{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,9]],"date-time":"2026-08-09T02:37:13Z","timestamp":1786243033745,"version":"3.56.0"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,2,28]],"date-time":"2013-02-28T00:00:00Z","timestamp":1362009600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Source Code Biol Med"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1751-0473-8-7","type":"journal-article","created":{"date-parts":[[2013,3,1]],"date-time":"2013-03-01T05:06:23Z","timestamp":1362114383000},"source":"Crossref","is-referenced-by-count":142,"title":["Git can facilitate greater reproducibility and increased transparency in science"],"prefix":"10.1186","volume":"8","author":[{"given":"Karthik","family":"Ram","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,2,28]]},"reference":[{"key":"88_CR1","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1525\/bio.2012.62.5.3","volume":"62","author":"CJ Vink","year":"2012","unstructured":"Vink CJ, Paquin P, Cruickshank RH: Taxonomy and irreproducible biological science. BioScience. 2012, 62: 451-452. Available: [ http:\/\/www.bioone.org\/doi\/abs\/10.1525\/bio.2012.62.5.3 ]","journal-title":"BioScience"},{"key":"88_CR2","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1126\/science.1213847","volume":"334","author":"RD Peng","year":"2011","unstructured":"Peng RD: Reproducible research in computational science. Science. 2011, 334: 1226-1227. 10.1126\/science.1213847. Available: [ http:\/\/www.sciencemag.org\/cgi\/doi\/10.1126\/science.1213847 ]","journal-title":"Science"},{"key":"88_CR3","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1038\/483531a","volume":"483","author":"CG Begley","year":"2012","unstructured":"Begley CG, Ellis LM: Drug development: Raise standards for preclinical cancer research. Nature. 2012, 483: 531-533. 10.1038\/483531a. Available: [ http:\/\/dx.doi.org\/10.1038\/483531a ]","journal-title":"Nature"},{"key":"88_CR4","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1109\/5992.881708","volume":"2","author":"M Schwab","year":"2000","unstructured":"Schwab M, Karrenbach M, Claerbout J: Making scientific computations reproducible. Comput Sci Eng. 2000, 2: 61-67. Available: [ http:\/\/ieeexplore.ieee.org\/lpdocs\/epic03\/wrapper.htm?arnumber=881708 ]","journal-title":"Comput Sci Eng"},{"key":"88_CR5","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1038\/nature10836","volume":"482","author":"DC Ince","year":"2012","unstructured":"Ince DC, Hatton L, Graham-Cumming J: The case for open computer programs. Nature. 2012, 482: 485-488. 10.1038\/nature10836. Available: [ http:\/\/dx.doi.org\/10.1038\/nature10836 ]","journal-title":"Nature"},{"issue":"7367","key":"88_CR6","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1038\/478006a","volume":"478","author":"Noorden Van R","year":"2011","unstructured":"Van Noorden: The trouble with retractions. Nature. 2011, 478 (7367): 6-8.","journal-title":"Nature"},{"key":"88_CR7","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1086\/650340","volume":"175","author":"MC Whitlock","year":"2010","unstructured":"Whitlock MC, McPeek MA, Rausher MD, Rieseberg L, Moore AJ: Data archiving. Am Nat. 2010, 175: 145-146. 10.1086\/650340. Available: [ http:\/\/www.jstor.org\/stable\/10.1086\/650340 ]","journal-title":"Am Nat"},{"key":"88_CR8","volume-title":"FASEB J","author":"TH Vines","year":"2013","unstructured":"Vines TH, Andrew RL, Bock DG, Franklin MT, Gilbert KJ: Mandateddata archiving greatly improves access to research data. FASEB J. 2013, [ http:\/\/dx.doi.org\/10.1096\/fj.12-218164 ]"},{"key":"88_CR9","doi-asserted-by":"publisher","first-page":"2102","DOI":"10.1111\/j.1365-2486.2012.02693.x","volume":"18","author":"EM Wolkovich","year":"2012","unstructured":"Wolkovich EM, Regetz J, O\u2019Connor MI: Advances in global change research require open science by individual researchers. Glob Change Biol. 2012, 18: 2102-2110. 10.1111\/j.1365-2486.2012.02693.x. Available: [ http:\/\/apps.webofknowledge.com\/full_record.do?product=UA&search_mode=GeneralSearch&qid=1&SID=1CfaPnJ9gbl5bo171Jc&page=1&doc=4 ]","journal-title":"Glob Change Biol"},{"key":"88_CR10","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/492348a","volume":"492","author":"C Neylon","year":"2012","unstructured":"Neylon C: Open access must enable open use. Nature. 2012, 492: 8-9.","journal-title":"Nature"},{"key":"88_CR11","volume-title":"Issues & Perspectives Scientists Embrace openness","author":"C Wald","year":"2010","unstructured":"Wald C: Issues & Perspectives Scientists Embrace openness. 2010, Available: [ http:\/\/sciencecareers.sciencemag.org\/career_magazine\/previous_issues\/articles\/2010_04_09\/caredit.a1000036 ] Accessed 16 Jan 2013."},{"key":"88_CR12","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1126\/science.1224988","volume":"337","author":"P Greenland","year":"2012","unstructured":"Greenland P, Fontanarosa PB: Ending honorary authorship. Science (New York, NY). 2012, 337: 1019-10.1126\/science.1224988. Available: [ http:\/\/www.sciencemag.org\/content\/337\/6098\/1019.short ]","journal-title":"Science (New York, NY)"},{"key":"88_CR13","doi-asserted-by":"crossref","unstructured":"Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, Gravel D: The case for open preprints in biology. PLoS Biol. Accepted","DOI":"10.1371\/journal.pbio.1001563"},{"key":"88_CR14","doi-asserted-by":"publisher","first-page":"e24914","DOI":"10.1371\/journal.pone.0024914","volume":"6","author":"SJ Schultheiss","year":"2011","unstructured":"Schultheiss SJ, M\u00fcnch M-C, Andreeva GD, R\u00e4tsch G: Persistence and availability of Web services in computational biology. PloS One. 2011, 6: e24914-10.1371\/journal.pone.0024914. Available: [ http:\/\/dx.plos.org\/10.1371\/journal.pone.0024914 ]","journal-title":"PloS One"},{"key":"88_CR15","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1093\/bioinformatics\/btg465","volume":"20","author":"JD Wren","year":"2004","unstructured":"Wren JD: 404 not found: the stability and persistence of URLs published in MEDLINE. Bioinformatics (Oxford, England). 2004, 20: 668-72. 10.1093\/bioinformatics\/btg465. Available: [ http:\/\/bioinformatics.oxfordjournals.org\/content\/20\/5\/668.abstract ]","journal-title":"Bioinformatics (Oxford, England)"},{"key":"88_CR16","doi-asserted-by":"publisher","first-page":"e1002802","DOI":"10.1371\/journal.pcbi.1002802","volume":"8","author":"A Prli\u0107","year":"2012","unstructured":"Prli\u0107 A, Procter JB: Ten simple rules for the open development of scientific software. PLoS Comput Biol. 2012, 8: e1002802-10.1371\/journal.pcbi.1002802. Available: [ http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002802 ]","journal-title":"PLoS Comput Biol"},{"key":"88_CR17","volume-title":"GitHub sees 3 millionth member account","author":"DP Pearson","year":"2013","unstructured":"Pearson DP: GitHub sees 3 millionth member account. 2013, Available: [ http:\/\/www.gamesindustry.biz\/articles\/2013-01-17-Github-sees-3-millionth-member-account ] Accessed 18 Jan 2013"},{"key":"88_CR18","volume-title":"Github Has surpassed sourceforge and Google code in popularity","author":"K Finley","year":"2011","unstructured":"Finley K: Github Has surpassed sourceforge and Google code in popularity. 2011, Available: [ http:\/\/readwrite.com\/2011\/06\/02\/github-has-passed-sourceforge ] Accessed 15 Jan 2013"},{"key":"88_CR19","unstructured":"The Octoverse in 2012 \u00b7 GitHub Blog. Available: [ https:\/\/github.com\/blog\/1359-the-octoverse-in-2012 ]. Accessed 01AD\u2013Feb 13AD"},{"key":"88_CR20","doi-asserted-by":"publisher","first-page":"e1002598","DOI":"10.1371\/journal.pcbi.1002598","volume":"8","author":"A Morin","year":"2012","unstructured":"Morin A, Urban J, Sliz P: A quick guide to software licensing for the scientist-programmer. PLoS Comput Biol. 2012, 8: e1002598-10.1371\/journal.pcbi.1002598. [ http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002598 ]","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"88_CR21","doi-asserted-by":"publisher","first-page":"e308","DOI":"10.1371\/journal.pone.0000308","volume":"2","author":"HA Piwowar","year":"2007","unstructured":"Piwowar HA, Day RS, Fridsma B: Sharing detailed research data is associated with increased citation rate. PLOS One. 2007, 2 (3): e308-10.1371\/journal.pone.0000308.","journal-title":"PLOS One"},{"key":"88_CR22","doi-asserted-by":"publisher","first-page":"e18657","DOI":"10.1371\/journal.pone.0018657","volume":"6","author":"HA Piwowar","year":"2011","unstructured":"Piwowar HA: Who shares? Who doesn\u2019t? Factors associated with openly archiving raw research data. PloS One. 2011, 6: e18657-10.1371\/journal.pone.0018657. Available: [ http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3135593&tool=pmcentrez&rendertype=abstract ]","journal-title":"PloS One"},{"key":"88_CR23","doi-asserted-by":"publisher","first-page":"e24357","DOI":"10.1371\/journal.pone.0024357","volume":"6","author":"W Qureshi","year":"2011","unstructured":"Qureshi W, Al-Mallah MH, Alsheikh-Ali, A a: Public availability of published research data in high-impact journals. PloS One. 2011, 6: e24357-10.1371\/journal.pone.0024357. Available: [ http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3168487&tool=pmcentrez&rendertype=abstract ]","journal-title":"PloS One"},{"key":"88_CR24","doi-asserted-by":"publisher","first-page":"e44913","DOI":"10.1371\/journal.pone.0044913","volume":"7","author":"THJ Niedermeyer","year":"2012","unstructured":"Niedermeyer THJ, Strohalm M: mMass as a software tool for the annotation of cyclic peptide tandem mass spectra. PloS one. 2012, 7: e44913-10.1371\/journal.pone.0044913. Available: [ http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3441486&tool=pmcentrez&rendertype=abstract ]","journal-title":"PloS one"},{"key":"88_CR25","unstructured":"US NSF - Dear Colleague Letter - Issuance of a new NSF Proposal & Award Policies and Procedures Guide (NSF13004). 2012, Available: [ http:\/\/www.nsf.gov\/pubs\/2013\/nsf13004\/nsf13004.jsp?WT.mc_id=USNSF_109 ] Accessed 11 Nov 2012"},{"key":"88_CR26","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/493159a","volume":"493","author":"H Piwowar","year":"2013","unstructured":"Piwowar H, Altmetrics: Value all research products. Nature. 2013, 493: 159-159. Available: [ http:\/\/www.nature.com\/doifinder\/10.1038\/493159a ]","journal-title":"Nature"},{"key":"88_CR27","unstructured":"Wilson G, Aruliah DA, Brown CT, Hong NPC, Davis M: Best practices for scientific computing. Arxiv. 6. [ http:\/\/arxiv.org\/abs\/1210.0530 ]"}],"container-title":["Source Code for Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1751-0473-8-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1751-0473-8-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1751-0473-8-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,10]],"date-time":"2019-07-10T02:55:28Z","timestamp":1562727328000},"score":1,"resource":{"primary":{"URL":"https:\/\/scfbm.biomedcentral.com\/articles\/10.1186\/1751-0473-8-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,2,28]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["88"],"URL":"https:\/\/doi.org\/10.1186\/1751-0473-8-7","relation":{},"ISSN":["1751-0473"],"issn-type":[{"value":"1751-0473","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,2,28]]},"article-number":"7"}}