Cargando…
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
Summary: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, so...
| Autores principales: | , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Oxford University Press
2012
|
| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315718/ https://www.ncbi.nlm.nih.gov/pubmed/22332238 http://dx.doi.org/10.1093/bioinformatics/bts080 |
| _version_ | 1782228277948055552 |
|---|---|
| author | Bonnal, Raoul J.P. Aerts, Jan Githinji, George Goto, Naohisa MacLean, Dan Miller, Chase A. Mishima, Hiroyuki Pagani, Massimiliano Ramirez-Gonzalez, Ricardo Smant, Geert Strozzi, Francesco Syme, Rob Vos, Rutger Wennblom, Trevor J. Woodcroft, Ben J. Katayama, Toshiaki Prins, Pjotr |
| author_facet | Bonnal, Raoul J.P. Aerts, Jan Githinji, George Goto, Naohisa MacLean, Dan Miller, Chase A. Mishima, Hiroyuki Pagani, Massimiliano Ramirez-Gonzalez, Ricardo Smant, Geert Strozzi, Francesco Syme, Rob Vos, Rutger Wennblom, Trevor J. Woodcroft, Ben J. Katayama, Toshiaki Prins, Pjotr |
| author_sort | Bonnal, Raoul J.P. |
| collection | PubMed |
| description | Summary: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Availability: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html Contact: bonnal@ingm.org |
| format | Online Article Text |
| id | pubmed-3315718 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2012 |
| publisher | Oxford University Press |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-33157182012-03-30 Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics Bonnal, Raoul J.P. Aerts, Jan Githinji, George Goto, Naohisa MacLean, Dan Miller, Chase A. Mishima, Hiroyuki Pagani, Massimiliano Ramirez-Gonzalez, Ricardo Smant, Geert Strozzi, Francesco Syme, Rob Vos, Rutger Wennblom, Trevor J. Woodcroft, Ben J. Katayama, Toshiaki Prins, Pjotr Bioinformatics Applications Note Summary: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Availability: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html Contact: bonnal@ingm.org Oxford University Press 2012-04-01 2012-02-12 /pmc/articles/PMC3315718/ /pubmed/22332238 http://dx.doi.org/10.1093/bioinformatics/bts080 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| spellingShingle | Applications Note Bonnal, Raoul J.P. Aerts, Jan Githinji, George Goto, Naohisa MacLean, Dan Miller, Chase A. Mishima, Hiroyuki Pagani, Massimiliano Ramirez-Gonzalez, Ricardo Smant, Geert Strozzi, Francesco Syme, Rob Vos, Rutger Wennblom, Trevor J. Woodcroft, Ben J. Katayama, Toshiaki Prins, Pjotr Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |
| title | Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |
| title_full | Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |
| title_fullStr | Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |
| title_full_unstemmed | Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |
| title_short | Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |
| title_sort | biogem: an effective tool-based approach for scaling up open source software development in bioinformatics |
| topic | Applications Note |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315718/ https://www.ncbi.nlm.nih.gov/pubmed/22332238 http://dx.doi.org/10.1093/bioinformatics/bts080 |
| work_keys_str_mv | AT bonnalraouljp biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT aertsjan biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT githinjigeorge biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT gotonaohisa biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT macleandan biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT millerchasea biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT mishimahiroyuki biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT paganimassimiliano biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT ramirezgonzalezricardo biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT smantgeert biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT strozzifrancesco biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT symerob biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT vosrutger biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT wennblomtrevorj biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT woodcroftbenj biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT katayamatoshiaki biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics AT prinspjotr biogemaneffectivetoolbasedapproachforscalingupopensourcesoftwaredevelopmentinbioinformatics |