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Title: Automating the JGI's Community Sequencing Program

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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
Report Number(s):
DOE Contract Number:
Resource Type:
Resource Relation:
Conference: 2nd Annual JGI User Meeting, Walnut Creek, CA
Country of Publication:
United States
99 GENERAL AND MISCELLANEOUS; CSP, Community Sequencing Program, AJAX

Citation Formats

Patil, Jayant, Fazo, Joni, Kobayashi, Art, Greiner, Annette, Voloshin, Arkady, Kale, Pat, Fenner, Marsha, Bruce, David, Cheng, Jan-Fang, and Bristow, Jim. Automating the JGI's Community Sequencing Program. United States: N. p., 2007. Web.
Patil, Jayant, Fazo, Joni, Kobayashi, Art, Greiner, Annette, Voloshin, Arkady, Kale, Pat, Fenner, Marsha, Bruce, David, Cheng, Jan-Fang, & Bristow, Jim. Automating the JGI's Community Sequencing Program. United States.
Patil, Jayant, Fazo, Joni, Kobayashi, Art, Greiner, Annette, Voloshin, Arkady, Kale, Pat, Fenner, Marsha, Bruce, David, Cheng, Jan-Fang, and Bristow, Jim. Mon . "Automating the JGI's Community Sequencing Program". United States. doi:.
title = {Automating the JGI's Community Sequencing Program},
author = {Patil, Jayant and Fazo, Joni and Kobayashi, Art and Greiner, Annette and Voloshin, Arkady and Kale, Pat and Fenner, Marsha and Bruce, David and Cheng, Jan-Fang and Bristow, Jim},
abstractNote = {},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Mar 26 00:00:00 EDT 2007},
month = {Mon Mar 26 00:00:00 EDT 2007}

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  • The Department of Energy's (DOE) Office of Site Closure, EM-30, houses the document library pertaining to sites that are related to the Formerly Utilized Sites Remedial Action Program (FUSRAP) and regularly addresses ongoing information demands, primarily from Freedom of Information Act (FOIA) requests, interested members of the public, the DOE, and other Federal Agencies. To address these demands more efficiently, DOE has begun to implement a new multi-phase, information management process known as e-FUSRAP. The first phase of e-FUSRAP, the development of the Considered Sites Database, summarizes and allows public access to complex information on over 600 sites considered asmore » candidates for FUSRAP. The second phase of e-FUSRAP, the development of the Document Indexing Database, will create an internal index of more than 10,000 documents in the FUSRAP library's case file, allowing more effective management and retrieval of case file documents. Together, the phases of e-FUSRAP will allow EM-30 to become an innovative leader in enhancing public information sources.« less
  • The problem of reducing the cost of developing, validating, and maintaining packages of numerical subroutines is a topic currently under investigation. Where such packages are to be made available in versions tailored to run on several different manufacturers' computers, the problem has been attacked by taking advantage of commonality; that is, the number of routines to be handled (and hence the cost) is reduced by creating a kind of prototype for each routine which can be processed automatically to produce the several required machine-tailored versions of that routine. It is shown here how these costs can often be further reducedmore » by taking a more general view of commonality. Packages frequently contain several subroutines which are the same program realized in different modes. The potential economies of commonality can be achieved by employing a program manipulation system which permits one to describe (and to automate) the construction of different realizations of the same prototype program. The capabilities of one such system are illustrated by considering in detail a program realization which trades structure for efficiency in some implementations: namely, the realization of prototype programs which call the Hanson, Krogh, and Lawson Basic Linear Algebra Modules, as programs with these calls replaced by in-line code. The analysis of this realization and the specification of transformations which guide the manipulation system in constructing it are described. Finally, some of the problems involved in trying to demonstrate the correctness of this automated realization are considered briefly. 15 figures.« less
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