The following list outlines various outreach activities the team is using to expand TVAP's reach.



  • The Cancer Genome Atlas 2nd Annual Scientific Symposium: Enabling Cancer Research Through TCGA (November 27-28, 2012). Title: Assessing Tumor Heterogeneity and Tracking Clonal Evolution Using Whole Genome or Exome Sequencing (Video Slides)


  • November 2011 at Genome Informatics (CSHL)


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).


  • Workshop: "iSeqTools to Demistify the Cloud and Genomics Analysis for Researchers Seeking Ways to Analyze High-Throughput DNA Sequencing Data". (2014). American Society of Human Genetics Annual Meeting.


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.


PathScan is written in Perl and is both freely distributed and supported by the Genome Institute's bioinformatics staff. Documentation and examples are widely available, e.g. on CPAN.


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.


  • September 2010 at Genome Informatics conference (Hinxton, UK)


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.