{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:35:02Z","timestamp":1732034102713},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1694,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"Abstract<\/jats:title>\n 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.<\/jats:p>\n 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.<\/jats:p>\n 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<\/jats:p>\n Contact: \u00a0bonnal@ingm.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts080","type":"journal-article","created":{"date-parts":[[2012,2,14]],"date-time":"2012-02-14T01:23:09Z","timestamp":1329182589000},"page":"1035-1037","source":"Crossref","is-referenced-by-count":21,"title":["Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics"],"prefix":"10.1093","volume":"28","author":[{"given":"Raoul J.P.","family":"Bonnal","sequence":"first","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Jan","family":"Aerts","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"George","family":"Githinji","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Naohisa","family":"Goto","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Dan","family":"MacLean","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Chase A.","family":"Miller","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Hiroyuki","family":"Mishima","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Massimiliano","family":"Pagani","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Ricardo","family":"Ramirez-Gonzalez","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Geert","family":"Smant","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Francesco","family":"Strozzi","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Rob","family":"Syme","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Rutger","family":"Vos","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Trevor J.","family":"Wennblom","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Ben J.","family":"Woodcroft","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Toshiaki","family":"Katayama","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. Box 230 - 80108, Kenya, 4 Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan, 5 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK, 6 Biology Department, Boston College, Chestnut Hill, 02467, Massachusetts, USA, 7 Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-852, Japan, 8 Sequence Informatics, Bioinformatics, The Genome Analysis Centre, Norwich, NR4 7UH, UK, 9 Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands, 10 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy, 11 Department of Env"}]},{"given":"Pjotr","family":"Prins","sequence":"additional","affiliation":[{"name":"1 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy, 2 ESAT\/SCD, Faculty of Engineering and IBBT Future Health Department, University of Leuven, Heverlee (Leuven) 3001, Belgium, 3Parasitology and Immunology Department, KEMRI-Wellcome Trust Research Program, Kilifi, P.O. 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