{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T15:06:41Z","timestamp":1774969601395,"version":"3.50.1"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have found that agile methods are well suited to the exploratory and iterative nature of scientific inquiry. They provide a robust framework for reproducing scientific results and for developing clinical support systems. The agile development approach also provides a model for collaboration between software engineers and researchers. We present our experience using agile methodologies in projects at six different biomedical software development organizations. The organizations include academic, commercial and government development teams, and included both bioinformatics and clinical support applications. We found that agile practices were a match for the needs of our biomedical projects and contributed to the success of our organizations.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We found that the agile development approach was a good fit for our organizations, and that these practices should be applicable and valuable to other biomedical software development efforts. Although we found differences in how agile methods were used, we were also able to identify a set of core practices that were common to all of the groups, and that could be a focus for others seeking to adopt these methods.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-273","type":"journal-article","created":{"date-parts":[[2006,5,31]],"date-time":"2006-05-31T10:19:53Z","timestamp":1149070793000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Agile methods in biomedical software development: a multi-site experience report"],"prefix":"10.1186","volume":"7","author":[{"given":"David W","family":"Kane","sequence":"first","affiliation":[]},{"given":"Moses M","family":"Hohman","sequence":"additional","affiliation":[]},{"given":"Ethan G","family":"Cerami","sequence":"additional","affiliation":[]},{"given":"Michael W","family":"McCormick","sequence":"additional","affiliation":[]},{"given":"Karl F","family":"Kuhlmman","sequence":"additional","affiliation":[]},{"given":"Jeff A","family":"Byrd","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,5,30]]},"reference":[{"key":"1012_CR1","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1109\/ICSE.2004.1317460","volume-title":"26th International Conference on Software Engineering (ICSE'04)","author":"P Manhart","year":"2004","unstructured":"Manhart P, Schneider K: Breaking the ice for agile development of embedded software: an industry experience report. In 26th International Conference on Software Engineering (ICSE'04). Edinburgh, Scotland, United Kingdom. IEEE; 2004:378\u2013386."},{"key":"1012_CR2","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1109\/ADEVC.2004.21","volume-title":"Agile Development Conference (ADC'04)","author":"NV Schooenderwoert","year":"2004","unstructured":"Schooenderwoert NV, Morsicato R: Taming the Embedded Tiger \u2013 Agile Test Techniques for Embedded Software. In Agile Development Conference (ADC'04). Sal Lake City, Utah. IEEE; 2004:120\u2013126."},{"key":"1012_CR3","first-page":"2","volume-title":"Agile Development Conference (ADC'03)","author":"B Freeman-Benson","year":"2003","unstructured":"Freeman-Benson B, Borning A: YP and Urban Simulation: Applying an Agile Programming Methodology in a Politically Tempestuous Domain. In Agile Development Conference (ADC'03). Salt Lake City, Utah. IEEE; 2003:2\u201311."},{"key":"1012_CR4","first-page":"60","volume-title":"Agile Development Conference (ADC'03)","author":"MK Spayd","year":"2003","unstructured":"Spayd MK: Evolving agile in the enterprise: implementing XP on a grand scale. In Agile Development Conference (ADC'03). Salt Lake City, Utah. IEEE; 2003:60\u201370."},{"key":"1012_CR5","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1109\/ADEVC.2004.15","volume-title":"Agile Development Conference (ADC'04)","author":"L Layman","year":"2004","unstructured":"Layman L, Williams L, Cunningham L: Exploring extreme programming in context: an industrial case study. In Agile Development Conference (ADC'04). Salt Lake City, Utah. IEEE; 2004:32\u201341."},{"key":"1012_CR6","doi-asserted-by":"crossref","unstructured":"Weinstein J 2005.","DOI":"10.1126\/stke.3002005tr24"},{"key":"1012_CR7","unstructured":"Manifesto for Agile Software Development[http:\/\/www.agilemanifesto.org]"},{"key":"1012_CR8","volume-title":"Test-driven development : by example","author":"K Beck","year":"2003","unstructured":"Beck K: Test-driven development : by example. Boston: Addison-Wesley; 2003."},{"key":"1012_CR9","volume-title":"Pragmatic unit testing in Java with JUnit","author":"A Hunt","year":"2003","unstructured":"Hunt A, Thomas D, Pragmatic Programmers (Firm): Pragmatic unit testing in Java with JUnit. Raleigh, NC: Pragmatic Bookshelf; 2003."},{"key":"1012_CR10","volume-title":"JUnit recipes : practical methods for programmer testing","author":"JB Rainsberger","year":"2005","unstructured":"Rainsberger JB, Stirling S: JUnit recipes : practical methods for programmer testing. Greenwich, CT: Manning; 2005."},{"key":"1012_CR11","volume-title":"Agile and iterative development : a manager's guide","author":"C Larman","year":"2004","unstructured":"Larman C: Agile and iterative development : a manager's guide. Boston: Addison-Wesley; 2004."},{"key":"1012_CR12","unstructured":"XPlanner[http:\/\/www.xplanner.org]"},{"key":"1012_CR13","volume-title":"Extreme programming explained : embrace change","author":"K Beck","year":"2004","unstructured":"Beck K, Andres C: Extreme programming explained : embrace change. 2nd edition. Boston, MA: Addison-Wesley; 2004.","edition":"2"},{"key":"1012_CR14","unstructured":"FitNesse: the fully integrated standalone wiki, and acceptance testing framework[http:\/\/www.fitnesse.org]"},{"key":"1012_CR15","volume-title":"Planning extreme programming","author":"K Beck","year":"2001","unstructured":"Beck K, Fowler M: Planning extreme programming. Boston: Addison-Wesley; 2001."},{"key":"1012_CR16","first-page":"132","volume-title":"Agile 2005","author":"MM Hohman","year":"2005","unstructured":"Hohman MM: Estimating in Actual Time. In Agile 2005; Denver, Colorado. IEEE Computer Society; 2005:132\u2013138."},{"key":"1012_CR17","unstructured":"Mock Objects[http:\/\/www.mockobjects.com]"},{"key":"1012_CR18","unstructured":"JUnit, Testing Resources for Extreme Programming[http:\/\/www.junit.org]"},{"key":"1012_CR19","unstructured":"CruiseControl: continuous integration toolkiit[http:\/\/cruisecontrol.sourceforge.net]"},{"key":"1012_CR20","volume-title":"Refactoring : improving the design of existing code","author":"M Fowler","year":"1999","unstructured":"Fowler M, Beck K: Refactoring : improving the design of existing code. Reading, MA: Addison-Wesley; 1999."},{"key":"1012_CR21","unstructured":"IntelliJ IDEA[http:\/\/www.jetbrains.com\/idea\/]"},{"key":"1012_CR22","unstructured":"Eclipse[http:\/\/www.eclipse.org]"},{"key":"1012_CR23","volume-title":"Fearless change : patterns for introducing new ideas","author":"ML Manns","year":"2005","unstructured":"Manns ML, Rising L: Fearless change : patterns for introducing new ideas. Boston: Addison-Wesley; 2005."},{"key":"1012_CR24","first-page":"16","volume":"18","author":"P McMahon","year":"2005","unstructured":"McMahon P: Extending Agile Methods: A Distributed Project and Organizational Improvement Perspective. Crosstalk 2005, 18: 16\u201319.","journal-title":"Crosstalk"},{"key":"1012_CR25","unstructured":"Scaling Agile Methods[http:\/\/www.newarchitectmag.com\/documents\/s=7576\/na1002e\/index.html]"},{"key":"1012_CR26","volume-title":"2003 Agile Development Conference; June 25\u201328, 2003","author":"MH G Alleman","year":"2003","unstructured":"G Alleman MH: \"Making Agile Development Work in a Government Contracting Environment\". In 2003 Agile Development Conference; June 25\u201328, 2003. Salt Lake City, UT; 2003."},{"key":"1012_CR27","volume-title":"Software architecture: organizational principles and patterns","author":"DM Dikel","year":"2001","unstructured":"Dikel DM, Kane D, Wilson JR: Software architecture: organizational principles and patterns. Upper Saddle River, NJ: Prentice Hall; 2001."},{"key":"1012_CR28","volume-title":"Agile software development with scrum","author":"K Schwaber","year":"2002","unstructured":"Schwaber K, Beedle M: Agile software development with scrum. Upper Saddle River, NJ: Prentice Hall; 2002."},{"key":"1012_CR29","volume-title":"Agile software development","author":"A Cockburn","year":"2002","unstructured":"Cockburn A: Agile software development. Boston: Addison-Wesley; 2002."},{"key":"1012_CR30","unstructured":"Feature Driven Development[http:\/\/www.featuredrivendevelopment.com]"},{"key":"1012_CR31","unstructured":"DSDM Consortium[http:\/\/www.dsdm.org]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-273.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:05:31Z","timestamp":1630494331000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-273"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,5,30]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["1012"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-273","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,5,30]]},"assertion":[{"value":"17 November 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"273"}}