skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: j5 v2.8.4

Abstract

j5 automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from (combinatorial) multi-part scar-less SLIC, Gibson, CPEC, Golden Gate assembly, or variants thereof, for which automation software does not currently exist, without the intense labor currently associated with the process. j5 inputs a list of the DNA sequences to be assembled, along with a Genbank, FASTA, jbei-seq, or SBOL v1.1 format sequence file for each DNA source. Given the list of DNA sequences to be assembled, j5 first determines the cost-minimizing assembly strategy for each part (direct synthesis, PCR/SOE, or oligo-embedding), designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 for CPEC) or optimized overhang sequences (Golden Gate) to the oligos and direct synthesis pieces, and utilizes BLAST to check against oligo mis-priming and assembly piece incompatibility events. After identifying DNA oligos that are already contained within a local collection for reuse, the program estimates the total cost of direct synthesis and new oligos to be ordered. In the instance that j5 identifies putative assembly piece incompatibilities (multiple pieces with high flanking sequence homology), the program suggests hierarchical subassemblies where possible. The program outputsmore » a comma-separated value (CSV) file, viewable via Excel or other spreadsheet software, that contains assembly design information (such as the PCR/SOE reactions to perform, their anticipated sizes and sequences, etc.) as well as a properly annotated genbank file containing the sequence resulting from the assembly, and appends the local oligo library with the oligos to be ordered j5 condenses multiple independent assembly projects into 96-well format for high-throughput liquid-handling robotics platforms, and generates configuration files for the PR-PR biology-friendly robot programming language. j5 thus provides a new way to design DNA assembly procedures much more productively and efficiently, not only in terms of time, but also in terms of cost. To a large extent, however, j5 does not allow people to do something that could not be done before by hand given enough time and effort. An exception to this is that, since the very act of using j5 to design the DNA assembly process standardizes the experimental details and workflow, j5 enables a single person to concurrently perform the independent DNA construction tasks of an entire group of researchers. Currently, this is not readily possible, since separate researchers employ disparate design strategies and workflows, and furthermore, their designs and workflows are very infrequently fully captured in an electronic format which is conducive to automation.« less

Authors:
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1261610
Report Number(s):
j5 v2.8.4; 004846MLTPL00
R&D Project: 2016-101
DOE Contract Number:
AC02-05CH11231
Resource Type:
Software
Software Revision:
00
Software Package Number:
004846
Software CPU:
MLTPL
Source Code Available:
No
Other Software Info:
Only LBNL reserves the right distribute this software.
Country of Publication:
United States

Citation Formats

Hillson, Nathan. j5 v2.8.4. Computer software. Vers. 00. USDOE. 29 Jun. 2016. Web.
Hillson, Nathan. (2016, June 29). j5 v2.8.4 (Version 00) [Computer software].
Hillson, Nathan. j5 v2.8.4. Computer software. Version 00. June 29, 2016.
@misc{osti_1261610,
title = {j5 v2.8.4, Version 00},
author = {Hillson, Nathan},
abstractNote = {j5 automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from (combinatorial) multi-part scar-less SLIC, Gibson, CPEC, Golden Gate assembly, or variants thereof, for which automation software does not currently exist, without the intense labor currently associated with the process. j5 inputs a list of the DNA sequences to be assembled, along with a Genbank, FASTA, jbei-seq, or SBOL v1.1 format sequence file for each DNA source. Given the list of DNA sequences to be assembled, j5 first determines the cost-minimizing assembly strategy for each part (direct synthesis, PCR/SOE, or oligo-embedding), designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 for CPEC) or optimized overhang sequences (Golden Gate) to the oligos and direct synthesis pieces, and utilizes BLAST to check against oligo mis-priming and assembly piece incompatibility events. After identifying DNA oligos that are already contained within a local collection for reuse, the program estimates the total cost of direct synthesis and new oligos to be ordered. In the instance that j5 identifies putative assembly piece incompatibilities (multiple pieces with high flanking sequence homology), the program suggests hierarchical subassemblies where possible. The program outputs a comma-separated value (CSV) file, viewable via Excel or other spreadsheet software, that contains assembly design information (such as the PCR/SOE reactions to perform, their anticipated sizes and sequences, etc.) as well as a properly annotated genbank file containing the sequence resulting from the assembly, and appends the local oligo library with the oligos to be ordered j5 condenses multiple independent assembly projects into 96-well format for high-throughput liquid-handling robotics platforms, and generates configuration files for the PR-PR biology-friendly robot programming language. j5 thus provides a new way to design DNA assembly procedures much more productively and efficiently, not only in terms of time, but also in terms of cost. To a large extent, however, j5 does not allow people to do something that could not be done before by hand given enough time and effort. An exception to this is that, since the very act of using j5 to design the DNA assembly process standardizes the experimental details and workflow, j5 enables a single person to concurrently perform the independent DNA construction tasks of an entire group of researchers. Currently, this is not readily possible, since separate researchers employ disparate design strategies and workflows, and furthermore, their designs and workflows are very infrequently fully captured in an electronic format which is conducive to automation.},
doi = {},
year = 2016,
month = 6,
note =
}

Software:
To order this software, request consultation services, or receive further information, please fill out the following request.

Save / Share:
  • This report presents the results of a customer telephone survey of the users of two software programs provided by the U. S. Department of Energy Federal Energy Management Program (FEMP) during calendar years 1995 and 1996. The primary purpose for the survey is to provide the Team Leader to FEMP Technical Assistance and members of the team with detailed customer feedback pertaining to how well selected FEMP software programs are being used and to identify areas for improvement. The information presented enables managers to see both the strengths of their software programs and software components that can be improved. Themore » survey was conducted during the fall of 1997 in conjunction with a FEMP workshop attendee survey. The results of the workshop survey are presented is a sister document entitled, ''An Evaluation of the Federal Energy Management Program's Technical Assistance Workshops.« less
  • By means of a literature survey, a comprehensive set of methods was identified for the verification and validation of conventional software. The 153 methods so identified were classified according to their appropriateness for various phases of a developmental life-cycle -- requirements, design, and implementation; the last category was subdivided into two, static testing and dynamic testing methods. The methods were then characterized in terms of eight rating factors, four concerning ease-of-use of the methods and four concerning the methods` power to detect defects. Based on these factors, two measurements were developed to permit quantitative comparisons among methods, a Cost-Benefit metricmore » and an Effectiveness Metric. The Effectiveness Metric was further refined to provide three different estimates for each method, depending on three classes of needed stringency of V&V (determined by ratings of a system`s complexity and required-integrity). Methods were then rank-ordered for each of the three classes by terms of their overall cost-benefits and effectiveness. The applicability was then assessed of each for the identified components of knowledge-based and expert systems, as well as the system as a whole.« less
  • By means of a literature survey, a comprehensive set of methods was identified for the verification and validation of conventional software. The 153 methods so identified were classified according to their appropriateness for various phases of a developmental life-cycle -- requirements, design, and implementation; the last category was subdivided into two, static testing and dynamic testing methods. The methods were then characterized in terms of eight rating factors, four concerning ease-of-use of the methods and four concerning the methods` power to detect defects. Based on these factors, two measurements were developed to permit quantitative comparisons among methods, a Cost-Benefit Metricmore » and an Effectiveness Metric. The Effectiveness Metric was further refined to provide three different estimates for each method, depending on three classes of needed stringency of V&V (determined by ratings of a system`s complexity and required-integrity). Methods were then rank-ordered for each of the three classes in terms of their overall cost-benefits and effectiveness. The applicability was then assessed of each method for the four identified components of knowledge-based and expert systems, as well as the system as a whole.« less
  • The Software Quality Forum is a triennial conference held by the Software Quality Assurance Subcommittee for the Department of Energy's Quality Managers. The forum centers on key issues, information, and technology important in software development for the Nuclear Weapons Complex. This year it will be opened up to include local information technology companies and software vendors presenting their solutions, ideas, and lessons learned. The Software Quality Forum 2000 will take on a more hands-on, instructional tone than those previously held. There will be an emphasis on providing information, tools, and resources to assist developers in their goal of producing nextmore » generation software.« less
  • The EPRI Information Monitoring and Applied Graphics Environment (IMAGE) system is designed for 'fast proto-typing' of advanced concepts for computer-aided plant operations tools. It is a flexible software system which can be used for rapidly creating, dynamically driving and evaluating advanced operator aid displays. The software is written to be both host computer and graphic device independent.

To initiate an order for this software, request consultation services, or receive further information, fill out the request form below. You may also reach us by email at: .

OSTI staff will begin to process an order for scientific and technical software once the payment and signed site license agreement are received. If the forms are not in order, OSTI will contact you. No further action will be taken until all required information and/or payment is received. Orders are usually processed within three to five business days.

Software Request

(required)
(required)
(required)
(required)
(required)
(required)
(required)
(required)