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Open-source code

A resource for users or producers of open-source code, software, and hardware for researchers in biomedical or life science

Finding open-source code & programs

The largest repository for open source code projects in the life sciences is currently GitHub. GitHub also has a spin-off environment called GitLab . GitHub allows browsing by topic. Browsing by "biology" or "medicine" can be helpful for discovering projects in the life sciences.  

Searching by programming language can be challenging in both PubMed and Google, however the programming language can be helpful in narrowing a search to a specific area, with Python and "R" being most popular in biology and Java/Javascript being most popular in medicine.

The journal, Source Code for Biology and Medicine (Source Code Biol Med) is a useful journal.

Search strategy

PubMed search strategy designed to capture new open source software reported in the biological and life sciences literature using the most frequently cited open source licenses. 

"Source Code Biol Med"[jour] OR (open-source OR copyleft OR sourceforge OR github OR gitlab OR bitbucket OR “coding.net”) OR (((creative-commons NOT "creativecommons.org") OR public-domain) AND (code OR coding OR tool OR toolkit OR “http://”)) OR ((open OR license) AND (Alioth OR Apache OR BSD OR CC0 OR CDDL OR CeCILL OR Codeplex OR Copyleft OR Drupal OR Expat OR FreeBSD OR Gna OR GNU OR GNUGPL OR “Google Code” OR GPL OR GFDL OR Kallithea OR Launchpad OR LGPL OR MIT OR MITX OR “MIT/X” OR Mozilla OR OpenBSD OR OpenLDAP OR X11 OR Zope)) ​

PubMed feed for open code & software

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