BioPartsBuilder

A synthetic biology tool for combinatorial assembly of biological parts

Kun Yang, Giovanni Stracquadanio, Jingchuan Luo, Jef D. Boeke, Joel S. Bader

Research output: Contribution to journalArticle

Abstract

Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)937-939
Number of pages3
JournalBioinformatics
Volume32
Issue number6
DOIs
StatePublished - Sep 11 2015

Fingerprint

Synthetic Biology
Fragment
DNA
Licensure
Bioinformatics
Computational Biology
Compliance
Web services
Web Services
Pathway
Fabrication
Availability
Contact
Design

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

BioPartsBuilder : A synthetic biology tool for combinatorial assembly of biological parts. / Yang, Kun; Stracquadanio, Giovanni; Luo, Jingchuan; Boeke, Jef D.; Bader, Joel S.

In: Bioinformatics, Vol. 32, No. 6, 11.09.2015, p. 937-939.

Research output: Contribution to journalArticle

Yang, Kun ; Stracquadanio, Giovanni ; Luo, Jingchuan ; Boeke, Jef D. ; Bader, Joel S. / BioPartsBuilder : A synthetic biology tool for combinatorial assembly of biological parts. In: Bioinformatics. 2015 ; Vol. 32, No. 6. pp. 937-939.
@article{27c6a5b2135c4940b19ae5972b4ba2dc,
title = "BioPartsBuilder: A synthetic biology tool for combinatorial assembly of biological parts",
abstract = "Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.",
author = "Kun Yang and Giovanni Stracquadanio and Jingchuan Luo and Boeke, {Jef D.} and Bader, {Joel S.}",
year = "2015",
month = "9",
day = "11",
doi = "10.1093/bioinformatics/btv664",
language = "English (US)",
volume = "32",
pages = "937--939",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "6",

}

TY - JOUR

T1 - BioPartsBuilder

T2 - A synthetic biology tool for combinatorial assembly of biological parts

AU - Yang, Kun

AU - Stracquadanio, Giovanni

AU - Luo, Jingchuan

AU - Boeke, Jef D.

AU - Bader, Joel S.

PY - 2015/9/11

Y1 - 2015/9/11

N2 - Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

AB - Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

UR - http://www.scopus.com/inward/record.url?scp=84962138875&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84962138875&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btv664

DO - 10.1093/bioinformatics/btv664

M3 - Article

VL - 32

SP - 937

EP - 939

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 6

ER -