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Biopython Project Update 2016

Brueffer, Christian LU orcid ; Antao, Tiago ; Cock, Peter ; Talevich, Eric ; de Hoon, Michiel ; Arindrarto, Wibowo ; Pritchard, Leighton ; Sharma, Anuj ; Rasche, Eric and Rosenfeld, Aaron , et al. (2016) Bioinformatics Open Source Conference, 2016
Abstract
The Biopython Project is a long-running distributed collaborative effort, supported by the Open Bioinformatics Foundation, which develops a freely available Python library for biological computation.
We present here details of the latest Biopython release - version 1.66. New features include: extended Bio.KEGG and Bio.Graphics modules to support drawing KEGG pathways with transparency; extended “abi” Bio.SeqIO parser to decode almost all documented fields used by ABIF instruments; a QCPSuperimposer module using the Quaternion Characteristic Polynomial algorithm for superimposing structures to Bio.PDB; and an extended Bio.Entrez module to implement the NCBI Entrez Citation Matching function and to support NCBI XML files with XSD... (More)
The Biopython Project is a long-running distributed collaborative effort, supported by the Open Bioinformatics Foundation, which develops a freely available Python library for biological computation.
We present here details of the latest Biopython release - version 1.66. New features include: extended Bio.KEGG and Bio.Graphics modules to support drawing KEGG pathways with transparency; extended “abi” Bio.SeqIO parser to decode almost all documented fields used by ABIF instruments; a QCPSuperimposer module using the Quaternion Characteristic Polynomial algorithm for superimposing structures to Bio.PDB; and an extended Bio.Entrez module to implement the NCBI Entrez Citation Matching function and to support NCBI XML files with XSD schemas. Additionally we fixed miscellaneous bugs, enhanced our test suite and continued our efforts to abide by the PEP8 coding style guidelines.
We are currently preparing a new release – version 1.67 – that will deprecate the ability to compare SeqRecord objects with “==”, which sometimes lead to surprising results. In addition it will feature a new experimental Bio.phenotype module for working with Phenotype Microarray data; updates to Bio.Data to
include NCBI genetic code table 25, covering Candidate Division SR1 and Gracilibacteria; an update to Bio.Restriction to include the REBASE May 2016 restriction enzyme list; updates to BioSQL to use foreign keys with SQLite3 databases; as well as corrections to the Bio.Entrez module and the MMCIF structure parser.
Our website has been migrated from MediaWiki to GitHub Pages and is now under version control. The continuous integration process on GitHub has been enhanced by including external services like Landscape, Quantified Code and Codecov to perform quality review, test coverage analysis and generation of quality metrics.
Finally, our range of Docker containers has been greatly enhanced. In addition to a basic container that includes Python 2 and 3 with Biopython and all its dependencies, as well as a BioSQL container, we now also provide two versions of Jupyter notebook containers: a basic one, and a version including the Biopython tutorial as notebooks. (Less)
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organization
publishing date
type
Contribution to conference
publication status
published
subject
keywords
Python, Programming, Computational tools, Bioinformatics, Computational Biology
conference name
Bioinformatics Open Source Conference, 2016
conference location
Orlando, United States
conference dates
2016-07-08 - 2016-07-09
DOI
10.7490/f1000research.1112611.1
language
English
LU publication?
yes
id
90ff3c56-f3a1-4237-bd0d-276db959930b
date added to LUP
2016-09-29 14:46:21
date last changed
2025-04-04 14:06:34
@misc{90ff3c56-f3a1-4237-bd0d-276db959930b,
  abstract     = {{The Biopython Project is a long-running distributed collaborative effort, supported by the Open Bioinformatics Foundation, which develops a freely available Python library for biological computation.<br/>We present here details of the latest Biopython release - version 1.66. New features include: extended Bio.KEGG and Bio.Graphics modules to support drawing KEGG pathways with transparency; extended “abi” Bio.SeqIO parser to decode almost all documented fields used by ABIF instruments; a QCPSuperimposer module using the Quaternion Characteristic Polynomial algorithm for superimposing structures to Bio.PDB; and an extended Bio.Entrez module to implement the NCBI Entrez Citation Matching function and to support NCBI XML files with XSD schemas. Additionally we fixed miscellaneous bugs, enhanced our test suite and continued our efforts to abide by the PEP8 coding style guidelines.<br/>We are currently preparing a new release – version 1.67 – that will deprecate the ability to compare SeqRecord objects with “==”, which sometimes lead to surprising results. In addition it will feature a new experimental Bio.phenotype module for working with Phenotype Microarray data; updates to Bio.Data to<br/>include NCBI genetic code table 25, covering Candidate Division SR1 and Gracilibacteria; an update to Bio.Restriction to include the REBASE May 2016 restriction enzyme list; updates to BioSQL to use foreign keys with SQLite3 databases; as well as corrections to the Bio.Entrez module and the MMCIF structure parser.<br/>Our website has been migrated from MediaWiki to GitHub Pages and is now under version control. The continuous integration process on GitHub has been enhanced by including external services like Landscape, Quantified Code and Codecov to perform quality review, test coverage analysis and generation of quality metrics.<br/>Finally, our range of Docker containers has been greatly enhanced. In addition to a basic container that includes Python 2 and 3 with Biopython and all its dependencies, as well as a BioSQL container, we now also provide two versions of Jupyter notebook containers: a basic one, and a version including the Biopython tutorial as notebooks.}},
  author       = {{Brueffer, Christian and Antao, Tiago and Cock, Peter and Talevich, Eric and de Hoon, Michiel and Arindrarto, Wibowo and Pritchard, Leighton and Sharma, Anuj and Rasche, Eric and Rosenfeld, Aaron and Skennerton, Connor and Galardini, Marco and Piotrowski, Markus}},
  keywords     = {{Python; Programming; Computational tools; Bioinformatics; Computational Biology}},
  language     = {{eng}},
  month        = {{07}},
  title        = {{Biopython Project Update 2016}},
  url          = {{http://dx.doi.org/10.7490/f1000research.1112611.1}},
  doi          = {{10.7490/f1000research.1112611.1}},
  year         = {{2016}},
}