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BioJava 5: A community driven open-source bioinformatics library
2019
PLoS Computational Biology
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BioJava is an open-source project that provides a Java library for processing biological data. ...
Since 2012, we have released two major versions of the library (4 and 5) that include many new features to tackle challenges with increasingly complex macromolecular structure data. ...
We would also like to thank the Open Bioinformatics Foundation (OBF) for continuously supporting the project. ...
doi:10.1371/journal.pcbi.1006791
fatcat:r2n3lfvg5rg6bm73fwa2nwhyje
Meeting Review: The Bioinformatics Open Source Conference 2001 (BOSC 2001)
2001
Comparative and Functional Genomics
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The BioPerl policy (one now adopted by much of the bioinformatics open source community) is that 'he who codes it, wins the argument'. ...
The general aim of the BOSC was to bring people up to date with what is happening in the open source community, which has representatives all over the world. ...
doi:10.1002/cfg.107
pmid:18629243
pmcid:PMC2448404
fatcat:o3k4jrcvozba7gbsozy2ar4hwq
An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities
2012
2012 Ninth International Conference on Information Technology - New Generations
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To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm ...
development, which generally focuses on the fields of machine learning, data processing, bioinformatics. ...
There are other existing examples, largely genome related, of functional programming work in the open-source bioinformatics community: The BioCaml project offers a variety of parsers for different genomic ...
doi:10.1109/itng.2012.21
pmid:25328913
pmcid:PMC4197993
dblp:conf/itng/FenwickSSEHVG12
fatcat:65szd4tidbf43dbskerudnvtfi
Community-driven development for computational biology at Sprints, Hackathons and Codefests
2014
BMC Bioinformatics
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Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment ...
We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. ...
Acknowledgements All scientific groups that support contributions to Open Source software are thanked. The events' hosting institutions are thanked for providing facilities and support. ...
doi:10.1186/1471-2105-15-s14-s7
pmid:25472764
pmcid:PMC4255748
fatcat:p7jbtuipnbdafo3zauaqrhu5sq
Sharing Programming Resources Between Bio* Projects
[chapter]
2019
Msphere
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In evolutionary bioinformatics, open-source software comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. ...
Open-source software encourages computer programmers to reuse software components written by others. ...
Acknowledgments We thank all open-source software developers for creating such great tools and libraries for the scientific community. ...
doi:10.1007/978-1-4939-9074-0_25
pmid:31278684
fatcat:sanqijnerzcx3llayblewitgza
The 2006 NESCent Phyloinformatics Hackathon: A Field Report
2007
Evolutionary Bioinformatics
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The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. ...
In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics ...
The identifi cation of specifi c commercial software products in this paper is for the purpose of specifying a protocol, and does not imply a recommendation or endorsement by the National Institute of ...
doi:10.1177/117693430700300016
fatcat:ycivqatp35fhhoeolsxqm5fpsu
JEnsembl: a version-aware Java API to Ensembl data systems
2012
Bioinformatics
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The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. ...
Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge ...
source Java libraries for bioinformatics where relevant (e.g. ...
doi:10.1093/bioinformatics/bts525
pmid:22945789
pmcid:PMC3476335
fatcat:ioudcycmgfbrnpcv2ppl4edeiy
Pegasys: software for executing and integrating analyses of biological sequences
2004
BMC Bioinformatics
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The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/. ...
We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. ...
DL is supported by the CIHR/MSFHR Strategic Training Program in Bioinformatics http://bioinformatics.bcgsc.ca. TX is supported by CIHR grant #MOP-53259. ...
doi:10.1186/1471-2105-5-40
pmid:15096276
pmcid:PMC406494
fatcat:nlg5rwy27vdxvjyymfwmts54xu
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
2018
Journal of Cheminformatics
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PyBioMed is a feature-rich and highly customized python library used for the characterization of various complex chemical and biological molecules and interaction samples. ...
Results: Herein, the python library PyBioMed is presented, which comprises functionalities for online download for various molecular objects by providing different IDs, the pretreatment of molecular structures ...
However, to our knowledge, no open source or freely available tool exists to perform all these functions above in a uniform framework. ...
doi:10.1186/s13321-018-0270-2
pmid:29556758
pmcid:PMC5861255
fatcat:ss76y77rcrbn5ayrondsyql77q
Community-driven computational biology with Debian Linux
2010
BMC Bioinformatics
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The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. ...
It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. ...
The traditional installation of Open Source software requires its compilation from source code. The skills and interest needed for packaging software are different from software development. ...
doi:10.1186/1471-2105-11-s12-s5
pmid:21210984
pmcid:PMC3040531
fatcat:kaccvasddbe37hywbddw36ppuq
Visual programming for next-generation sequencing data analytics
2016
BioData Mining
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An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent ...
Text: Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter ...
The SeqAn library is written in C++ and licensed as an open source. ...
doi:10.1186/s13040-016-0095-3
pmid:27127540
pmcid:PMC4848821
fatcat:tvbjlx36hbgblb5x5dl7tah6fe
Integrating biological data – the Distributed Annotation System
2008
BMC Bioinformatics
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The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. ...
DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics. ...
Acknowledgements We would like to acknowledge the contribution of all those who provide data to the community via DAS, without which the system would not function. ...
doi:10.1186/1471-2105-9-s8-s3
pmid:18673527
pmcid:PMC2500094
fatcat:neywzrq2mnggzddq3oxipfnddu
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software
2019
GigaScience
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, code documentation, a standard open source software license, software revision control, and containerization. ...
Bionitio is released as open source software under the MIT License and is available at https://github.com/bionitio-team/bionitio. ...
Acknowledgements The authors would like to thank Melbourne Bioinformatics for providing computing resources for the development of Bionitio, and the many users of the tool who have provided feedback about ...
doi:10.1093/gigascience/giz109
pmid:31544213
pmcid:PMC6755254
fatcat:6o6iyirqvfemtkd2oaegnkvddy
Web services in the life sciences
2005
Drug Discovery Today
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Web services provide a standard way of publishing applications and data sources over the internet, enabling mass dissemination of knowledge. ...
In the life sciences, the web-service approach is seen as being a road to standardizing the multitude of tools available from different providers. ...
This could be addressed, in part, by making use of the efforts of the Open Bioinformatics Foundation (http://www.open-bio.org/), which produces libraries for Perl, Java, Ruby and Python (called, unsurprisingly ...
doi:10.1016/s1359-6446(05)03481-1
pmid:15970269
pmcid:PMC7185667
fatcat:5dhg6mza4rbdlevq5hyyrf4qia
Native structure-based modeling and simulation of biomolecular systems per mouse click
2014
BMC Bioinformatics
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Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research. ...
This video shows how to construct a workflow for finding the folding temperature of a protein. Additional file 3: Demonstration of installation and usage of the SBM GridBean: Part 3. ...
BioJava [65] is another library that we have integrated into the SBM GridBean. ...
doi:10.1186/1471-2105-15-292
pmid:25176255
pmcid:PMC4162935
fatcat:diorayfnhfcg3eennkdd62w5ny
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