National Library of Energy BETA

Sample records for annotated manual interactive

  1. EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

    SciTech Connect (OSTI)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Here the comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15–25% and helps curators to detect terms that would otherwise have been missed.

  2. EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, wellmore » documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Here the comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15–25% and helps curators to detect terms that would otherwise have been missed.« less

  3. Integrated Fuel-Coolant Interaction (IFCI 6.0) code. User`s manual

    SciTech Connect (OSTI)

    Davis, F.J.; Young, M.F.

    1994-04-01

    The integrated Fuel-Coolant interaction (IFCI) computer code is being developed at Sandia National Laboratories to investigate the fuel-coolant interaction (FCI) problem at large scale using a two-dimensional, four-field hydrodynamic framework and physically based models. IFCI will be capable of treating all major FCI processes in an integrated manner. This document is a product of the effort to generate a stand-alone version of IFCI, IFCI 6.0. The User`s Manual describes in detail the hydrodynamic method and physical models used in IFCI 6.0. Appendix A is an input manual, provided for the creation of working decks.

  4. CORCON-MOD3: An integrated computer model for analysis of molten core-concrete interactions. User`s manual

    SciTech Connect (OSTI)

    Bradley, D.R.; Gardner, D.R.; Brockmann, J.E.; Griffith, R.O.

    1993-10-01

    The CORCON-Mod3 computer code was developed to mechanistically model the important core-concrete interaction phenomena, including those phenomena relevant to the assessment of containment failure and radionuclide release. The code can be applied to a wide range of severe accident scenarios and reactor plants. The code represents the current state of the art for simulating core debris interactions with concrete. This document comprises the user`s manual and gives a brief description of the models and the assumptions and limitations in the code. Also discussed are the input parameters and the code output. Two sample problems are also given.

  5. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect (OSTI)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  6. Algal functional annotation tool

    SciTech Connect (OSTI)

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG

  7. Algal functional annotation tool

    Energy Science and Technology Software Center (OSTI)

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations tomore » interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on

  8. Algal functional annotation tool

    SciTech Connect (OSTI)

    Lopez, D.; Casero, D.; Cokus, S. J.; Merchant, S. S.; Pellegrini, M.

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  9. Implementation Manual

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Skip navigation links BPA Energy Efficiency Plan BPA Post-2011 EE Role Implementation Manual Archives IM Document Library Interim Solution 2.0 Files Low Income Efficiency...

  10. Biosafety Manual

    SciTech Connect (OSTI)

    King, Bruce W.

    2010-05-18

    Work with or potential exposure to biological materials in the course of performing research or other work activities at Lawrence Berkeley National Laboratory (LBNL) must be conducted in a safe, ethical, environmentally sound, and compliant manner. Work must be conducted in accordance with established biosafety standards, the principles and functions of Integrated Safety Management (ISM), this Biosafety Manual, Chapter 26 (Biosafety) of the Health and Safety Manual (PUB-3000), and applicable standards and LBNL policies. The purpose of the Biosafety Program is to protect workers, the public, agriculture, and the environment from exposure to biological agents or materials that may cause disease or other detrimental effects in humans, animals, or plants. This manual provides workers; line management; Environment, Health, and Safety (EH&S) Division staff; Institutional Biosafety Committee (IBC) members; and others with a comprehensive overview of biosafety principles, requirements from biosafety standards, and measures needed to control biological risks in work activities and facilities at LBNL.

  11. Utah Code Annotated | Open Energy Information

    Open Energy Info (EERE)

    Code Ann. DOI Not Provided Check for DOI availability: http:crossref.org Online Internet link for Utah Code Annotated Citation Utah Code Annotated (2014). Retrieved from...

  12. Next Generation Models for Storage and Representation of Microbial Biological Annotation

    SciTech Connect (OSTI)

    Quest, Daniel J; Land, Miriam L; Brettin, Thomas S; Cottingham, Robert W

    2010-01-01

    Background Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused on generating high quality annotation submissions to GenBank/EMBL supported by expert manual curation. The exponential growth of sequence data drives a growing need for increasingly higher quality and automatically generated annotation. Typical annotation pipelines utilize traditional database technologies, clustered computing resources, Perl, C, and UNIX file systems to process raw sequence data, identify genes, and predict and categorize gene function. These technologies tightly couple the annotation software system to hardware and third party software (e.g. relational database systems and schemas). This makes annotation systems hard to reproduce, inflexible to modification over time, difficult to assess, difficult to partition across multiple geographic sites, and difficult to understand for those who are not domain experts. These systems are not readily open to scrutiny and therefore not scientifically tractable. The advent of Semantic Web standards such as Resource Description Framework (RDF) and OWL Web Ontology Language (OWL) enables us to construct systems that address these challenges in a new comprehensive way. Results Here, we develop a framework for linking traditional data to OWL-based ontologies in genome annotation. We show how data standards can decouple hardware and third party software tools from annotation pipelines, thereby making annotation pipelines easier to reproduce and assess. An illustrative example shows how TURTLE (Terse RDF Triple Language) can be used as a human readable, but also semantically-aware, equivalent to GenBank/EMBL files. Conclusions The power of this approach lies in its ability to assemble annotation data from multiple databases across multiple locations into a representation that is understandable to

  13. Audit Manual (Release 8)

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Deputy Inspector General for Audits and Inspections AUDIT MANUAL Release 8 Revised 2014 Revised 2014 TOC-1 Release 8 OFFICE OF INSPECTOR GENERAL OFFICE OF AUDITS AUDIT MANUAL TABLE OF CONTENTS Page List of Acronyms ...................................................................................................................LOA-1 PART I -- INTRODUCTION CHAPTER 1 -- INTRODUCTION TO THE AUDIT MANUAL A. Purpose of the Audit Manual

  14. Fermilab at Work | Manuals and Forms

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Policy Guide Engineering Manual Engineering Manual Engineering Manual Appendices Risk Assessment Spreadsheet Engineering Manual Rollout Teamcenter Rollout Facilities Request Form...

  15. Automatic annotation of organellar genomes with DOGMA

    SciTech Connect (OSTI)

    Wyman, Stacia; Jansen, Robert K.; Boore, Jeffrey L.

    2004-06-01

    Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of extra-nuclear organellar (chloroplast and animal mitochondrial) genomes. It is a web-based package that allows the use of comparative BLAST searches to identify and annotate genes in a genome. DOGMA presents a list of putative genes to the user in a graphical format for viewing and editing. Annotations are stored on our password-protected server. Complete annotations can be extracted for direct submission to GenBank. Furthermore, intergenic regions of specified length can be extracted, as well the nucleotide sequences and amino acid sequences of the genes.

  16. Nuclear Explosive Safety Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-04-14

    This Manual provides supplemental details to support the requirements of DOE O 452.2D, Nuclear Explosive Safety.

  17. Directives System Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1998-01-30

    This Manual provides detailed requirements to supplement DOE O 251.1A, Directives System, dated 1-30-98.

  18. GRSAC Users Manual

    SciTech Connect (OSTI)

    Ball, S.J.; Nypaver, D.J.

    1999-02-01

    An interactive workstation-based simulation code (GRSAC) for studying postulated severe accidents in gas-cooled reactors has been developed to accommodate user-generated input with ''smart front-end'' checking. Code features includes on- and off-line plotting, on-line help and documentation, and an automated sensitivity study option. The code and its predecessors have been validated using comparisons with a variety of experimental data and similar codes. GRSAC model features include a three-dimensional representation of the core thermal hydraulics, and optional ATWS (anticipated transients without scram) capabilities. The user manual includes a detailed description of the code features, and includes four case studies which guide the user through four different examples of the major uses of GRSAC: an accident case; an initial conditions setup and run; a sensitivity study; and the setup of a new reactor model.

  19. KDYNA user's manual

    SciTech Connect (OSTI)

    Levatin, J.A.L.; Attia, A.V.; Hallquist, J.O.

    1990-09-28

    This report is a complete user's manual for KDYNA, the Earth Sciences version of DYNA2D. Because most features of DYNA2D have been retained in KDYNA much of this manual is identical to the DYNA2D user's manual.

  20. Audit Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Manual Audit Manual 2014 Office of Inspector General Audit Manual PDF icon Audit Manual More Documents & Publications Audit Peer Review 2009 Audit Report: OAS-L-04-13 Audit Report: ...

  1. nGASP - the nematode genome annotation assessment project

    SciTech Connect (OSTI)

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome

  2. EMS Programs Manual

    Broader source: Energy.gov [DOE]

    The Environmental Management System Programs Manual (LMS/POL/S04388-3.0) is obsolete and has been removed from the LM website.

  3. Radiological Control Manual

    SciTech Connect (OSTI)

    Not Available

    1993-04-01

    This manual has been prepared by Lawrence Berkeley Laboratory to provide guidance for site-specific additions, supplements, and clarifications to the DOE Radiological Control Manual. The guidance provided in this manual is based on the requirements given in Title 10 Code of Federal Regulations Part 835, Radiation Protection for Occupational Workers, DOE Order 5480.11, Radiation Protection for Occupational Workers, and the DOE Radiological Control Manual. The topics covered are (1) excellence in radiological control, (2) radiological standards, (3) conduct of radiological work, (4) radioactive materials, (5) radiological health support operations, (6) training and qualification, and (7) radiological records.

  4. Directives System Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1995-10-16

    This Manual provides detailed requirements to supplement DOE O 251.1, which establishes requirements for the development, coordination, and sunset review of DOE directives.

  5. DOE Explosives Safety Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1996-03-29

    This Manual describes DOE's explosives safety requirements applicable to operations involving the development, testing, handling, and processing of explosives or assemblies containing explosives.

  6. Mail Services User's Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2000-07-12

    This Manual provides detailed information on using the Department of Energy (DOE) mail services. Canceled by DOE G 573.1-1.

  7. Making web annotations persistent over time

    SciTech Connect (OSTI)

    Sanderson, Robert; Van De Sompel, Herbert

    2010-01-01

    As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

  8. AIRMaster+ User Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    User Manual AIRMaster+ User Manual This user manual is designed to help users understand the AIRMaster+ compressed air software. AIRMaster+ User Manual (2000) (2.39

  9. Cost Study Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Cost Study Manual Cost Study Manual Update 62912. PDF icon Memo regarding Cost Study Manual PDF icon Cost Study Manual More Documents & Publications Contractor Human Resources ...

  10. Personnel Security Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1998-05-22

    This Manual provides detailed requirements and procedures to supplement DOE O 472.1B, Personnel Security Activities, which establishes the overall objectives, requirements, and responsibilities for implementation and operation of the Personnel Security Program and the Personnel Security Assurance Program in the Department of Energy (DOE). This Manual addresses only the Personnel Security Program.

  11. Federal Employee Training Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2001-10-11

    This Manual provides detailed requirements to supplement DOE O 360.1B, FEDERAL EMPLOYEE TRAINING. The information in this Manual is intended to assist in improving Federal workforce performance under Department of Energy (DOE) managed Federal employee training. Cancels DOE M 360.1A-1. Canceled by DOE O 360.1C.

  12. Federal Employee Training Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-09-21

    This Manual provides detailed requirements to supplement DOE O 360.1A, Federal Employee Training, dated 9-21-99. The information in this Manual is intended to assist in improving Federal workforce performance under Department of Energy (DOE) managed Federal employee training. Canceled by DOE M 360.1-1B.

  13. Automated Knowledge Annotation for Dynamic Collaborative Environments

    SciTech Connect (OSTI)

    Cowell, Andrew J.; Gregory, Michelle L.; Marshall, Eric J.; McGrath, Liam R.

    2009-05-19

    This paper describes the Knowledge Encapsulation Framework (KEF), a suite of tools to enable automated knowledge annotation for modeling and simulation projects. This framework can be used to capture evidence (e.g., facts extracted from journal articles and government reports), discover new evidence (from similar peer-reviewed material as well as social media), enable discussions surrounding domain-specific topics and provide automatically generated semantic annotations for improved corpus investigation. The current KEF implementation is presented within a wiki environment, providing a simple but powerful collaborative space for team members to review, annotate, discuss and align evidence with their modeling frameworks.

  14. Salinas : theory manual.

    SciTech Connect (OSTI)

    Walsh, Timothy Francis; Reese, Garth M.; Bhardwaj, Manoj Kumar

    2004-08-01

    This manual describes the theory behind many of the constructs in Salinas. For a more detailed description of how to use Salinas , we refer the reader to Salinas, User's Notes. Many of the constructs in Salinas are pulled directly from published material. Where possible, these materials are referenced herein. However, certain functions in Salinas are specific to our implementation. We try to be far more complete in those areas. The theory manual was developed from several sources including general notes, a programer-notes manual, the user's notes and of course the material in the open literature.

  15. Fire Protection Program Manual

    SciTech Connect (OSTI)

    Sharry, J A

    2012-05-18

    This manual documents the Lawrence Livermore National Laboratory (LLNL) Fire Protection Program. Department of Energy (DOE) Orders 420.1B, Facility Safety, requires LLNL to have a comprehensive and effective fire protection program that protects LLNL personnel and property, the public and the environment. The manual provides LLNL and its facilities with general information and guidance for meeting DOE 420.1B requirements. The recommended readers for this manual are: fire protection officers, fire protection engineers, fire fighters, facility managers, directorage assurance managers, facility coordinators, and ES and H team members.

  16. User' Software Manual

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    MM-Group Home MMG Advisory Committees 4-ID-D Home Recent Publications Beamline Info Optics Instrumentation Software User Info FAQs 4-ID-D Beamline Software Manual Introduction...

  17. Nuclear Material Packaging Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-03-07

    The manual provides detailed packaging requirements for protecting workers from exposure to nuclear materials stored outside of an approved engineered contamination barrier. Does not cancel/supersede other directives. Certified 11-18-10.

  18. Media Sanitization Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-12-23

    The Manual establishes minimum technical and management requirements for the sanitization of electronic media, hardware, and devices and a risk-based approach to sanitization. Does not cancel other directives.

  19. Budget Execution Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1995-09-30

    The manual provides the user with a single source for references, definitions, and detailed procedures for distributing and controlling Department funds.Canceled by DOE M 135.1-1A. Does not cancel other directives.

  20. Geochemical engineering reference manual

    SciTech Connect (OSTI)

    Owen, L.B.; Michels, D.E.

    1984-01-01

    The following topics are included in this manual: physical and chemical properties of geothermal brine and steam, scale and solids control, processing spent brine for reinjection, control of noncondensable gas emissions, and goethermal mineral recovery. (MHR)

  1. Policies, Manuals & References

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    03-00203-0311.tif-277x300 Key Berkeley Lab Policy Documents Regulations & Procedures Manual (RPM) : The RPM is the primary policy document for Berkeley Lab and links out to many...

  2. Cost Study Manual

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    2 Cost Study Manual Executive Summary This Cost Study Manual documents the procedures for preparing a Cost Study to compare the cost of a contractor's employee benefits to the industry average from a broad-based national benefit cost survey. The annual Employee Benefits Cost Study Comparison (Cost Study) assists with the analysis of contractors' employee benefits costs. The Contracting Officer (CO) may require corrective action when the average benefit per capita cost or the benefit cost as a

  3. Critical Assessment of Function Annotation Meeting, 2011

    SciTech Connect (OSTI)

    Friedberg, Iddo

    2015-01-21

    The Critical Assessment of Function Annotation meeting was held July 14-15, 2011 at the Austria Conference Center in Vienna, Austria. There were 73 registered delegates at the meeting. We thank the DOE for this award. It helped us organize and support a scientific meeting AFP 2011 as a special interest group (SIG) meeting associated with the ISMB 2011 conference. The conference was held in Vienna, Austria, in July 2011. The AFP SIG was held on July 15-16, 2011 (immediately preceding the conference). The meeting consisted of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component provided a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA).

  4. Salinas : theory manual.

    SciTech Connect (OSTI)

    Walsh, Timothy Francis; Reese, Garth M.; Bhardwaj, Manoj Kumar

    2011-11-01

    Salinas provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of structural systems. This manual describes the theory behind many of the constructs in Salinas. For a more detailed description of how to use Salinas, we refer the reader to Salinas, User's Notes. Many of the constructs in Salinas are pulled directly from published material. Where possible, these materials are referenced herein. However, certain functions in Salinas are specific to our implementation. We try to be far more complete in those areas. The theory manual was developed from several sources including general notes, a programmer notes manual, the user's notes and of course the material in the open literature.

  5. Genomic Data and Annotation from the SEED

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The projects subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  6. Toward a standard in structural genome annotation for prokaryotes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tripp, H. James; Sutton, Granger; White, Owen; Wortman, Jennifer; Pati, Amrita; Mikhailova, Natalia; Ovchinnikova, Galina; Payne, Samuel H.; Kyrpides, Nikos C.; Ivanova, Natalia

    2015-07-25

    In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, we collected 1,004,576 peptides from various publicly available resources, and these were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicons with an average GC content from 31 % to 74 %, biased toward higher GC content genomes. Automated, manual, and semi-manual methods were used to tally errors in three widely used gene calling methods, as evidenced by peptides mapped outside the boundaries of called genes. We found thatmore » the consensus set of identical genes predicted by the three methods constitutes only about 70 % of the genes predicted by each individual method (with start and stop required to coincide). Peptide data was useful for evaluating some of the differences between gene callers, but not reliable enough to make the results conclusive, due to limitations inherent in any proteogenomic study. A single, unambiguous, unanimous best practice did not emerge from this analysis, since the available proteomics data were not adequate to provide an objective measurement of differences in the accuracy between these methods. However, as a result of this study, software, reference data, and procedures have been better matched among participants, representing a step toward a much-needed standard. In the absence of sufficient amount of experimental data to achieve a universal standard, our recommendation is that any of these methods can be used by the community, as long as a single method is employed across all datasets to be compared.« less

  7. Quality Assurance Manual

    SciTech Connect (OSTI)

    McGarrah, J.E.

    1995-05-01

    In order to provide clients with quality products and services, Pacific Northwest Laboratory (PNL) has established and implemented a formal quality assurance program. These management controls are documented in this manual (PNL-MA-70) and its accompanying standards and procedures. The QA Program meets the basic requirements and supplements of ANSI/ASME NQA-1, Quality Assurance Program Requirements for Nuclear Facilities, as interpreted for PNL activities. Additional, the quality requirements are augmented to include the Total Quality approach defined in the Department of Energy Order 5700.6C, Quality Assurance. This manual provides requirements and an overview of the administrative procedures that apply to projects and activities.

  8. Keystone coal industry manual

    SciTech Connect (OSTI)

    Not Available

    1993-01-01

    The 1994 Keystone Coal Industry Manual is presented. Keystone has served as the one industry reference authority for the many diverse organizations concerned with the supply and utilization of coal in the USA and Canada. Through the continuing efforts of coal producers, buyers, users, sellers, and equipment designers and manufacturers, the coal industry supplies an abundant and economical fuel that is indispensable in meeting the expanding energy needs of North America. The manual is divided into the following sections: coal sales companies, coal export, transportation of coal, consumer directories, coal associations and groups, consulting and financial firms, buyers guide, industry statistics and ownership, coal preparation, coal mine directory, and coal seams.

  9. Radioactive Waste Management Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-07-09

    This Manual further describes the requirements and establishes specific responsibilities for implementing DOE O 435.1, Radioactive Waste Management, for the management of DOE high-level waste, transuranic waste, low-level waste, and the radioactive component of mixed waste. The purpose of the Manual is to catalog those procedural requirements and existing practices that ensure that all DOE elements and contractors continue to manage DOE's radioactive waste in a manner that is protective of worker and public health and safety, and the environment. Does not cancel other directives.

  10. New Mexico Interconnection Manual | Open Energy Information

    Open Energy Info (EERE)

    Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library General: New Mexico Interconnection Manual Abstract This manual sets forth common interconnection...

  11. Voluntary Protection Program Manuals | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Manuals Voluntary Protection Program Manuals Voluntary Protection Program Manual U.S. Department Of Energy Approval Memo Issuing Revised VPP Program Documents (May 2012) Part I: ...

  12. Electrical Safety Manual | The Ames Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Electrical Safety Manual Version Number: 0 Document Number: Manual 10200.007 Effective Date: 032012 File (public): PDF icon manual10200.007rev0.pdf...

  13. Manually operated coded switch

    DOE Patents [OSTI]

    Barnette, Jon H.

    1978-01-01

    The disclosure relates to a manually operated recodable coded switch in which a code may be inserted, tried and used to actuate a lever controlling an external device. After attempting a code, the switch's code wheels must be returned to their zero positions before another try is made.

  14. Information Security Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-01-16

    This Manual establishes security requirements for the protection and control of matter required to be classified or controlled by statutes, regulations, or U.S. Department of Energy directives. Cancels DOE M 470.4-4 Chg 1. DOE M 470.4-4A Chg 1 issued 10-12-10.

  15. Information Security Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2010-10-12

    The Manual establishes security requirements for the protection and control of matter required to be classified or controlled by statutes, regulations, or U.S. Department of Energy (DOE) directives. Original dated dated 1-16-09. Canceled by DOE O 471.6--except for Section D.

  16. Nuclear Explosive Safety Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-04-14

    This Department of Energy (DOE) Manual provides supplemental details on selected topics to support the requirements of DOE O 452.2D, Nuclear Explosive Safety, dated 4/14/09. Cancels DOE M 452.2-1. Admin Chg 1, dated 7-10-13, cancels DOE M 452.2-1A.

  17. Federal Technical Capability Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2000-06-05

    The Federal Technical Capability Manual provides the process for the recruitment, deployment, development, and retention of Federal personnel with the demonstrated technical capability to safely accomplish the Departments missions and responsibilities at defense nuclear facilities. Canceled by DOE M 426.1-1A. Does not cancel other directives.

  18. Media Sanitization Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-12-23

    The Manual establishes minimum technical and management requirements for the sanitization of electronic media, hardware, and devices and a risk-based approach to sanitization. Admin Chg 1 dated 9-1-09; Admin Chg 2 dated 12-22-09. Canceled by DOE O 205.1B

  19. Media Sanitization Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-12-23

    The Manual establishes minimum technical and management requirements for the sanitization of electronic media, hardware, and devices and a risk-based approach to sanitization. Admin Chg 1 dated 9-1-09. Canceled by DOE O 205.1B.

  20. National Security System Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2007-03-08

    The manual provides baseline requirements and controls for the graded protection of the confidentiality, integrity, and availability of classified information and information systems used or operated by the Department of Energy (DOE), contractors, and any other organization on behalf of DOE, including the National Nuclear Security Administration. Cancels DOE M 471.2-2. Canceled by DOE O 205.1B.

  1. DOE Explosives Safety Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2006-01-09

    The Manual describes the Departments explosive safety requirements applicable to operations involving the development, testing, handling, and processing of explosives or assemblies containing explosives. Cancels DOE M 440.1-1. Canceled by DOE O 440.1B Chg 1.

  2. Ontological Annotation with WordNet

    SciTech Connect (OSTI)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  3. Automating Ontological Annotation with WordNet

    SciTech Connect (OSTI)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  4. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    SciTech Connect (OSTI)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  5. Proteus-SN user manual

    SciTech Connect (OSTI)

    Shemon, Emily R.; Smith, Micheal A.; Lee, Changho

    2015-07-31

    This user manual describes how to set up a neutron transport simulation with the PROTEUS-SN code. A companion methodology manual describes the theory and algorithms within PROTEUS-SN.

  6. Cyber Security Process Requirements Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-08-12

    The Manual establishes the minimum implementation standards for cyber security management processes throughout the Department. No cancellation.

  7. State Energy Program Operations Manual

    Broader source: Energy.gov [DOE]

    The State Energy Program Operations Manual is a reference tool for the SEP network states and program officials within DOE.

  8. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    SciTech Connect (OSTI)

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, III, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  9. ASPEN costing manual

    SciTech Connect (OSTI)

    Schwint, K.J.

    1986-07-25

    The ASPEN program contains within it a Cost Estimation System (CES) which estimates the purchase cost and utility consumption rates for major pieces of equipment in a process flowsheet as well as installed equipment costs. These estimates are ''preliminary-study grade'' with an accuracy of plus or minus 30%. The ASPEN program also contains within it an Economic Evaluation System (EES) which estimates overall capital investment costs, annual operating expenses and profitability indices for a chemical plant. This ASPEN costing manual has been written as a guide for those inexperienced in the use of ASPEN and unfamiliar with standard cost estimating techniques who want to use the ASPEN CES and EES. The ASPEN Costing Manual is comprised of the following sections: (1) Introduction, (2) ASPEN Input Language, (3) ASPEN Cost Estimation System (CES), (4) ASPEN Cost Blocks; and (5) ASPEN Economic Evaluation System (EES).

  10. Personnel Security Program Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2001-07-12

    This Manual provides detailed requirements and procedures to supplement DOE O 472.1B, Personnel Security Activities, which establishes the overall objectives, requirements, and responsibilities for implementation and operation of the Personnel Security Program and the Personnel Security Assurance Program in the Department of Energy (DOE), including the National Nuclear Security Administration (NNSA). Extended until 7-7-06 by DOE N 251.64, dated 7-7-05 Cancels: DOE M 472.1-1A.

  11. Radioactive Waste Management Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-07-09

    This Manual further describes the requirements and establishes specific responsibilities for implementing DOE O 435.1, Radioactive Waste Management, for the management of DOE high-level waste, transuranic waste, low-level waste, and the radioactive component of mixed waste. Change 1 dated 6/19/01 removes the requirement that Headquarters is to be notified and the Office of Environment, Safety and Health consulted for exemptions for use of non-DOE treatment facilities. Certified 1-9-07.

  12. Project Records Information System (PRIS) user's manual

    SciTech Connect (OSTI)

    Smith, P.S.; Nations, J.A.; Short, R.D.

    1991-08-01

    The Projects Record Information System (PRIS) is an interactive system developed for the Information Services Division (ISD) of Martin Marietta Energy Systems, Inc., to perform indexing, maintenance, and retrieval of information about Engineering project record documents for which they are responsible. This PRIS User's Manual provides instruction on the use of this system. Section 2.0 of this manual presents an overview of PRIS, describing the system's purpose; the data that it handles, functions it performs; hardware, software, and access; and help and error functions. Section 3.0 describes the interactive menu-driven operation of PRIS. Appendixes A, B,C, and D contain the data dictionary, help screens, report descriptions, and a primary menu structure diagram, respectively.

  13. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect (OSTI)

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  14. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect (OSTI)

    David J. States

    1998-08-01

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  15. CHRPR Operations Manual

    SciTech Connect (OSTI)

    Windsor, Bradford T.; Woodring, Mitchell L.; Myjak, Mitchell J.

    2012-08-21

    proportional to the amplitude, via voltage to pulse width converters (VPW). These time widths are then digitized by a field programmable gate array (FPGA) and transmitted over Ethernet to a data acquisition computer. The CHRPR records the magnitude of each pulse to a continuous event mode file on or each detector and occupancy sensor This manual begins with CHRPR installation instructions, then a section on CHRPR software. Afterward is a brief overview of how the TSA system works, then an explanation of the CHRPR. This manual is meant as a supplement to the TSA VM-250AGN manual, which can be found at http://tsasystems.com/library/manuals/pm700agn-vm250agn_manual.pdf . That manual is the manufacturers guide for the installation, programming, and maintenance of the portal system.

  16. RADTRAN 6 technical manual.

    SciTech Connect (OSTI)

    Weiner, Ruth F.; Neuhauser, Karen Sieglinde; Heames, Terence John; O'Donnell, Brandon M.; Dennis, Matthew L.

    2014-01-01

    This Technical Manual contains descriptions of the calculation models and mathematical and numerical methods used in the RADTRAN 6 computer code for transportation risk and consequence assessment. The RADTRAN 6 code combines user-supplied input data with values from an internal library of physical and radiological data to calculate the expected radiological consequences and risks associated with the transportation of radioactive material. Radiological consequences and risks are estimated with numerical models of exposure pathways, receptor populations, package behavior in accidents, and accident severity and probability.

  17. SHAFT79 user's manual

    SciTech Connect (OSTI)

    Pruess, K.; Schroeder, R.C.

    1980-03-01

    SHAFT79 (Simultaneous Heat And Fluid Transport) is an integrated finite difference program for computing two-phase non-isothermal flow in porous media. The principal application for which SHAFT79 is designed is in geothermal reservoir simulation. SHAFT79 solves the same equations as an earlier version, called SHAFT78, but uses much more efficient mathematical and numerical methods. The present SHAFT79 user's manual gives a brief account of equations and numerical methods and then describes in detail how to set up input decks for running the program. The application of SHAFT79 is illustrated by means of a few sample problems. (MHR)

  18. Radioactive Waste Management Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-07-09

    This Manual further describes the requirements and establishes specific responsibilities for implementing DOE O 435.1, Radioactive Waste Management, for the management of DOE high-level waste, transuranic waste, low-level waste, and the radioactive component of mixed waste. Change 1 dated 6/19/01 removes the requirement that Headquarters is to be notified and the Office of Environment, Safety and Health consulted for exemptions for use of non-DOE treatment facilities. Certified 1-9-07. Admin Chg 2, dated 6-8-11, supersedes DOE M 435.1-1 Chg 1.

  19. TALENT user's manual.

    SciTech Connect (OSTI)

    Merchant, Bion John

    2012-01-01

    The Ground-Based Monitoring R and E Component Evaluation project performs testing on the hardware components that make up Seismic and Infrasound monitoring systems. The majority of the testing is focused on the Digital Waveform Recorder (DWR), Seismic Sensor, and Infrasound Sensor. The software tool used to capture and analyze the data collected from testing is called TALENT: Test and Analysis Evaluation Tool. This document is the manual for using TALENT. Other reports document the testing procedures that are in place (Kromer, 2007) and the algorithms employed in the test analysis (Merchant, 2011).

  20. Radiological control manual. Revision 1

    SciTech Connect (OSTI)

    Kloepping, R.

    1996-05-01

    This Lawrence Berkeley National Laboratory Radiological Control Manual (LBNL RCM) has been prepared to provide guidance for site-specific additions, supplements and interpretation of the DOE Radiological Control Manual. The guidance provided in this manual is one methodology to implement the requirements given in Title 10 Code of Federal Regulations Part 835 (10 CFR 835) and the DOE Radiological Control Manual. Information given in this manual is also intended to provide demonstration of compliance to specific requirements in 10 CFR 835. The LBNL RCM (Publication 3113) and LBNL Health and Safety Manual Publication-3000 form the technical basis for the LBNL RPP and will be revised as necessary to ensure that current requirements from Rules and Orders are represented. The LBNL RCM will form the standard for excellence in the implementation of the LBNL RPP.

  1. State Energy Program Operations Manual

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    PROGRAM Operations Manual (This page intentionally left blank) Introduction 3 Table of Contents Introduction: Using the Manual 3 Table of Contents, Using the Manual, Terms, Acronyms Chapter 1: State Energy Program Review 6 This chapter describes the types of funding vehicles and federal regulations applicable to the program. Chapter 2: Annual Formula Grants and Formula Grant Application 15 This chapter provides application rules and procedures for SEP Annual Formula funding. Chapter 3: Program

  2. Cyber Security Process Requirements Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-08-12

    The Manual establishes the minimum implementation standards for cyber security management processes throughout the Department. No cancellation. Admin Chg 1 dated 9-1-09.

  3. MELCOR computer code manuals

    SciTech Connect (OSTI)

    Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.; Stuart, D.S.; Thompson, S.L.; Hodge, S.A.; Hyman, C.R.; Sanders, R.L.

    1995-03-01

    MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.

  4. Automated manual transmission controller

    DOE Patents [OSTI]

    Lawrie, Robert E.; Reed, Jr., Richard G.; Bernier, David R.

    1999-12-28

    A powertrain system for a hybrid vehicle. The hybrid vehicle includes a heat engine, such as a diesel engine, and an electric machine, which operates as both an electric motor and an alternator, to power the vehicle. The hybrid vehicle also includes a manual-style transmission configured to operate as an automatic transmission from the perspective of the driver. The engine and the electric machine drive an input shaft which in turn drives an output shaft of the transmission. In addition to driving the transmission, the electric machine regulates the speed of the input shaft in order to synchronize the input shaft during either an upshift or downshift of the transmission by either decreasing or increasing the speed of the input shaft. When decreasing the speed of the input shaft, the electric motor functions as an alternator to produce electrical energy which may be stored by a storage device. Operation of the transmission is controlled by a transmission controller which receives input signals and generates output signals to control shift and clutch motors to effect smooth launch, upshift shifts, and downshifts of the transmission, so that the transmission functions substantially as an automatic transmission from the perspective of the driver, while internally substantially functioning as a manual transmission.

  5. Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Leung, Elo; Huang, Amy; Cadag, Eithon; Montana, Aldrin; Soliman, Jan Lorenz; Zhou, Carol L. Ecale

    2016-01-20

    In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

  6. Genomic Data and Annotation from the SEED

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project is a cooperative effort to annotate ever-expanding genomic data so researchers can conduct effective comparative analyses of genomes. Launched in 2003 by the Fellowship for Interpretation of Genomes (FIG), the project is one of several initiatives in ongoing development of data curation systems. SEED is designed to be used by scientists from numerous centers and with varied research objectives. As such, several institutions have since joined FIG in a consortium, including the University of Chicago, DOE’s Argonne National Laboratory (ANL), the University of Illinois at Urbana-Champaign, and others. As one example, ANL has used SEED to develop the National Microbial Pathogen Data Resource. Other agencies and institutions have used the project to discover genome components and clarify gene functions such as metabolism. SEED also has enabled researchers to conduct comparative analyses of closely related genomes and has supported derivation of stoichiometric models to understand metabolic processes. The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  7. Annotations in Refseq (GSC8 Meeting)

    ScienceCinema (OSTI)

    Tatusova, Tatiana

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  8. Work Plans & Manuals | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Work Plans & Manuals Work Plans & Manuals This list contains audit and inspections manuals and a list of planned reviews to be conducted by the Office of Audits and Inspections. Documents Available for Download November 20, 2014 Work Plan FY 2016 Planned Audits and Inspections for FY 2016 December 23, 2014 Audit Manual 2014 Office of Inspector General Audit Manual

  9. Towards a Library of Standard Operating Procedures (SOPs) for (meta)genomic annotation

    SciTech Connect (OSTI)

    Kyrpides, Nikos; Angiuoli, Samuel V.; Cochrane, Guy; Field, Dawn; Garrity, George; Gussman, Aaron; Kodira, Chinnappa D.; Klimke, William; Kyrpides, Nikos; Madupu, Ramana; Markowitz, Victor; Tatusova, Tatiana; Thomson, Nick; White, Owen

    2008-04-01

    Genome annotations describe the features of genomes and accompany sequences in genome databases. The methodologies used to generate genome annotation are diverse and typically vary amongst groups. Descriptions of the annotation procedure are helpful in interpreting genome annotation data. Standard Operating Procedures (SOPs) for genome annotation describe the processes that generate genome annotations. Some groups are currently documenting procedures but standards are lacking for structure and content of annotation SOPs. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse a central online repository of SOPs.

  10. FRMAC Operations Manual

    SciTech Connect (OSTI)

    Frandsen, K.

    2010-05-01

    In the event of a major radiological incident, the Federal Radiological Monitoring and Assessment Center (FRMAC) will coordinate the federal agencies that have various statutory responsibilities. The FRMAC is responsible for coordinating all environmental radiological monitoring, sampling, and assessment activities for the response. This manual describes the FRMAC’s response activities in a radiological incident. It also outlines how FRMAC fits in the National Incident Management System (NIMS) under the National Response Framework (NRF) and describes the federal assets and subsequent operational activities which provide federal radiological monitoring and assessment of the affected areas. In the event of a potential or existing major radiological incident, the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) is responsible for establishing and managing the FRMAC during the initial phases.

  11. OSH technical reference manual

    SciTech Connect (OSTI)

    Not Available

    1993-11-01

    In an evaluation of the Department of Energy (DOE) Occupational Safety and Health programs for government-owned contractor-operated (GOCO) activities, the Department of Labor`s Occupational Safety and Health Administration (OSHA) recommended a technical information exchange program. The intent was to share written safety and health programs, plans, training manuals, and materials within the entire DOE community. The OSH Technical Reference (OTR) helps support the secretary`s response to the OSHA finding by providing a one-stop resource and referral for technical information that relates to safe operations and practice. It also serves as a technical information exchange tool to reference DOE-wide materials pertinent to specific safety topics and, with some modification, as a training aid. The OTR bridges the gap between general safety documents and very specific requirements documents. It is tailored to the DOE community and incorporates DOE field experience.

  12. RCRA orientation manual, 1990 edition

    SciTech Connect (OSTI)

    Clay, D.R.

    1990-01-01

    The U.S. Environmental Protection Agency (EPA) developed the manual to provide introductory information on the solid and hazardous waste management programs under the Resource Conservation and Recovery Act (RCRA). The manual outlines the basic framework of the regulatory program for new EPA and State employees, those persons new to RCRA assignments, and others interested in the Act. The manual is not, however, meant to replace in-depth analysis of the statute and its associated regulations and Agency guidance. The manual is an update of the original RCRA Orientation Manual issued in 1986. Revisions contained in the update reflect the many regulatory changes that have resulted from both the Hazardous and Solid Waste Amendments (HSWA) of 1984 and the Medical Waste Tracking Act of 1988 (RCRA Subtitle J).

  13. TEC Working Group Topic Groups Manual Review

    Broader source: Energy.gov [DOE]

    This group is responsible for the update of DOE Manual 460.2-1, Radioactive Material Transportation Practices Manual.  This manual was issued on September 23, 2002, and establishes a set of...

  14. Radiometer Calibration and Characterization (RCC) User's Manual...

    Office of Scientific and Technical Information (OSTI)

    (RCC) User's Manual: Windows Version 4.0 Citation Details In-Document Search Title: Radiometer Calibration and Characterization (RCC) User's Manual: Windows Version 4.0 ...

  15. WYDOT - Utility Accommodation Regulation Manual | Open Energy...

    Open Energy Info (EERE)

    Regulation ManualPermittingRegulatory GuidanceGuideHandbook Abstract This manual sets forth the processes and procedures for utility accommodation on WYDOT rights-of-way. Author...

  16. Caltrans Transportation Permits Manual | Open Energy Information

    Open Energy Info (EERE)

    Transportation Permits Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library Legal Document- OtherOther: Caltrans Transportation Permits ManualLegal Abstract...

  17. HOPSPACK 2.0 user manual.

    SciTech Connect (OSTI)

    Plantenga, Todd D.

    2009-09-01

    HOPSPACK (Hybrid Optimization Parallel Search PACKage) solves derivative-free optimization problems using an open source, C++ software framework. The framework enables parallel operation using MPI or multithreading, and allows multiple solvers to run simultaneously and interact to find solution points. HOPSPACK comes with an asynchronous pattern search solver that handles general optimization problems with linear and nonlinear constraints, and continuous and integer-valued variables. This user manual explains how to install and use HOPSPACK to solve problems, and how to create custom solvers within the framework.

  18. Manual braille writer

    DOE Patents [OSTI]

    Hawk, Lawrence S.; Turner, Joe H.

    1992-01-01

    A manual-type braille writer that provides for both writing and reading in a normal left-to-right manner. In the preferred form, this braille writer has a clip board type base, and in the preferred embodiment a guide plate assembly can be moved to, and releasable fixed at, selected vertical locations along this base. The guide plate assembly is provided with a plurality of character cells uniformly spaced along rows across the guide plate assembly as well as in uniformly spaced rows. This guide plate assembly has a lower portion to be placed under a sheet of paper positioned on the clip board base and an upper portion to be positioned on top of the sheet. This upper portion is hinged with respect to the lower portion. Each character cell is typically made up of six appropriately spaced pins extending up from the lower portion that are aligned with a rosette-shaped cutout in the upper portion. A stylus member is provided that has a distal end to be fitted into the cutout of the character cell so that a recess in the end thereof presses the writing paper over the pin associated with that recess to produce a braille dot at that location. When desired, the upper portion can be lifted up so that the text already written can be read or to determine the place for initiating writing when writing has been interrupted.

  19. Manual braille writer

    DOE Patents [OSTI]

    Hawk, L.S.; Turner, J.H.

    1992-07-28

    A manual-type braille writer is described that provides for both writing and reading in a normal left-to-right manner. In the preferred form, this braille writer has a clip board type base, and in the preferred embodiment a guide plate assembly can be moved to, and releasable fixed at, selected vertical locations along this base. The guide plate assembly is provided with a plurality of character cells uniformly spaced along rows across the guide plate assembly as well as in uniformly spaced rows. This guide plate assembly has a lower portion to be placed under a sheet of paper positioned on the clip board base and an upper portion to be positioned on top of the sheet. This upper portion is hinged with respect to the lower portion. Each character cell is typically made up of six appropriately spaced pins extending up from the lower portion that are aligned with a rosette-shaped cutout in the upper portion. A stylus member is provided that has a distal end to be fitted into the cutout of the character cell so that a recess in the end thereof presses the writing paper over the pin associated with that recess to produce a braille dot at that location. When desired, the upper portion can be lifted up so that the text already written can be read or to determine the place for initiating writing when writing has been interrupted. 10 figs.

  20. JSATS Decoder Software Manual

    SciTech Connect (OSTI)

    Flory, Adam E.; Lamarche, Brian L.; Weiland, Mark A.

    2013-05-01

    The Juvenile Salmon Acoustic Telemetry System (JSATS) Decoder is a software application that converts a digitized acoustic signal (a waveform stored in the .bwm file format) into a list of potential JSATS Acoustic MicroTransmitter (AMT) tagcodes along with other data about the signal including time of arrival and signal to noise ratios (SNR). This software is capable of decoding single files, directories, and viewing raw acoustic waveforms. When coupled with the JSATS Detector, the Decoder is capable of decoding in ‘real-time’ and can also provide statistical information about acoustic beacons placed within receive range of hydrophones within a JSATS array. This document details the features and functionality of the software. The document begins with software installation instructions (section 2), followed in order by instructions for decoder setup (section 3), decoding process initiation (section 4), then monitoring of beacons (section 5) using real-time decoding features. The last section in the manual describes the beacon, beacon statistics, and the results file formats. This document does not consider the raw binary waveform file format.

  1. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; et al

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offersmore » a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.« less

  2. T-580: Apache Tomcat May Ignore @ServletSecurity Annotation Protections

    Broader source: Energy.gov [DOE]

    Apache Tomcat May Ignore @ServletSecurity Annotation Protections. A remote user may be able to bypass @ServletSecurity annotation protections.

  3. GETEM Manuals and Revision Notes

    Broader source: Energy.gov [DOE]

    Please refer to these manuals and revision notes prior to downloading and running the Geothermal Electricity Technology Evaluation Model (GETEM). Because this is a beta version, you are urged to...

  4. Cyber Security Process Requirements Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-08-12

    The Manual establishes minimum implementation standards for cyber security management processes throughout the Department. Admin Chg 1 dated 9-1-09; Admin Chg 2 dated 12-22-09. Canceled by DOE O 205.1B. No cancellations.

  5. Manual for Identifying Classified Information

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2007-08-28

    The Manual provides detailed requirements to supplement DOE O 475.2, Identifying Classified Information, dated 8/28/07. Cancels DOE M 475.1-1A; canceled by DOE O 475.2A

  6. Manual on indoor air quality

    SciTech Connect (OSTI)

    Diamond, R.C.; Grimsrud, D.T.

    1983-12-01

    This reference manual was prepared to assist electric utilities in helping homeowners, builders, and new home buyers to understand a broad range of issues related to indoor air quality. The manual is directed to technically knowledgeable persons employed by utility companies - the customer service or marketing representative, applications engineer, or technician - who may not have specific expertise in indoor air quality issues. In addition to providing monitoring and control techniques, the manual summarizes the link between pollutant concentrations, air exchange, and energy conservation and describes the characteristics and health effects of selected pollutants. Where technical information is too lengthy or complex for inclusion in this volume, reference sources are given. Information for this manual was gathered from technical studies, manufacturers' information, and other materials from professional societies, institutes, and associations. The aim has been to provide objective technical and descriptive information that can be used by utility personnel to make informed decisions about indoor air quality issues.

  7. Surface Environmental Surveillance Procedures Manual

    SciTech Connect (OSTI)

    Hanf, RW; Dirkes, RL

    1990-02-01

    This manual establishes the procedures for the collection of environmental samples and the performance of radiation surveys and other field measurements. Responsibilities are defined for those personnel directly involved in the collection of samples and the performance of field measurements.

  8. Integrated Safety Management System Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2006-11-01

    This manual provides requirements and guidance for DOE and contractors to ensure development and implementation of an effective Integrated Safety Management system that is periodically reviewed and continuously improved. Canceled by DOE O 450.2.

  9. Geothermal XML Product Data Services Manual | OSTI, US Dept of...

    Office of Scientific and Technical Information (OSTI)

    Geothermal XML Product Data Services Manual Available Downloads: PDF icon GeothermalXMLDataServicesManual0

  10. State authorization manual. Volume 1

    SciTech Connect (OSTI)

    Brugler-Jones, S.

    1990-10-01

    The State Authorization Manual (SAM) (Vol. I) provides guidance for States applying for program revisions to their authorized RCRA State program. The SAM is an updated version of the 1988 State Consolidated RCRA Authorization Manual (SCRAM). It focuses on program revision applications rather than initial applications since most States have received initial authorization for the RCRA program. The SCRAM should continue to be used to assist States not yet authorized under the RCRA program.

  11. Value Study Desk Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Value Study Desk Manual Value Study Desk Manual Updated September 26, 2012. Memo from Robert Myers regarding DOE Benefit Value Desk Manual (56.76 KB) Value Study Desk Manual (1005.83 KB) More Documents & Publications Contractor Human Resources Management VALUE STUDY VALUE STUDY

  12. Towards Experimental Annotation of Genes by High Throughput Sequencing

    SciTech Connect (OSTI)

    Bradbury, Andrew

    2010-06-03

    Andrew Bradbury of Los Alamos National Laboratory discusses turning annotation into a sequencing pipeline on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  13. Geothermal wetlands: an annotated bibliography of pertinent literature

    SciTech Connect (OSTI)

    Stanley, N.E.; Thurow, T.L.; Russell, B.F.; Sullivan, J.F.

    1980-05-01

    This annotated bibliography covers the following topics: algae, wetland ecosystems; institutional aspects; macrophytes - general, production rates, and mineral absorption; trace metal absorption; wetland soils; water quality; and other aspects of marsh ecosystems. (MHR)

  14. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  15. AmiGO: online access to ontology and annotation data

    SciTech Connect (OSTI)

    Carbon, Seth; Ireland, Amelia; Mungall, Christopher J.; Shu, ShengQiang; Marshall, Brad; Lewis, Suzanna

    2009-01-15

    AmiGO is a web application that allows users to query, browse, and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium; it can also be downloaded and installed to browse local ontologies and annotations. AmiGO is free open source software developed and maintained by the GO Consortium.

  16. SOWFA + Super Controller User's Manual

    SciTech Connect (OSTI)

    Fleming, P.; Gebraad, P.; Churchfield, M.; Lee, S.; Johnson, K.; Michalakes, J.; van Wingerden, J. W.; Moriarty, P.

    2013-08-01

    SOWFA + Super Controller is a modification of the NREL's SOWFA tool which allows for a user to apply multiturbine or centralized wind plant control algorithms within the high-fidelity SOWFA simulation environment. The tool is currently a branch of the main SOWFA program, but will one day will be merged into a single version. This manual introduces the tool and provides examples such that a user can implement their own super controller and set up and run simulations. The manual only discusses enough about SOWFA itself to allow for the customization of controllers and running of simulations, and details of SOWFA itself are reported elsewhere Churchfield and Lee (2013); Churchfield et al. (2012). SOWFA + Super Controller, and this manual, are in alpha mode.

  17. Sierra Structural Dynamics Theory Manual

    SciTech Connect (OSTI)

    Reese, Garth M.

    2015-10-19

    Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of structural systems. This manual describes the theory behind many of the constructs in Sierra/SD. For a more detailed description of how to use Sierra/SD , we refer the reader to Sierra/SD, User's Notes . Many of the constructs in Sierra/SD are pulled directly from published material. Where possible, these materials are referenced herein. However, certain functions in Sierra/SD are specific to our implementation. We try to be far more complete in those areas. The theory manual was developed from several sources including general notes, a programmer notes manual, the user's notes and of course the material in the open literature. This page intentionally left blank.

  18. Metagenomic gene annotation by a homology-independent approach

    SciTech Connect (OSTI)

    Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

    2011-06-02

    Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

  19. SOLDESIGN user's manual copyright

    SciTech Connect (OSTI)

    Pillsbury, R.D. Jr.

    1991-02-01

    SOLDESIGN is a general purpose program for calculating and plotting magnetic fields, Lorentz body forces, resistances and inductances for a system of coaxial uniform current density solenoidal elements. The program was originally written in 1980 and has been evolving ever since. SOLDESIGN can be used with either interactive (terminal) or file input. Output can be to the terminal or to a file. All input is free-field with comma or space separators. SOLDESIGN contains an interactive help feature that allows the user to examine documentation while executing the program. Input to the program consists of a sequence of word commands and numeric data. Initially, the geometry of the elements or coils is defined by specifying either the coordinates of one corner of the coil or the coil centroid, a symmetry parameter to allow certain reflections of the coil (e.g., a split pair), the radial and axial builds, and either the overall current density or the total ampere-turns (NI). A more general quadrilateral element is also available. If inductances or resistances are desired, the number of turns must be specified. Field, force, and inductance calculations also require the number of radial current sheets (or integration points). Work is underway to extend the field, force, and, possibly, inductances to non-coaxial solenoidal elements.

  20. DOE Manual 442.1-1 Differing Professional Opinions Manual for...

    Office of Environmental Management (EM)

    Issues Involving Environment, Safety, and Health DOE Manual 442.1-1 Differing Professional Opinions Manual for Technical Issues Involving Environment, Safety, and Health ...

  1. Memorandum, Implementation of Department of Energy Manual 450...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Implementation of Department of Energy Manual 450.4-1, Integrated Safety Management System Manual Memorandum, Implementation of Department of Energy Manual 450.4-1, Integrated ...

  2. Hydrogen Fuel Cell Engines and Related Technologies Course Manual...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Engines and Related Technologies Course Manual Hydrogen Fuel Cell Engines and Related Technologies Course Manual This course manual features technical information on the use of ...

  3. Maintenance neutron coincidence counter manual

    SciTech Connect (OSTI)

    Krick, M.S.; Polk, P.J.; Atencio, J.D.

    1989-09-01

    A compact thermal-neutron coincidence counter has been constructed specifically for use by the International Atomic Energy Agency as a reference neutron detector for maintenance activities. The counter is designed for use only with {sup 252}Cf sources in SR-CF-100 capsules. This manual describes the detector's mechanical and electrical components and its operating characteristics. 2 refs., 8 figs.

  4. Cyber Security Incident Management Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-01-08

    The manual establishes minimum requirements for a structured cyber security incident detection and management process for detecting, identifying, categorizing, containing, reporting, and mitigating cyber security incidents involving DOE information and information systems operated by DOE or by contractors on behalf of the Department. No cancellations. Admin Chg 1 dated 9-1-09.

  5. Cyber Security Incident Management Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-01-08

    The manual establishes minimum requirements for a structured cyber security incident detection and management process for detecting, identifying, categorizing, containing, reporting, and mitigating cyber security incidents involving DOE information and information systems operated by DOE or by contractors on behalf of the Department. No cancellations.

  6. Radioactive Material Transportation Practices Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-06-04

    This Manual establishes standard transportation practices for the Department of Energy, including National Nuclear Security Administration to use in planning and executing offsite shipments of radioactive materials and waste. The revision reflects ongoing collaboration of DOE and outside organizations on the transportation of radioactive material and waste. Supersedes DOE M 460.2-1.

  7. PNNL Hoisting and Rigging Manual

    SciTech Connect (OSTI)

    Haynie, Todd O.; Fullmer, Michael W.

    2008-12-29

    This manual describes the safe and cost effective operation, inspection, maintenance, and repair requirements for cranes, hoists, fork trucks, slings, rigging hardware, and hoisting equipment. It is intended to be a user's guide to requirements, codes, laws, regulations, standards, and practices that apply to Pacific Northwest National Laboratory (PNNL) and its subcontractors.

  8. COE1 Calorimeter Operations Manual

    SciTech Connect (OSTI)

    Santi, Peter Angelo

    2015-12-15

    The purpose of this manual is to describe the operations of the COE1 calorimeter which is used to measure the thermal power generated by the radioactive decay of plutonium-bearing materials for the purposes of assaying the amount of plutonium within the material.

  9. NPDES Permit Writers Manual | Open Energy Information

    Open Energy Info (EERE)

    Permit Writers Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library Web Site: NPDES Permit Writers Manual Abstract This website contains the PDF version of the...

  10. Users Manual for the FEHMN application

    SciTech Connect (OSTI)

    Zyvoloski, G.A.; Robinson, B.A.; Dash, Z.V.; Trease, L.L.

    1996-09-01

    The user`s manual documents the use of the Yucca Mountain Site Characterization Projects Finite element heat and mass transfer code (FEHMN) application. The manual covers: Program considerations, data files, input data, output, system interface, and examples.

  11. Explosive Safety Manual, to a New Order

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2010-12-02

    This memorandum provides justification for the conversion of Department of Energy (DOE) Manual (M) 440.1-1A, DOE Explosives Safety Manual, dated 1-9-06, into a new DOE Order.

  12. Departmental Directives Program Manual - DOE Directives, Delegations...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    M 251.1-1B, Departmental Directives Program Manual by Website Administrator Functional areas: Information Technology, The Manual supplements DOE O 251.1B. Cancels DOE M 251.1-1A....

  13. RAVEN User Manual

    SciTech Connect (OSTI)

    Mandelli, Diego; Rabiti, Cristian; Cogliati, Joshua Joseph; Kinoshita, Robert Arthur; Alfonsi, Andrea; Sen, Ramazan Sonat

    2015-10-01

    RAVEN is a generic software framework to perform parametric and probabilistic analysis based on the response of complex system codes. The initial development was aimed to provide dynamic risk analysis capabilities to the Thermo-Hydraulic code RELAP-7, currently under development at the Idaho National Laboratory (INL). Although the initial goal has been fully accomplished, RAVEN is now a multi-purpose probabilistic and uncertainty quantification platform, capable to agnostically communicate with any system code. This agnosticism includes providing Application Programming Interfaces (APIs). These APIs are used to allow RAVEN to interact with any code as long as all the parameters that need to be perturbed are accessible by inputs files or via python interfaces. RAVEN is capable of investigating the system response, and investigating the input space using Monte Carlo, Grid, or Latin Hyper Cube sampling schemes, but its strength is focused toward system feature discovery, such as limit surfaces, separating regions of the input space leading to system failure, using dynamic supervised learning techniques. The development of RAVEN has started in 2012, when, within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the need to provide a modern risk evaluation framework became stronger. RAVEN principal assignment is to provide the necessary software and algorithms in order to employ the concept developed by the Risk Informed Safety Margin Characterization (RISMC) program. RISMC is one of the pathways defined within the Light Water Reactor Sustainability (LWRS) program. In the RISMC approach, the goal is not just the individuation of the frequency of an event potentially leading to a system failure, but the closeness (or not) to key safety-related events. Hence, the approach is interested in identifying and increasing the safety margins related to those events. A safety margin is a numerical value quantifying the probability that a safety metric (e.g. for

  14. Fan System Assessment Tool User Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    User Manual Fan System Assessment Tool User Manual This user manual will help users understand how to use AMO's Fan System Assessment Tool. Fan System Assessment Tool User Manual ...

  15. PUB-3000 | BERKELEY LAB HEALTH AND SAFETY MANUAL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ES&H MANUAL (PUB-3000) Berkeley Lab Table of Contents Guide to Using the ES&H Manual Responsible Authors Log of ES&H Manual Changes Requesting a Change to the ES&H Manual Search...

  16. DOE Manual 442.1-1 Differing Professional Opinions Manual for Technical

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Issues Involving Environment, Safety, and Health | Department of Energy Manual 442.1-1 Differing Professional Opinions Manual for Technical Issues Involving Environment, Safety, and Health DOE Manual 442.1-1 Differing Professional Opinions Manual for Technical Issues Involving Environment, Safety, and Health Stakeholders: DOE Employees, contractors, and subcontractors Scope: DOE Manual 442.1-1 seeks to establish a Differing Professional Opinion (DPO) process. This process is to encourage DOE

  17. Internal dosimetry technical basis manual

    SciTech Connect (OSTI)

    Not Available

    1990-12-20

    The internal dosimetry program at the Savannah River Site (SRS) consists of radiation protection programs and activities used to detect and evaluate intakes of radioactive material by radiation workers. Examples of such programs are: air monitoring; surface contamination monitoring; personal contamination surveys; radiobioassay; and dose assessment. The objectives of the internal dosimetry program are to demonstrate that the workplace is under control and that workers are not being exposed to radioactive material, and to detect and assess inadvertent intakes in the workplace. The Savannah River Site Internal Dosimetry Technical Basis Manual (TBM) is intended to provide a technical and philosophical discussion of the radiobioassay and dose assessment aspects of the internal dosimetry program. Detailed information on air, surface, and personal contamination surveillance programs is not given in this manual except for how these programs interface with routine and special bioassay programs.

  18. Cyber Security Incident Management Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-01-08

    The manual establishes minimum requirements for a structured cyber security incident detection and management process for detecting, identifying, categorizing, containing, reporting, and mitigating cyber security incidents involving DOE information and information systems operated by DOE or by contractors on behalf of the Department. Admin Chg 1 dated 9-1-09; Admin Chg 2 dated 12-22-09. Canceled by DOE O 205.1B.

  19. Plutonium nitrate bottle counter manual

    SciTech Connect (OSTI)

    Menlove, H.O.; Adams, E.L.; Holbrooks, O.R.

    1984-03-01

    A neutron coincidence counter has been designed for plutonium nitrate assay in large storage bottles. This assay system can be used in the reprocessing plant or in the nitrate-to-oxide conversion facility. The system is based on the family of neutron detectors similar to the high-level neutron coincidence counter. This manual describes the system and gives performance and calibration parameters for typical applications. 4 references, 11 figures, 9 tables.

  20. Surface Environmental Surveillance Procedures Manual

    SciTech Connect (OSTI)

    RW Hanf; TM Poston

    2000-09-20

    Environmental surveillance data are used in assessing the impact of current and past site operations on human health and the environment, demonstrating compliance with applicable local, state, and federal environmental regulations, and verifying the adequacy of containment and effluent controls. SESP sampling schedules are reviewed, revised, and published each calendar year in the Hanford Site Environmental Surveillance Master Sampling Schedule. Environmental samples are collected by SESP staff in accordance with the approved sample collection procedures documented in this manual.

  1. Vegetation Change Analysis User's Manual

    SciTech Connect (OSTI)

    D. J. Hansen; W. K. Ostler

    2002-10-01

    Approximately 70 percent of all U.S. military training lands are located in arid and semi-arid areas. Training activities in such areas frequently adversely affect vegetation, damaging plants and reducing the resilience of vegetation to recover once disturbed. Fugitive dust resulting from a loss of vegetation creates additional problems for human health, increasing accidents due to decreased visibility, and increasing maintenance costs for roads, vehicles, and equipment. Diagnostic techniques are needed to identify thresholds of sustainable military use. A cooperative effort among U.S. Department of Energy, U.S. Department of Defense, and selected university scientists was undertaken to focus on developing new techniques for monitoring and mitigating military impacts in arid lands. This manual focuses on the development of new monitoring techniques that have been implemented at Fort Irwin, California. New mitigation techniques are described in a separate companion manual. This User's Manual is designed to address diagnostic capabilities needed to distinguish between various degrees of sustainable and nonsustainable impacts due to military training and testing and habitat-disturbing activities in desert ecosystems. Techniques described here focus on the use of high-resolution imagery and the application of image-processing techniques developed primarily for medical research. A discussion is provided about the measurement of plant biomass and shrub canopy cover in arid. lands using conventional methods. Both semiquantitative methods and quantitative methods are discussed and reference to current literature is provided. A background about the use of digital imagery to measure vegetation is presented.

  2. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema (OSTI)

    White, Owen [University of Maryland

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  3. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

    SciTech Connect (OSTI)

    Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.; Chia, Nicholas; Price, Nathan D.; Maranas, Costas D.

    2014-10-16

    Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary to

  4. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Benedict, Matthew N.; Mundy, Michael B.; Henry, Christopher S.; Chia, Nicholas; Price, Nathan D.; Maranas, Costas D.

    2014-10-16

    Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genesmore » and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary

  5. Manual

    Office of Environmental Management (EM)

    Sites | Department of Energy Managing Legacy Records for Formerly Utilized Sites Remedial Action Program Sites Managing Legacy Records for Formerly Utilized Sites Remedial Action Program Sites Managing Legacy Records for Formerly Utilized Sites Remedial Action Program Sites (Waste Management Conference 2008) Managing Legacy Records for Formerly Utilized Sites Remedial Action Program Sites (317.04 KB) More Documents & Publications FUSRAP Overview Recent Developments in DOE FUSRAP Process

  6. Manual

    Office of Environmental Management (EM)

    Emergency Management at the Savannah River Site January 2010 Office of Independent Oversight Office of Health, Safety and Security Office of Health, Safety and Security HSS Independent Oversight Abbreviations i 1 Introduction 1 2 Results 3 3 Conclusions 6 Appendix A - Supplemental Information 9 Appendix B - Emergency Planning 11 Appendix C - Emergency Preparedness 19 Appendix D - Emergency Response 28 Appendix E - Readiness Assurance 37 | table Of cOntents table of contents Independent Oversight

  7. Manual

    Office of Environmental Management (EM)

    Environment, Safety, and Health Programs at the Savannah River Operations Office and Savannah River Site January 2010 Office of Independent Oversight Office of Health, Safety and Security Office of Health, Safety and Security HSS Independent Oversight Abbreviations i 1 Introduction 1 2 Positive Attributes 5 3 Weaknesses 9 4 Results 12 4.1 Work Planning and Control 12 4.2 Focus Areas 14 4.3 Feedback and Improvement 16 5 Conclusions 20 Appendix A - Supplemental Information 22 | table Of cOntents

  8. Manual

    Energy Savers [EERE]

    were missed or not adequately communicated to the workers for hazards including noise, welding activities, and electrical arc flashes. In addition, some work controls are not...

  9. Manual

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... SRNS is enhancing the effectiveness of their ... errors to identify underlying contributing organizational and systemic ... improvement concepts and techniques are ...

  10. Manual

    Energy Savers [EERE]

    and Development RMWMF Radioactive and Mixed Waste Management Facility RWNMDD Regulated WasteNuclear Material Disposition Department SAC Specific Administrative Control SME...

  11. Manual

    Office of Environmental Management (EM)

    Appendix A - Supplemental Information 9 Appendix B - Emergency Planning 11 Appendix C - ... identifying and correcting problems, as well as facilitating improvements ...

  12. Manual

    Energy Savers [EERE]

    to larger materials). These more reactive particles can enter the body through the lungs or digestive tract, and nanomaterials may also enter the body through absorption...

  13. Classified Information Systems Security Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-08-03

    This Manual provides requirements and implementation instructions for the graded protection of the confidentiality, integrity, and availability of information processed on all automated information systems used to collect, create, process, transmit, store, and disseminate classified information by, or on behalf of, the Department of Energy (DOE). DOE N 205.4 cancels Chapter III section 8, Incident Reporting, and DOE N 205.3 cancels Chapter VI, paragraph 4j(2), 4j(6); and Chapter VII, paragraph 12a(2)(a). Cancels: DOE M 5639.6A-1. Canceled by DOE M 205.1-4.

  14. Sierra/SM theory manual.

    SciTech Connect (OSTI)

    Crane, Nathan Karl

    2013-07-01

    Presented in this document are the theoretical aspects of capabilities contained in the Sierra/SM code. This manuscript serves as an ideal starting point for understanding the theoretical foundations of the code. For a comprehensive study of these capabilities, the reader is encouraged to explore the many references to scientific articles and textbooks contained in this manual. It is important to point out that some capabilities are still in development and may not be presented in this document. Further updates to this manuscript will be made as these capabilites come closer to production level.

  15. Power Marketing Administration Emergency Management Program Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2008-09-18

    This Manual establishes emergency management policy and requirements for emergency planning, preparedness, readiness assurance, and response for the Department's Power Marketing Administrations. Supersedes DOE O 5500.11.

  16. Pumping System Assessment Tool User Manual

    Broader source: Energy.gov [DOE]

    The Pumping System Assessment Tool (PSAT) user manual gives basic information about the data entry items, the calculated results, and assorted control button features.

  17. WYDOT Access Manual | Open Energy Information

    Open Energy Info (EERE)

    search OpenEI Reference LibraryAdd to library PermittingRegulatory Guidance - GuideHandbook: WYDOT Access ManualPermittingRegulatory GuidanceGuideHandbook Abstract...

  18. ODEQ - Construction Stormwater Application and Forms Manual ...

    Open Energy Info (EERE)

    search OpenEI Reference LibraryAdd to library PermittingRegulatory Guidance - GuideHandbook: ODEQ - Construction Stormwater Application and Forms ManualPermitting...

  19. PUCT DG Interconnection Manual | Open Energy Information

    Open Energy Info (EERE)

    search OpenEI Reference LibraryAdd to library PermittingRegulatory Guidance - GuideHandbook: PUCT DG Interconnection ManualPermittingRegulatory GuidanceGuideHandbook...

  20. Incident Prevention, Warning, and Response (IPWAR) Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2004-09-30

    This Manual defines a structured, cohesive, and consistent process for performing incident prevention, warning, and response for DOE's Federal information systems and is consistent with the requirements of Federal laws, Executive orders, national security directives, and other regulations. The Manual also provides requirements and implementation instructions for the Department's Incident Prevention, Warning and Response process, and supplements DOE O 205.1, Department of Energy Cyber Security Management Program, dated 3-21-03. DOE N 205.17 cancels this manual. This manual cancels DOE N 205.4, Handling Cyber Security Alerts and Advisories and Reporting Cyber Security Incidents, dated 3/18/2002.

  1. Radiological Control Manual. Revision 0, January 1993

    SciTech Connect (OSTI)

    Not Available

    1993-04-01

    This manual has been prepared by Lawrence Berkeley Laboratory to provide guidance for site-specific additions, supplements, and clarifications to the DOE Radiological Control Manual. The guidance provided in this manual is based on the requirements given in Title 10 Code of Federal Regulations Part 835, Radiation Protection for Occupational Workers, DOE Order 5480.11, Radiation Protection for Occupational Workers, and the DOE Radiological Control Manual. The topics covered are (1) excellence in radiological control, (2) radiological standards, (3) conduct of radiological work, (4) radioactive materials, (5) radiological health support operations, (6) training and qualification, and (7) radiological records.

  2. ODEQ - Construction Stormwater Best Management Practices Manual...

    Open Energy Info (EERE)

    Best Management Practices Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library PermittingRegulatory Guidance - GuideHandbook: ODEQ - Construction Stormwater...

  3. Hanford Hoisting and Rigging Manual - Hanford Site

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to use and reproduce portions of standards relating to crane operation and safety. ... from the Mobile Crane Manual by courtesy of Construction Safety Association of Ontario. ...

  4. Automated manual transmission clutch controller

    DOE Patents [OSTI]

    Lawrie, Robert E.; Reed, Jr., Richard G.; Rausen, David J.

    1999-11-30

    A powertrain system for a hybrid vehicle. The hybrid vehicle includes a heat engine, such as a diesel engine, and an electric machine, which operates as both an electric motor and an alternator, to power the vehicle. The hybrid vehicle also includes a manual-style transmission configured to operate as an automatic transmission from the perspective of the driver. The engine and the electric machine drive an input shaft which in turn drives an output shaft of the transmission. In addition to driving the transmission, the electric machine regulates the speed of the input shaft in order to synchronize the input shaft during either an upshift or downshift of the transmission by either decreasing or increasing the speed of the input shaft. When decreasing the speed of the input shaft, the electric motor functions as an alternator to produce electrical energy which may be stored by a storage device. Operation of the transmission is controlled by a transmission controller which receives input signals and generates output signals to control shift and clutch motors to effect smooth launch, upshift shifts, and downshifts of the transmission, so that the transmission functions substantially as an automatic transmission from the perspective of the driver, while internally substantially functioning as a manual transmission.

  5. Memorandum, Implementation of Department of Energy Manual 450.4-1, Integrated Safety Management System Manual

    Broader source: Energy.gov [DOE]

    Memorandum, Implementation of Department of Energy Manual 450.401, "Integrated Safety Management System Manual". January 4, 2007. Identifies and institutionalizes requirements and responsibilities for the development and implementation of ISM systems throughout DOE.

  6. Fermilab | Director's Policy Manual | Home

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Financial Management Freedom of Information Act Requests Inclement Weather and Snow Policy Interactions with Legislators Issues Management Maintenance MOUs Between...

  7. ROOT CAUSE ANALYSIS PROGRAM MANUAL

    SciTech Connect (OSTI)

    Gravois, Melanie C.

    2007-05-02

    Root Cause Analysis (RCA) identifies the cause of an adverse condition that, if corrected, will preclude recurrence or greatly reduce the probability of recurrence of the same or similar adverse conditions and thereby protect the health and safety of the public, the workers, and the environment. This procedure sets forth the requirements for management determination and the selection of RCA methods and implementation of RCAs that are a result of significant findings from Price-Anderson Amendments Act (PAAA) violations, occurrences/events, Significant Adverse Conditions, and external oversight Corrective Action Requests (CARs) generated by the Office of Enforcement (PAAA headquarters), the U.S. Environmental Protection Agency, and other oversight entities against Lawrence Berkeley National Laboratory (LBNL). Performance of an RCA may result in the identification of issues that should be reported in accordance with the Issues Management Program Manual.

  8. Hoisting and rigging manual: Uncontrolled document

    SciTech Connect (OSTI)

    1991-05-01

    This document is a draft copy of a Hoisting and Rigging Manual for the Department of Energy. The manual is divided into ten chapters. The chapter titles follow: terminology and definitions; operator training and qualification; overhead and gantry cranes; mobile cranes; forklift trucks; hoists; hooks; wire rope, slings, and rigging accessories; construction hoisting and rigging equipment requirements; references.

  9. Davis PV plant operation and maintenance manual

    SciTech Connect (OSTI)

    1994-09-01

    This operation and maintenance manual contains the information necessary to run the Photovoltaics for Utility Scale Applications (PVUSA) test facility in Davis, California. References to more specific information available in drawings, data sheets, files, or vendor manuals are included. The PVUSA is a national cooperative research and demonstration program formed in 1987 to assess the potential of utility scale photovoltaic systems.

  10. EPA - NPDES Permit Writers Manual | Open Energy Information

    Open Energy Info (EERE)

    Permit Writers Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library Web Site: EPA - NPDES Permit Writers Manual Abstract This manual provides an overview of...

  11. TxDOT Access Management Manual | Open Energy Information

    Open Energy Info (EERE)

    Access Management Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library Legal Document- OtherOther: TxDOT Access Management ManualLegal Abstract Manual prepared...

  12. General Renewable Energy-Legal Documents and Operation Manuals...

    Open Energy Info (EERE)

    and Operation Manuals Jump to: navigation, search Tool Summary LAUNCH TOOL Name: General Renewable Energy-Legal Documents and Operation Manuals AgencyCompany Organization: World...

  13. Estimating the Opportunity Cost of REDD+: A Training Manual ...

    Open Energy Info (EERE)

    the Opportunity Cost of REDD+: A Training Manual Jump to: navigation, search Tool Summary LAUNCH TOOL Name: Estimating the Opportunity Cost of REDD+: A Training Manual Agency...

  14. Manual for Quantitative Evaluation of the Co-Benefits Approach...

    Open Energy Info (EERE)

    Manual for Quantitative Evaluation of the Co-Benefits Approach to Climate Change Jump to: navigation, search Tool Summary LAUNCH TOOL Name: Manual for Quantitative Evaluation of...

  15. New DOE IH Manual Chapter on Exposure Assessment | Department...

    Office of Environmental Management (EM)

    New DOE IH Manual Chapter on Exposure Assessment New DOE IH Manual Chapter on Exposure Assessment August 2009 Presenter: Danny Field, National Nuclear Security Administration Track...

  16. DOepatents XML Product Data Services Manual | OSTI, US Dept of...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DOepatents XML Product Data Services Manual Document Files and References Available Downloads for this Document: applicationpdf icon DOepatentsXMLDataServicesManual.pdf Last...

  17. EPA Section 401 Water Quality Certification Manual | Open Energy...

    Open Energy Info (EERE)

    Section 401 Water Quality Certification Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library Reference: EPA Section 401 Water Quality Certification Manual...

  18. Update of identification and estimation of socioeconomic impacts resulting from perceived risks and changing images: An annotated bibliography

    SciTech Connect (OSTI)

    Nieves, L.A.; Clark, D.E.; Wernette, D.

    1991-08-01

    This annotated bibliography reviews selected literature published through August 1991 on the identification of perceived risks and methods for estimating the economic impacts of risk perception. It updates the literature review found in Argonne National Laboratory report ANL/EAIS/TM-24 (February 1990). Included in this update are (1) a literature review of the risk perception process, of the relationship between risk perception and economic impacts, of economic methods and empirical applications, and interregional market interactions and adjustments; (2) a working bibliography (that includes the documents abstracted in the 1990 report); (3) a topical index to the abstracts found in both reports; and (4) abstracts of selected articles found in this update.

  19. HTGR Cost Model Users' Manual

    SciTech Connect (OSTI)

    A.M. Gandrik

    2012-01-01

    The High Temperature Gas-Cooler Reactor (HTGR) Cost Model was developed at the Idaho National Laboratory for the Next Generation Nuclear Plant Project. The HTGR Cost Model calculates an estimate of the capital costs, annual operating and maintenance costs, and decommissioning costs for a high-temperature gas-cooled reactor. The user can generate these costs for multiple reactor outlet temperatures; with and without power cycles, including either a Brayton or Rankine cycle; for the demonstration plant, first of a kind, or nth of a kind project phases; for a single or four-pack configuration; and for a reactor size of 350 or 600 MWt. This users manual contains the mathematical models and operating instructions for the HTGR Cost Model. Instructions, screenshots, and examples are provided to guide the user through the HTGR Cost Model. This model was design for users who are familiar with the HTGR design and Excel. Modification of the HTGR Cost Model should only be performed by users familiar with Excel and Visual Basic.

  20. 1982 Oregon energy resource manual

    SciTech Connect (OSTI)

    Ebert, R.; Ebert, J. (eds.)

    1982-01-01

    This manual is divided into three distinct sections. Part one contains 40 passive solar home plans designed for the Pacific Northwest by Oregon architects and designers. Floor plans and exterior renderings of multi-family and single-family dwellings, earth sheltered and bermed designs, and light commercial structures are included. The degree of solar contribution each residence achieves is graphically presented for ease of understanding. Part two, renewable-energy-resource guide, is primarily designed as a locator to indepth publications that explain specific energy resources in detail. It contains illustrated book reviews of pertinent private and government publications available. Various tables, forms, diagrams, energy system evaluation criteria, an illustrated glossary, BPA energy programs, utility programs, financial outlooks and non-profit organizations are included. The product locator index makes up part three. This indexed directory contains the listings of businesses, including the address, phone number, contact person and a 30 to 50 word description of the product or services currently offered. These renewable energy companies range from architectural and engineering services to research and development firms.

  1. Home audit program: management manual

    SciTech Connect (OSTI)

    Not Available

    1980-09-01

    Many public power systems have initiated home energy audit programs in response to the requests of their consumers. The manual provides smaller public power systems with the information and specific skills needed to design and develop a program of residential energy audits. The program is based on the following precepts: locally owned public systems are the best, and in many cases the only agencies available to organize and coordinate energy conservation programs in many smaller communities; consumers' rights to energy conservation information and assistance should not hinge on the size of the utility that serves them; in the short run, public power systems of all sizes should offer residential energy conservation assistance to their consumers, because such assistance is desirable, necessary, and in the public interest; and in the long run, such programs will complement national energy goals and will produce economic benefits for both consumers and the public power system. A detailed description of home audit program planning, organization, and management are given. (MCW)

  2. DOE Manual Studies Terrestrial Carbon Sequestration

    Broader source: Energy.gov [DOE]

    There is considerable opportunity and growing technical sophistication to make terrestrial carbon sequestration both practical and effective, according to the latest carbon capture and storage "best practices" manual issued by the U.S. Department of Energy.

  3. BLM Manual 2802 | Open Energy Information

    Open Energy Info (EERE)

    search OpenEI Reference LibraryAdd to library PermittingRegulatory Guidance - GuideHandbook: BLM Manual 2802PermittingRegulatory GuidanceGuideHandbook Author BLM...

  4. Alternative Fuel Driver Training Companion Manual

    SciTech Connect (OSTI)

    Not Available

    2005-09-01

    Training manual serves as a companion to alternative fuel training presentations on the fueling and use of vehicles that run on compressed natural gas, biodiesel, E85, and propane.

  5. Safety Management Functions, Responsibilities, and Authorities Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2003-12-31

    This Manual defines safety management functions, responsibilities, and authorities for DOE senior management with responsibilities for line, support, oversight, and enforcement actions. Cancels DOE M 411.1-1B. Canceled by DOE O 450.2.

  6. Safety Management Functions, Responsibilities, and Authorities Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1997-10-08

    This Manual defines safety management functions, responsibilities, and authorities for DOE senior management with responsibilities for line, support, oversight, and enforcement actions. Canceled by DOE M 411.1-1A. Does not cancel other directives.

  7. Environment, Safety, and Health Reporting Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1996-11-07

    This Manual provides detailed requirements to supplement DOE O 231.1, ENVIRONMENT, SAFETY AND HEALTH REPORTING, which establishes management objectives and requirements for reporting environment, safety and health information. Chg 1, 11-7-96.

  8. Environment Safety and Health Reporting Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1995-09-30

    This Manual provides detailed requirements to supplement DOE O 231.1, Environment, Safety and Health Reporting, which establishes management objectives and requirements for reporting environment, safety and health information. Does not cancel other directives.

  9. Jefferson Lab Project Control System Manual

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    IP > Project Control System Manual Privacy and Security Notice Skip over navigation Search the JLab Site Search Please upgrade your browser. This site's design is only visible in a graphical browser that supports web standards, but its content is accessible to any browser. Concerns? Jefferson Lab Navigation Home Search print version LINKS CEBAF 12 GeV Upgrade FEL Contact Our Staff Directorate Project Control System Manual Technical Engineering Development Facility (TEDF) Utilities

  10. IMG ER: A System for Microbial Genome Annotation Expert Review and Curation

    SciTech Connect (OSTI)

    Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.; Chu, Ken; Kyrpides, Nikos C.

    2009-05-25

    A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

  11. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; et al

    2015-10-26

    The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

  12. Operations and Maintenance Manual for Large Aperture Scanner System

    SciTech Connect (OSTI)

    Jones, Anthony M.; Hall, Thomas E.

    2010-04-08

    Operations and maintenance manual includes detailed instructions for system assembly, use, and maintenance.

  13. MotorMaster+ User Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    User Manual MotorMaster+ User Manual This user manual is designed to help users understand the MotorMaster+ software tool. MotorMaster+ User Manual (1.92 MB) More Documents & Publications MotorMaster+ International Fact Sheet Replacing an Oversized and Underloaded Electric Motor MotorMaster+ Fact Sheet

  14. Annotated bibliography of coal in the Caribbean region. [Lignite

    SciTech Connect (OSTI)

    Orndorff, R.C.

    1985-01-01

    The purpose of preparing this annotated bibliography was to compile information on coal localities for the Caribbean region used for preparation of a coal map of the region. Also, it serves as a brief reference list of publications for future coal studies in the Caribbean region. It is in no way an exhaustive study or complete listing of coal literature for the Caribbean. All the material was gathered from published literature with the exception of information from Cuba which was supplied from a study by Gordon Wood of the US Geological Survey, Branch of Coal Resources. Following the classification system of the US Geological Survey (Wood and others, 1983), the term coal resources has been used in this report for reference to general estimates of coal quantities even though authors of the material being annotated may have used the term coal reserves in a similar denotation. The literature ranges from 1857 to 1981. The countries listed include Colombia, Mexico, Venezuela, Cuba, the Dominican Republic, Haiti, Jamaica, Puerto Rico, and the countries of Central America.

  15. Pioneer Plants Study User's Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Pioneer Plants Study User's Manual Pioneer Plants Study User's Manual This manual supplies the material needed to apply the results of the Pioneer Plants Study analysis. It is a companion piece to Understanding Cost Growth and Performance Shortfalls in Pioneer Process Plants. Members of both private industry and government could find this manual a useful tool in predicting the cost growth and performance of first-of-a-kind process plants. Pioneer Plants Study User's Manual (3.01 MB) More

  16. FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J. P.; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; et al

    2016-06-13

    In this study, nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. Here, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same datamore » format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. In conclusion, our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

  17. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J. P.; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; et al

    2016-06-13

    Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. In this paper, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data formatmore » to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Finally, data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

  18. The Wheeling and Transmission Manual, Second Edition

    SciTech Connect (OSTI)

    Weiss, L.; Spiewak, S.

    1991-01-01

    The Wheeling and Transmission Manual addresses the key issues involved in the debate: the need for coordination, the extent to which access should be permitted, various pricing methodologies which might be employed, obstacles to the addition of new transmission capacity, and contractual matters which should be considered in negotiations between the parties. As one shall see, these matters are all interrelated and the resolution of any of them may affect the outcome of the others. The Manual is designed to give an overview of the issues involved. It is not intended exclusively for the expert engineer or attorney, although both might benefit from it. Rather, the Manual was written with the objective of providing decisionmakers and policymakers with detailed, timely and understandable materials to evaluate the specific circumstances affecting their companies. Each chapter of the book is indexed separately.

  19. NV/YMP RADIOLOGICAL CONTROL MANUAL

    SciTech Connect (OSTI)

    U.S. DEPARTMENT OF ENERGY, NATIONAL NUCLEAR SECURITY ADMINISTRATION NEVADA SITE OFFICE; BECHTEL NEVADA

    2004-11-01

    This manual contains the radiological control requirements to be used for all radiological activities conducted by programs under the purview of the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) and the Yucca Mountain Office of Repository Development (YMORD). Compliance with these requirements will ensure compliance with Title 10 Code of Federal Regulations Part 835 (10 CFR 835), Occupational Radiation Protection. Programs covered by this manual are located at the Nevada Test Site (NTS); Nellis Air Force Base and North Las Vegas, Nevada; Santa Barbara and Pleasanton, California; and at Andrews Air Force Base, Maryland. In addition, field work by NNSA/NSO at other locations is also covered by this manual.

  20. Hanford Waste Vitrification Plant technical manual

    SciTech Connect (OSTI)

    Larson, D.E.; Watrous, R.A.; Kruger, O.L.

    1996-03-01

    A key element of the Hanford waste management strategy is the construction of a new facility, the Hanford Waste Vitrification Plant (HWVP), to vitrify existing and future liquid high-level waste produced by defense activities at the Hanford Site. The HWVP mission is to vitrify pretreated waste in borosilicate glass, cast the glass into stainless steel canisters, and store the canisters at the Hanford Site until they are shipped to a federal geological repository. The HWVP Technical Manual (Manual) documents the technical bases of the current HWVP process and provides a physical description of the related equipment and the plant. The immediate purpose of the document is to provide the technical bases for preparation of project baseline documents that will be used to direct the Title 1 and Title 2 design by the A/E, Fluor. The content of the Manual is organized in the following manner. Chapter 1.0 contains the background and context within which the HWVP was designed. Chapter 2.0 describes the site, plant, equipment and supporting services and provides the context for application of the process information in the Manual. Chapter 3.0 provides plant feed and product requirements, which are primary process bases for plant operation. Chapter 4.0 summarizes the technology for each plant process. Chapter 5.0 describes the engineering principles for designing major types of HWVP equipment. Chapter 6.0 describes the general safety aspects of the plant and process to assist in safe and prudent facility operation. Chapter 7.0 includes a description of the waste form qualification program and data. Chapter 8.0 indicates the current status of quality assurance requirements for the Manual. The Appendices provide data that are too extensive to be placed in the main text, such as extensive tables and sets of figures. The Manual is a revision of the 1987 version.

  1. Solid waste disposal facility criteria. Technical manual

    SciTech Connect (OSTI)

    Not Available

    1993-11-01

    The technical manual has been developed to assist municipal solid waste landfill (MSWLF) owners and operators in achieving compliance with the revised MSWLF Criteria, promulgated on October 9, 1991 in Title 40, Part 258, of the Code of Federal Regulations (CFR). The manual is not a regulatory document, and does not provide mandatory technical guidance, but does provide assistance for coming into compliance with the technical aspects of the revised landfill Criteria. The document is intended for use by landfill owners/operators and their consultants and contractors who provide advice on demonstrating compliance with the Part 258 standards.

  2. Innovative and Alternative Technology Assessment Manual

    SciTech Connect (OSTI)

    1980-02-01

    This four chapter, six appendix manual presents the procedures and methodology as well as the baseline costs and energy information necessary for the analysis and evaluation of innovative and alternative technology applications submitted for federal grant assistance under the innovative and alternative technology provisions of the Clean Water Act of 1977. The manual clarifies and interprets the intent of Congress and the Environmental Protection Agency in carrying out the mandates of the innovative and alternative provisions of the Clean Water Act of 1977. [DJE 2005

  3. DOE Manual - Advisory Committee Management Program

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    MANUAL DOE M 515.1-1 Approved: 10-22-07 ADVISORY COMMITTEE MANAGEMENT PROGRAM U.S. DEPARTMENT OF ENERGY Office of Management AVAILABLE ONLINE AT: INITIATED BY: www.directives.doe.gov Office of Management i DOE M 515.1-1 10-22-07 ADVISORY COMMITTEE MANAGEMENT PROGRAM 1. PURPOSE. This Manual supplements the Federal Advisory Committee Act (FACA), Title 5 United States Code (U.S.C.), Appendix 2, as amended, and the General Services Administration's (GSA's) final rule "Federal Advisory Committee

  4. DOE Cooperative Research and Development Agreements Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2001-01-12

    This Manual provides detailed requirements to supplement DOE O 483.1, DOE Cooperative Research and Development Agreements, dated 1-12-01, which establishes requirements for the performance of technology transfer through the use of Cooperative Research and Development Agreements (CRADAs). Canceled by DOE O 483.1A.

  5. Classified Matter Protection and Control Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2001-04-17

    This Manual supplements DOE O 471.2A, Information Security Program, and provides detailed requirements for the protection and control of classified matter. Cancels DOE M 471.2-1B except Chapter III paragraphs 1 and 2, and Chapter IV.

  6. Security Controls for Unclassified Information Systems Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-01-05

    The Manual establishes minimum implementation standards for cyber security technical, management, and operational controls that will be followed in all information systems operated by DOE and the information systems. Admin Chg 1 dated 9-1-09. Canceled by DOE O 205.1B.

  7. Nevada Test Site Radiological Control Manual

    SciTech Connect (OSTI)

    Radiological Control Managers' Council - Nevada Test Site

    2009-10-01

    This document supersedes DOE/NV/11718--079, “NV/YMP Radiological Control Manual,” Revision 5 issued in November 2004. Brief Description of Revision: A complete revision to reflect the recent changes in compliance requirements with 10 CFR 835, and for use as a reference document for Tenant Organization Radiological Protection Programs.

  8. Safety Management Functions, Responsibilities, and Authorities Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-10-18

    This Manual is a mechanism for implementing the Department's guiding principles established in DOE P 450.4 and the safety management functions outlined in DOE P 411.1 Cancels DOE M 411.1-1. Canceled by DOE M 411.1-1B.

  9. Environment, Safety, and Health Reporting Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2004-03-19

    This Manual supplements DOE O 231.1A and provides detailed requirements for implementing Department of Energy reporting requirements, including time schedules for reporting and data elements to be reported. Cancels DOE M 231.1-1, DOE N 231.1.

  10. Security Controls for Unclassified Information Systems Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-01-05

    The Manual establishes minimum implementation standards for cyber security technical, management, and operational controls that will be followed in all information systems operated by DOE and the information systems. Does not cancel other directives. Canceled by DOE O 205.1B

  11. Security Controls for Unclassified Information Systems Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2009-01-05

    The Manual establishes minimum implementation standards for cyber security technical, management, and operational controls that will be followed in all information systems operated by DOE and the information systems. Admin Chg 1 dated 9-1-09; Admin Chg 2 dated 12-22-09. Canceled by DOE O 205.1B.

  12. State authorization manual. Volume 2. Appendices

    SciTech Connect (OSTI)

    Brugler-Jones, S.

    1990-10-01

    The document provides the supportive appendices for Volume 1 of the State Authorization Manual (SAM), which provides guidance for States applying for program revisions to their authorized RCRA State program. Among the appendices are: various program checklists, lists of revision checklists by cluster, model Federal Register Notices, guidance for State Authorization Files, and guidance for using Wordperfect files and for CFR files.

  13. DOE explosives safety manual. Revision 7

    SciTech Connect (OSTI)

    Not Available

    1994-08-01

    This manual prescribes the Department of Energy (DOE) safety rules used to implement the DOE safety policy for operations involving explosives. This manual is applicable to all DOE facilities engaged in operations of development, manufacturing, handling, storage, transportation, processing, or testing of explosives, pyrotechnics and propellants, or assemblies containing these materials. The standards of this manual deal with the operations involving explosives, pyrotechnics and propellants, and the safe management of such operations. The design of all new explosives facilities shall conform to the requirements established in this manual and implemented in DOE 6430.1A, ``General Design Criteria Manual.`` It is not intended that existing physical facilities be changed arbitrarily to comply with these provisions, except as required by law. Existing facilities that do not comply with these standards may continue to be used for the balance of their functional life, as long as the current operation presents no significantly greater risk than that assumed when the facility was originally designed and it can be demonstrated clearly that a modification to bring the facility into compliance is not feasible. However, in the case of a major renovation, the facility must be brought into compliance with current standards. The standards are presented as either mandatory or advisory. Mandatory standards, denoted by the words ``shall,`` ``must,`` or ``will,`` are requirements that must be followed unless written authority for deviation is granted as an exemption by the DOE. Advisory standards denoted by ``should`` or ``may`` are standards that may be deviated from with a waiver granted by facility management.

  14. Clean Air Act: Confidential business information security manual (revised). Procedures manual

    SciTech Connect (OSTI)

    Toomer, M.W.

    1998-08-01

    The procedures in this manual provide Federal, contractor, and subcontractor employees with the information necessary to utilize Confidential Business Information to perform their assigned duties without violating applicable Federal regulations protecting the rights of its owners.

  15. Reference Manual and Procedures for Implementation of PURPA Standards...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    EPACT 2005 (March 2006) Reference Manual and Procedures for Implementation of PURPA Standards in EPACT 2005 (March 2006) This reference manual is intended to be used as an aid to state ...

  16. Cancellation Notice for Policies, Notices, Orders or Manuals - DOE

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Directives, Delegations, and Requirements Notice for Policies, Notices, Orders or Manuals by Website Administrator Microsoft Word Document icon CancellationNotice-PoliciesNoticesOrdersManuals (2).doc - Microsoft Word Document, 30 KB (3123

  17. Low-Level Waste Disposal Facility Federal Review Group Manual...

    Office of Environmental Management (EM)

    Low-Level Waste Disposal Facility Federal Review Group Manual Low-Level Waste Disposal Facility Federal Review Group Manual This Revision 3 of the Low-Level Waste Disposal Facility ...

  18. SCRA Oversize/Overweight Permit Manual | Open Energy Information

    Open Energy Info (EERE)

    SCRA OversizeOverweight Permit Manual Jump to: navigation, search OpenEI Reference LibraryAdd to library Legal Document- OtherOther: SCRA OversizeOverweight Permit ManualLegal...

  19. Data collection system. Volume 1, Overview and operators manual; Volume 2, Maintenance manual; Appendices

    SciTech Connect (OSTI)

    Caudell, R.B.; Bauder, M.E.; Boyer, W.B.; French, R.E.; Isidoro, R.J.; Kaestner, P.C.; Perkins, W.G.

    1993-09-01

    Sandia National Laboratories (SNL) Instrumentation Development Department was tasked by the Defense Nuclear Agency (DNA) to record data on Tektronix RTD720 Digitizers on the HUNTERS TROPHY field test conducted at the Nevada Test Site (NTS) on September 18, 1992. This report contains a overview and description of the computer hardware and software that was used to acquire, reduce, and display the data. The document is divided into two volumes: an overview and operators manual (Volume 1) and a maintenance manual (Volume 2).

  20. Energy and Environmental Issues in Eastern Europe and Central Asia: An Annotated Guide to Information Resources

    SciTech Connect (OSTI)

    Gant, K.S.

    2000-10-09

    Energy and environmental problems undermine the potential for sustained economic development and contribute to political and economic instability in the strategically important region surrounding the Caspian and Black Seas. Many organizations supporting efforts to resolve problems in this region have found that consensus building--a prerequisite for action--is a difficult process. Reaching agreement on priorities for investment, technical collaboration, and policy incentives depends upon informed decision-making by governments and local stakeholders. And while vast quantities of data and numerous analyses and reports are more accessible than ever, wading through the many potential sources in search of timely and relevant data is a formidable task. To facilitate more successful data searches and retrieval, this document provides annotated references to over 200 specific information sources, and over twenty primary search engines and data retrieval services, that provide relevant and timely information related to the environment, energy, and economic development around the Caspian and Black Seas. This document is an advance copy of the content that Oak Ridge National Laboratory (ORNL) plans to transfer to the web in HTML format to facilitate interactive search and retrieval of information using standard web-browser software.

  1. Suspect/Counterfeit Items Awareness Training Manual | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Suspect/Counterfeit Items Awareness Training Manual Suspect/Counterfeit Items Awareness Training Manual June 2007 The Suspect/Counterfeit Items Awareness Training manual provides information on individual components identified as suspect or counterfeit. The DOE Office of Environmental Protection, Sustainability Support & Corporate Safety Analysis has taken a corporate leadership role and is accountable for ensuring the effective implementation of the Department's S/CI process. The manual

  2. Reimbursable Work for Non-Federal Sponsors Process Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1996-09-30

    This Manual provides detailed requirements to supplement DOE O 481.1. Does not cancel other directives.

  3. Low-level radioactive waste technology: a selected, annotated bibliography

    SciTech Connect (OSTI)

    Fore, C.S.; Vaughan, N.D.; Hyder, L.K.

    1980-10-01

    This annotated bibliography of 447 references contains scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on environmental transport, disposal site, and waste treatment studies. The publication covers both domestic and foreign literature for the period 1952 to 1979. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology and Site Resources; Regulatory and Economic Aspects; Transportation Technology; Waste Production; and Waste Treatment. Specialized data fields have been incorporated into the data file to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the Measured Radionuclides field, and specific parameters which affect the migration of these radionuclides are presented in the Measured Parameters field. In addition, each document referenced in this bibliography has been assigned a relevance number to facilitate sorting the documents according to their pertinence to low-level radioactive waste technology. The documents are rated 1, 2, 3, or 4, with 1 indicating direct applicability to low-level radioactive waste technology and 4 indicating that a considerable amount of interpretation is required for the information presented to be applied. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. Indexes are provide for (1) author(s), (2) keywords, (3) subject category, (4) title, (5) geographic location, (6) measured parameters, (7) measured radionuclides, and (8) publication description.

  4. Casting Annotation as an Optimization Problem (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Overbeek, Ross

    2011-06-08

    Ross Overbeek of the Fellowship for Interpretation of Genomes gives a presentation on "Casting Annotation as an Optimization Problem" at the JGI/Argonne HPC Workshop on January 25, 2010.

  5. Next-Gen Annotation Based on Transcriptomics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Cottingham, Bob [ORNL

    2011-06-08

    Bob Cottingham of the Oak Ridge National Laboratory gives a presentation on "Next-Gen Annotation based on Transcriptomics" at the JGI/Argonne HPC Workshop on January 25, 2010.

  6. Casting Annotation as an Optimization Problem (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Overbeek, Ross

    2010-01-25

    Ross Overbeek of the Fellowship for Interpretation of Genomes gives a presentation on "Casting Annotation as an Optimization Problem" at the JGI/Argonne HPC Workshop on January 25, 2010.

  7. Annotation of Plant Genomes using RNA-seq Data (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Pellegrinni, Matteo [UCLA

    2011-06-08

    Matteo Pellegrini from University of California, Los Angeles gives a presentation on "Annotation of Plant Genomes using RNA-seq Data" at the JGI/Argonne HPC Workshop on January 25, 2010.

  8. Annotated bibliography for gas-mask and chemical-defense-gear related papers. Interim report

    SciTech Connect (OSTI)

    Kelly, T.L.; Sucec, A.A.; Englund, C.E.

    1988-01-15

    This is an annotated bibliography of papers that relate to the characteristics and effects of gas masks and other chemical-defense gear. Psychological, physiological, and cognitive performance effects are included.

  9. SciTech XML Data Services Manual | OSTI, US Dept of Energy Office...

    Office of Scientific and Technical Information (OSTI)

    SciTech XML Data Services Manual Available Downloads: PDF icon SciTech Connect XML Data Services Manual

  10. New local potential useful for genome annotation and 3D modeling (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Journal Article: New local potential useful for genome annotation and 3D modeling Citation Details In-Document Search Title: New local potential useful for genome annotation and 3D modeling A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The

  11. Revegetation manual for the environmental restoration contractor

    SciTech Connect (OSTI)

    McLendon, T.; Redente, E.F.

    1997-02-01

    The purpose of this manual is to provide guidance and general guidelines for the revegetation of remediation waste sites and other disturbed areas on the Hanford Site. Specific revegetation plans will be developed using guidance from this manual. Locations, resources, and funding will dictate the specific revegetation design at each disturbed area. Disturbances have occurred to some of the ecological communities of the Hanford Site. Many of these disturbances are the result of operations of the Hanford Site, including Comprehensive Environmental Response, Compensation, and Liability Act of 1980 waste sites on small portions of the Hanford Site. There were, however, extensive disturbances to the native vegetation prior to operations of the facility. These resulted from cultivation, grazing, fire, and the introduction of exotics. Revegetation planning must take into account these early disturbances, as well as the later ones.

  12. Demonstration and Validation Assets: User Manual Development

    SciTech Connect (OSTI)

    2008-06-30

    This report documents the development of a database-supported user manual for DEMVAL assets in the NSTI area of operations and focuses on providing comprehensive user information on DEMVAL assets serving businesses with national security technology applications in southern New Mexico. The DEMVAL asset program is being developed as part of the NSPP, funded by both Department of Energy (DOE) and NNSA. This report describes the development of a comprehensive user manual system for delivering indexed DEMVAL asset information to be used in marketing and visibility materials and to NSTI clients, prospective clients, stakeholders, and any person or organization seeking it. The data about area DEMVAL asset providers are organized in an SQL database with updateable application structure that optimizes ease of access and customizes search ability for the user.

  13. Radiological Emergency Response Health and Safety Manual

    SciTech Connect (OSTI)

    D. R. Bowman

    2001-05-01

    This manual was created to provide health and safety (H&S) guidance for emergency response operations. The manual is organized in sections that define each aspect of H and S Management for emergency responses. The sections are as follows: Responsibilities; Health Physics; Industrial Hygiene; Safety; Environmental Compliance; Medical; and Record Maintenance. Each section gives guidance on the types of training expected for managers and responders, safety processes and procedures to be followed when performing work, and what is expected of managers and participants. Also included are generic forms that will be used to facilitate or document activities during an emergency response. These ensure consistency in creating useful real-time and archival records and help to prevent the loss or omission of information.

  14. Universal Fast Breeder Reactor Subassembly Counter manual

    SciTech Connect (OSTI)

    Menlove, H.O.; Eccleston, G.W.; Swansen, J.E.; Goris, P.; Abedin-Zadeh, R.; Ramalho, A.

    1984-08-01

    A neutron coincidence counter has been designed for the measurement of fast breeder reactor fuel assemblies. This assay system can accommodate the full range of geometries and masses found in fast breeder subassemblies under IAEA safeguards. The system's high-performance capability accommodates high plutonium loadings of up to 16 kg. This manual describes the system and its operation and gives performance and calibration parameters for typical applications.

  15. Transportable Xenon Laboratory (TXL-1) Operations Manual

    SciTech Connect (OSTI)

    Thompson, Robert C.; Stewart, Timothy L.; Willett, Jesse A.; Woods, Vincent T.

    2011-03-07

    The Transportable Xenon Laboratory Operations Manual is a guide to set up and shut down TXL, a fully contained laboratory made up of instruments to identify and measure concentrations of the radioactive isotopes of xenon by taking air samples and analyzing them. The TXL is housed in a standard-sized shipping container. TXL can be shipped to and function in any country in the world.

  16. Alternative Fuel Driver Training Companion Manual

    Alternative Fuels and Advanced Vehicles Data Center [Office of Energy Efficiency and Renewable Energy (EERE)]

    EPAct Regulated Fleets Alternative Fuel Driver Training Companion Manual Notice This report was prepared as an account of work sponsored by an agency of the United States government. Neither the United States government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use

  17. DOE - NNSA/NFO -- FRMAC Manuals

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    FRMAC NNSA/NFO Language Options U.S. DOE/NNSA - Nevada Field Office FRMAC Documents These documents are pertinent to the operation, monitoring, analysis, and assessment capabilities of the U. S. Department of Energy, National Nuclear Security Administration Nevada Field Office's Federal Radiological Monitoring and Assessment Center (FRMAC). Overall, these manuals provide a general guidance, some specific diagrams and forms, and are intended to provide enough guidance for stand-alone use without

  18. Environment, Safety and Health Reporting Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2004-03-19

    This Manual supplements DOE O 231.1A and provides detailed requirement for implementing Department of Energy reporting requirements, including time schedules for reporting and data elements to be reported. The page change modifies policy previously established that requires recording and reporting occupational injuries and illnesses of subcontractors employees. Change 1 dated 9-9-04. Change 2 dated 6-12-07. Canceled by DOE O 231.1B

  19. Nevada National Security Site Radiological Control Manual

    SciTech Connect (OSTI)

    Radiological Control Managers’ Council

    2012-03-26

    This document supersedes DOE/NV/25946--801, 'Nevada Test Site Radiological Control Manual,' Revision 1 issued in February 2010. Brief Description of Revision: A complete revision to reflect a recent change in name for the NTS; changes in name for some tenant organizations; and to update references to current DOE policies, orders, and guidance documents. Article 237.2 was deleted. Appendix 3B was updated. Article 411.2 was modified. Article 422 was re-written to reflect the wording of DOE O 458.1. Article 431.6.d was modified. The glossary was updated. This manual contains the radiological control requirements to be used for all radiological activities conducted by programs under the purview of the U.S. Department of Energy (DOE) and the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). Compliance with these requirements will ensure compliance with Title 10 Code of Federal Regulations (CFR) Part 835, 'Occupational Radiation Protection.' Programs covered by this manual are located at the Nevada National Security Site (NNSS); Nellis Air Force Base and North Las Vegas, Nevada; Santa Barbara and Livermore, California; and Andrews Air Force Base, Maryland. In addition, fieldwork by NNSA/NSO at other locations is covered by this manual. Current activities at NNSS include operating low-level radioactive and mixed waste disposal facilities for United States defense-generated waste, assembly and execution of subcritical experiments, assembly/disassembly of special experiments, the storage and use of special nuclear materials, performing criticality experiments, emergency responder training, surface cleanup and site characterization of contaminated land areas, environmental activity by the University system, and nonnuclear test operations, such as controlled spills of hazardous materials at the Hazardous Materials Spill Center. Currently, the major potential for occupational radiation exposure is associated with the burial of

  20. UMTRA Project document control system manual

    SciTech Connect (OSTI)

    Not Available

    1994-09-01

    This manual defines the Project Document Control System (PDCS) operated by the US DOE Uranium Mill tailings Remedial Action (UMTRA) project Office. The purpose of the PDCS is to provide an active and continuing program for acquiring, controlling, retaining, retrieving, retiring and disposing of all UMTRA Project documents. The PDCS also provides guidance and coordination in transferring documents by various UMTRA Projection document control centers to a central location.

  1. Environment, Safety, and Health Reporting Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2000-01-28

    This Manual provides detailed requirements to supplement DOE O 231.1, Environment, Safety and Health Reporting, which establishes management objectives and requirements for reporting environment, safety and health information. (Paragraphs 2a, 2a(1), 2a(2), 2b, 2b(1), 2b(2), and 2i(3)(a) through 2i(3)(d) of Chapter II, and Appendix A canceled by DOE N 231.1; Chapter IV canceled by DOE O 470.2A.)

  2. Project Records Information System (PRIS) user`s manual. Revision 2

    SciTech Connect (OSTI)

    Schwarz, R.K.; Cline, B.E.; Smith, P.S.

    1993-10-01

    The Project Records Information System (PRIS) is an interactive system developed for the Information Services Division (ISD) of Martin Marietta Energy Systems, Inc., to perform indexing, maintenance, and retrieval of information about Engineering project record documents for which they are responsible. This PRIS User`s Manual provides instruction on the use of this system. Section 2.0 of this manual presents an overview of PRIS, describing the system`s purpose; the data that it handles; functions it performs; hardware, software, and access; and help and error functions. Section 3.0 describes the interactive menu-driven operation of PRIS. Appendixes A, B, and C contain help screens, report descriptions, and the data dictionary, respectively.

  3. Measuring semantic similarities by combining gene ontology annotations and gene co-function networks

    SciTech Connect (OSTI)

    Peng, Jiajie; Uygun, Sahra; Kim, Taehyong; Wang, Yadong; Rhee, Seung Y.; Chen, Jin

    2015-02-14

    Background: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the limited proportion of genes that are annotated to GO in most organisms. Results: We introduce a novel approach called NETSIM (network-based similarity measure) that incorporates information from gene co-function networks in addition to using the GO structure and annotations. Using metabolic reaction maps of yeast, Arabidopsis, and human, we demonstrate that NETSIM can improve the accuracy of GO term similarities. We also demonstrate that NETSIM works well even for genomes with sparser gene annotation data. We applied NETSIM on large Arabidopsis gene families such as cytochrome P450 monooxygenases to group the members functionally and show that this grouping could facilitate functional characterization of genes in these families. Conclusions: Using NETSIM as an example, we demonstrated that the performance of a semantic similarity measure could be significantly improved after incorporating genome-specific information. NETSIM incorporates both GO annotations and gene co-function network data as a priori knowledge in the model. Therefore, functional similarities of GO terms that are not explicitly encoded in GO but are relevant in a taxon-specific manner become measurable when GO annotations are limited.

  4. Measuring semantic similarities by combining gene ontology annotations and gene co-function networks

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Peng, Jiajie; Uygun, Sahra; Kim, Taehyong; Wang, Yadong; Rhee, Seung Y.; Chen, Jin

    2015-02-14

    Background: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the limited proportion of genes that are annotated to GO in most organisms. Results: We introduce a novel approach called NETSIM (network-based similarity measure) that incorporates information from gene co-function networks in addition to using the GO structure and annotations. Using metabolic reaction maps of yeast, Arabidopsis, and human, we demonstrate that NETSIM can improve the accuracy of GO term similarities. We also demonstratemore » that NETSIM works well even for genomes with sparser gene annotation data. We applied NETSIM on large Arabidopsis gene families such as cytochrome P450 monooxygenases to group the members functionally and show that this grouping could facilitate functional characterization of genes in these families. Conclusions: Using NETSIM as an example, we demonstrated that the performance of a semantic similarity measure could be significantly improved after incorporating genome-specific information. NETSIM incorporates both GO annotations and gene co-function network data as a priori knowledge in the model. Therefore, functional similarities of GO terms that are not explicitly encoded in GO but are relevant in a taxon-specific manner become measurable when GO annotations are limited.« less

  5. Theoretical manual for DYNA3D

    SciTech Connect (OSTI)

    Hallquist, J.O.

    1983-03-01

    This report provides a theoretical manual for DYNA3D, a vectorized explicit three-dimensional finite element code for analyzing the large deformation dynamic response of inelastic solids. A contact-impact algorithm that permits gaps and sliding along material interfaces is described. By a specialization of this algorithm, such interfaces can be rigidly tied to admit variable zoning without the need of transition regions. Spatial discretization is achieved by the use of 8-node solid elements, and the equations-of-motion are integrated by the central difference method. DYNA3D is operational on the CRAY-1 and CDC7600 computers.

  6. UQTk version 2.0 user manual.

    SciTech Connect (OSTI)

    Debusschere, Bert J.; Sargsyan, Khachik; Safta, Cosmin

    2013-10-01

    The UQ Toolkit (UQTk) is a collection of libraries and tools for the quanti cation of uncer- tainty in numerical model predictions. Version 2.0 o ers intrusive and non-intrusive methods for propagating input uncertainties through computational models, tools for sensitivity anal- ysis, methods for sparse surrogate construction, and Bayesian inference tools for inferring parameters from experimental data. This manual discusses the download and installation process for UQTk, provides pointers to the UQ methods used in the toolkit, and describes some of the examples provided with the toolkit.

  7. Classified Matter Protection and Control Manual

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2004-07-14

    This Manual supplements DOE O 471.2A, Information Security Program, dated 3-27-97, and provides detailed requirements for the protection and control of classified matter. Cancels DOE M 471.2-1B, dated 1-6-99, except Chapter III paragraphs 1 and 2 and Chapter IV. DOE M 471.2-1B Chapter IV was canceled by DOE O 471.4, Incidents of Security Concern, dated 3-17-04. Change 1, dated 7-14-2004, modifies requirements in Chapter II, paragraph 8c. Extended until 5-11-06 by DOE N 251.63, dated 5-11-05.

  8. Rooftop Unit Comparison Calculator User Manual

    SciTech Connect (OSTI)

    Miller, James D.

    2015-04-30

    This document serves as a user manual for the Packaged rooftop air conditioners and heat pump units comparison calculator (RTUCC) and is an aggregation of the calculator’s website documentation. Content ranges from new-user guide material like the “Quick Start” to the more technical/algorithmic descriptions of the “Methods Pages.” There is also a section listing all the context-help topics that support the features on the “Controls” page. The appendix has a discussion of the EnergyPlus runs that supported the development of the building-response models.

  9. Torque limited drive for manual valves

    DOE Patents [OSTI]

    Elliott, Philip G.; Underwood, Daniel E.

    1989-01-01

    The present invention is directed to a torque-limiting handwheel device for preventing manual valves from being damaged due to the application of excessive torque during the opening or closing operation of the valves. Torque can only be applied when ridges in the handwheel assembly engage in channels machined in the face of the baseplate. The amount of torque required for disengagement of the ridges from the channels is determined by the force exerted by various Bellville springs and the inclination of the side faces of the channels.

  10. Torque limited drive for manual valves

    DOE Patents [OSTI]

    Elliott, Philip G.; Underwood, Daniel E.

    1989-06-06

    The present invention is directed to a torque-limiting handwheel device for preventing manual valves from being damaged due to the application of excessive torque during the opening or closing operation of the valves. Torque can only be applied when ridges in the handwheel assembly engage in channels machined in the face of the baseplate. The amount of torque required for disengagement of the ridges from the channels is determined by the force exerted by various Bellville springs and the inclination of the side faces of the channels.