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BioJava 5: A community driven open-source bioinformatics library

Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley (+2 others)
2019 PLoS Computational Biology  
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)

K. Cara Woodwark
2001 Comparative and Functional Genomics  
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

Matthew Fenwick, Colbert Sesanker, Martin R. Schiller, Heidi JC Ellis, M. Lee Hinman, Jay Vyas, Michael R. Gryk
2012 2012 Ninth International Conference on Information Technology - New Generations  
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

Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján (+16 others)
2014 BMC Bioinformatics  
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]

Raoul J. P. Bonnal, Andrew Yates, Naohisa Goto, Laurent Gautier, Scooter Willis, Christopher Fields, Toshiaki Katayama, Pjotr Prins
2019 Msphere  
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

Hilmar Lapp, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, Alisha Holloway, Toshiaki Katayama, Paul O. Lewis, Aaron J. Mackey, Brian I. Osborne (+12 others)
2007 Evolutionary Bioinformatics  
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

T. Paterson, A. Law
2012 Bioinformatics  
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

Sohrab P Shah, David Y M He, Jessica N Sawkins, Jeffrey C Druce, Gerald Quon, Drew Lett, Grace X Y Zheng, Tao Xu, B F Francis Ouellette
2004 BMC Bioinformatics  
The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at  ...  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 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

Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F. Chen, Dong-Sheng Cao
2018 Journal of Cheminformatics  
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

Steffen Möller, Hajo Krabbenhöft, Andreas Tille, David Paleino, Alan Williams, Katy Wolstencroft, Carole Goble, Richard Holland, Dominique Belhachemi, Charles Plessy
2010 BMC Bioinformatics  
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

Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
2016 BioData Mining  
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

Andrew M Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D Finn, Henning Hermjakob, Tim JP Hubbard, Rafael C Jimenez, Philip Jones, Andreas Kähäri, Eugene Kulesha (+3 others)
2008 BMC Bioinformatics  
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

Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope
2019 GigaScience  
, 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  ...  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

Vasa Curcin, Moustafa Ghanem, Yike Guo
2005 Drug Discovery Today  
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 (, 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

Benjamin Lutz, Claude Sinner, Stefan Bozic, Ivan Kondov, Alexander Schug
2014 BMC Bioinformatics  
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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