The following list outlines various outreach activities the team is using to expand TVAP's reach.
CMDS has been requested/used worldwide by researchers from such as Hamamatsu University School of Medicine (Japan), Beijing Institute of Genomics (China), The Arthur and Sonia Labatt Brain Tumor Research Centre (Canada), Nutrigenetics Unlimited, Inc. (USA), Baylor College of Medicine's Human Genome Sequencing Center (USA).
A series of classes called Genome Model Basics have been presented at the Genome Institute during the first quarter of 2013. An additional series tentatively titled Genome Model Not So Basic is also scheduled. These presentations are meant to be the basis of presentations tailored for external users of the GMS and to extend and expand the general GMS documentation.
The following is a list of invited talks about Pindel:
* October 2012: Wuhan University, Wuhan, China
* December 2011: Peking University, Beijing, China
* December 2011: Chinese Academic of Science, Beijing, China
* December 2011: Huazhong University of Science and Technology, Wuhan, China
* December 2011: Beijing Forestry University, Beijing, China
* December 2011: 301 hospital, Beijing, China
* November 2010: University of Washington, Seattle, WA
* October 2010: EMBL, Heidelberg, Germany
* September 2010: Gregor Mendel Institute of Molecular Plant Biology, Austria
* July 2010: Boston College, Boston, MA
* May 2010: The Genome Institute at Washington University, St. Louis, MO
* October 2009: Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany
Sourcecode available on github
Debian repo and help available from GMT website
Actively monitoring questions posed on Biostars and SeqAnswers as well as personal communications. Screencast on compiling.
The ongoing development and improvement of VarScan 2 benefits from a wide community of active users. More than a dozen code updates have been released since 2010, many in response to user feedback and bug reports. For example, we made VarScan compatible with Variant Call Format (VCF) upon request. The web site at http://varscan.sourceforge.net includes variant calling tutorials, documentation, and software downloads. We interact with users by e-mail, on the SourceForge Help forum, and on bioinformatics communities such as BioStars and SeqAnswers.