{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T12:17:04Z","timestamp":1763468224468},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"S14","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-s14-s7","type":"journal-article","created":{"date-parts":[[2014,11,27]],"date-time":"2014-11-27T10:04:14Z","timestamp":1417082654000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Community-driven development for computational biology at Sprints, Hackathons and Codefests"],"prefix":"10.1186","volume":"15","author":[{"given":"Steffen","family":"M\u00f6ller","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enis","family":"Afgan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Banck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raoul JP","family":"Bonnal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy","family":"Booth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Chilton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter JA","family":"Cock","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Gumbel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nomi","family":"Harris","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Holland","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mat\u00fa\u0161","family":"Kala\u0161","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L\u00e1szl\u00f3","family":"Kaj\u00e1n","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eri","family":"Kibukawa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David R","family":"Powel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pjotr","family":"Prins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacqueline","family":"Quinn","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Sallou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Strozzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Torsten","family":"Seemann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clare","family":"Sloggett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stian","family":"Soiland-Reyes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William","family":"Spooner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sascha","family":"Steinbiss","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Tille","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony J","family":"Travis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roman Valls","family":"Guimera","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Toshiaki","family":"Katayama","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brad A","family":"Chapman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,11,27]]},"reference":[{"issue":"1","key":"6718_CR1","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/2041-1480-1-8","volume":"1","author":"T Katayama","year":"2010","unstructured":"Katayama T, Arakawa K: The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J Biomed Semantics. 2010, 1 (1): 8-10.1186\/2041-1480-1-8.","journal-title":"J Biomed Semantics"},{"issue":"2","key":"6718_CR2","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/2041-1480-2-4","volume":"2","author":"T Katayama","year":"2011","unstructured":"Katayama T, Wilkinson MD: The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics. 2011, 2 (2): 4-","journal-title":"J Biomed Semantics"},{"issue":"1","key":"6718_CR3","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/2041-1480-4-6","volume":"4","author":"T Katayama","year":"2013","unstructured":"Katayama T, Wilkinson MD: The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics. 2013, 4 (1): 6-10.1186\/2041-1480-4-6.","journal-title":"J Biomed Semantics"},{"issue":"10","key":"6718_CR4","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1101\/gr.361602","volume":"12","author":"JE Stajich","year":"2002","unstructured":"Stajich JE, Block D: The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002, 12 (10): 1611-1618. 10.1101\/gr.361602.","journal-title":"Genome Res"},{"issue":"22","key":"6718_CR5","doi-asserted-by":"publisher","first-page":"3005","DOI":"10.1093\/bioinformatics\/btp493","volume":"25","author":"B N\u00e9ron","year":"2009","unstructured":"N\u00e9ron B, M\u00e9nager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C: Mobyle: a new full web bioinformatics framework. Bioinformatics. 2009, 25 (22): 3005-3011. 10.1093\/bioinformatics\/btp493.","journal-title":"Bioinformatics"},{"key":"6718_CR6","unstructured":"Lebo T, Sahoo S, McGuinness D, Belhajjame K, Cheney J, Corsar D, Garijo D, Soiland-Reyes S, Zednik S, Zhao J: PROV-O: The PROV Ontology. W3C Recommendation. 30 April 2013 \n                    http:\/\/www.w3.org\/TR\/2013\/REC-prov-o-20130430\/"},{"issue":"10","key":"6718_CR7","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1093\/bioinformatics\/btt113","volume":"29","author":"J Ison","year":"2013","unstructured":"Ison J, Kala\u0161 M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P: EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 2013, 29 (10): 1325-1332. 10.1093\/bioinformatics\/btt113.","journal-title":"Bioinformatics"},{"issue":"6","key":"6718_CR8","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1038\/nbt.2891","volume":"32","author":"M Galdzicki","year":"2014","unstructured":"Galdzicki M, Clancy KP: The Synthetic Biology Open Language Visual (SBOL) provides a community standard for communicating designs in synthetic biology. Nat Biotechnol. 2014, 32 (6): 545-550. 10.1038\/nbt.2891.","journal-title":"Nat Biotechnol"},{"issue":"14","key":"6718_CR9","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T: Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014, 30 (14): 2068-2069. 10.1093\/bioinformatics\/btu153.","journal-title":"Bioinformatics"},{"issue":"Database","key":"6718_CR10","doi-asserted-by":"publisher","first-page":"D1","DOI":"10.1093\/nar\/gks1297","volume":"41","author":"XM Fern\u00e1ndez-Su\u00e1rez","year":"2013","unstructured":"Fern\u00e1ndez-Su\u00e1rez XM, Galperin MY: The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res. 2013, 41 (Database): D1-7.","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"6718_CR11","doi-asserted-by":"publisher","first-page":"2693","DOI":"10.1093\/bioinformatics\/bts494","volume":"28","author":"A Prli\u0107","year":"2012","unstructured":"Prli\u0107 A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandst\u00e4tter-M\u00fcller H, Bourne PE, Willis S: BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012, 28 (20): 2693-2695. 10.1093\/bioinformatics\/bts494.","journal-title":"Bioinformatics"},{"issue":"11","key":"6718_CR12","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJ Cock","year":"2009","unstructured":"Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ: Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009, 25 (11): 1422-1423. 10.1093\/bioinformatics\/btp163.","journal-title":"Bioinformatics"},{"issue":"20","key":"6718_CR13","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1093\/bioinformatics\/btq475","volume":"26","author":"N Goto","year":"2010","unstructured":"Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T: BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 2010, 26 (20): 2617-2619. 10.1093\/bioinformatics\/btq475.","journal-title":"Bioinformatics"},{"issue":"7","key":"6718_CR14","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1093\/bioinformatics\/bts080","volume":"28","author":"RJ Bonnal","year":"2012","unstructured":"Bonnal RJ, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P: Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics. 2012, 28 (7): 1035-1037. 10.1093\/bioinformatics\/bts080.","journal-title":"Bioinformatics"},{"key":"6718_CR15","volume-title":"Packaging Software for Use in Medicine","author":"A Tille","year":"2001","unstructured":"Tille A: Packaging Software for Use in Medicine. 2001, Libre Software Meeting. Bordeaux, France"},{"issue":"S-12","key":"6718_CR16","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-11-S12-S5","volume":"11","author":"S M\u00f6ller","year":"2010","unstructured":"M\u00f6ller S, Krabbenh\u00f6ft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C: Community-driven computational biology with Debian Linux. BMC Bioinformatics. 2010, 11 (S-12): S5-","journal-title":"BMC Bioinformatics"},{"key":"6718_CR17","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1038\/nbt0706-801","volume":"24","author":"D Field","year":"2006","unstructured":"Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M: Open software for biologists: from famine to feast. Nat Biotechnol. 2006, 24: 801-803. 10.1038\/nbt0706-801.","journal-title":"Nat Biotechnol"},{"key":"6718_CR18","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/1471-2105-13-42","volume":"13","author":"K Krampis","year":"2012","unstructured":"Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE: Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics. 2012, 13: 42-10.1186\/1471-2105-13-42.","journal-title":"BMC Bioinformatics"},{"key":"6718_CR19","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1109\/GRID.2004.14","volume-title":"Proceedings of the 5th IEEE\/ACM Workshop on Grid Computing","author":"DP Anderson","year":"2004","unstructured":"Anderson DP: BOINC: A System for Public-Resource Computing and Storage. Proceedings of the 5th IEEE\/ACM Workshop on Grid Computing. 2004, 4-10."},{"key":"6718_CR20","first-page":"617","volume-title":"PDP","author":"DM Balan","year":"2012","unstructured":"Balan DM, Malinauskas T, Prins P, M\u00f6ller S: High-throughput Molecular Docking Now in Reach for a Wider Biochemical Community. PDP. 2012, 617-621."},{"issue":"3","key":"6718_CR21","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1109\/TCBB.2013.68","volume":"10","author":"G Gremme","year":"2013","unstructured":"Gremme G, Steinbiss S, Kurtz S: GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. IEEE\/ACM Trans Comp Biol Bioinf. 2013, 10 (3): 645-656.","journal-title":"IEEE\/ACM Trans Comp Biol Bioinf"},{"key":"6718_CR22","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1186\/1471-2105-13-187","volume":"13","author":"DS Standage","year":"2012","unstructured":"Standage DS, Brendel VP: ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics. 2012, 13: 187-10.1186\/1471-2105-13-187.","journal-title":"BMC Bioinformatics"},{"key":"6718_CR23","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/1759-8753-3-18","volume":"3","author":"S Steinbiss","year":"2012","unstructured":"Steinbiss S, Kastens S, Kurtz S: LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Mobile DNA. 2012, 3: 18-10.1186\/1759-8753-3-18.","journal-title":"Mobile DNA"},{"key":"6718_CR24","first-page":"398968","volume-title":"BioMed Research International","author":"L Kaj\u00e1n","year":"2013","unstructured":"Kaj\u00e1n L, Yachdav G, Vicedo S, Steinegger M, Mirdita M, Angerm\u00fcller C, B\u00f6hm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B: Cloud Prediction of Protein Structure and Function with PredictProtein for Debian. BioMed Research International. 2013, 398968-"},{"issue":"11","key":"6718_CR25","doi-asserted-by":"publisher","first-page":"e1003355","DOI":"10.1371\/journal.pcbi.1003355","volume":"9","author":"M Stobbe","year":"2013","unstructured":"Stobbe M, Mishra T, Macintyre G: Breaking the Ice and Forging Links: The Importance of Socializing in Research. PLoS Comput Biol. 2013, 9 (11): e1003355-10.1371\/journal.pcbi.1003355.","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"6718_CR26","doi-asserted-by":"publisher","first-page":"e18","DOI":"10.5334\/jors.bc","volume":"2","author":"EH Trainer","year":"2014","unstructured":"Trainer EH, Chaihirunkarn C, Herbsleb JD: The Big Effects of Short-term Efforts: Mentorship and Code Integration in Open Source Scientific Software. Journal of Open Research Software. 2014, 2 (1): e18-\n                    http:\/\/openresearchsoftware.metajnl.com\/article\/view\/jors.bc\/57\n                    \n                  ,","journal-title":"Journal of Open Research Software"},{"key":"6718_CR27","first-page":"btu413","volume-title":"Bioinformatics","author":"NL Harris","year":"2014","unstructured":"Harris NL, Cock PJA, Chapman BA, Goecks J, Hotz H-R, Lapp H: The Bioinformatics Open Source Conference (BOSC) 2013. Bioinformatics. 2014, btu413-"},{"issue":"12","key":"6718_CR28","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.1101\/gr.126599.111","volume":"21","author":"D Earl","year":"2011","unstructured":"Earl D, Bradnam K: Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011, 21 (12): 2224-2241. 10.1101\/gr.126599.111.","journal-title":"Genome Res"},{"issue":"7","key":"6718_CR29","doi-asserted-by":"publisher","first-page":"e1002554","DOI":"10.1371\/journal.pcbi.1002554","volume":"8","author":"Pavelin Katrina","year":"2012","unstructured":"Katrina Pavelin, Cham Jennifer A: Bioinformatics Meets User-Centred Design: A Perspective. PLoS Comput Biol. 2012, 8 (7): e1002554-10.1371\/journal.pcbi.1002554.","journal-title":"PLoS Comput Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S14-S7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T01:39:04Z","timestamp":1548207544000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S14-S7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,27]]},"references-count":29,"journal-issue":{"issue":"S14","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6718"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s14-s7","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,27]]},"assertion":[{"value":"27 November 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S7"}}