The main vehicle for training at the Division of Informatics is the weekly workshop. It is also listed as a credit-earning course by the UAB's graduate school as GBS755 Integrative Informatics (catalog entry, schedule listing, there is also a UAB blackboard, not used much). This is a hands on activity* that takes place every Wednesday where participants bring their laptops, code, and systems biology / integrative biomedicine problems to an "extreme programming" environment. Each participant is encouraged to maintain his or her own version-controlled repositories, ideally cloned from the shared repository at

*TCGA club - in response to multiple requests, the third hour of the hands-on workshop, (i.e. 11-noon) is focused on The Cancer Genome Atlas.


The workshop takes place every Wednesday from 9 am to noon at one of these two locations (current room is highlighted):

Online participation

Desktop sharing:

Some introductory reading material:
  • Programming the Semantic Web.Toby Segaran, Colin Evans, Jamie Taylor. O'Reilly Media (July 14, 2009).
  • Deus HF, DF Veiga, PR Freire, JN Weinstein, GB Mills, JS Almeida (2010) Exposing The Cancer Genome Atlas as a SPARQL endpoint. Journal Biomedical Informatics [PMID 20851208].
  • Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315].


  • David Robbins (robbinsd at mathbiol dot org) - Dept Electrical and Computer Engineering. 
  • Alexander Gruneberg (agrueneberg at mathbiol dot org) - Div Informatics, Dept Pathology.
  • Bade Iriabho (ebade at mathbiol dot org) - Div Informatics, Dept Pathology.
  • David Crossman (dkcrossm at uab dot edu) - ...
  • Vinodh Srinivasa (vinodh at uab dot edu) - Statistical Genetics Section of Dept Biostatistics.
  • Jonas S Almeida (jalmeida at uab dot edu) - Div Informatics, Dept Pathology.
  • Young So Song (lifen at uab dot edu)  - Div Informatics, Dept Pathology.
  • John Paul Robinson - Research Computing 
  • Jingyu Guo (jguo at uab dot edu) - Div Research, Dept Genetics.
  • Curtis Hendrickson (curtish at uab dot edu) - CCTS Biomedical Informatics / Microbiology
  • John Osborne (ozborn at uab dot edu) - CCTS Biomedical Informatics / Microbiology
  • Sean Wilkinson (wilkinson at uab dot edu) - Div Informatics, Dept Pathology; Dept Biomedical Engineering
  • Alex M. Dussaq (adussaq at uab dot edu) - Dib Informatic, Dept Pathology, PBMM, MSTP student
  • Emanuel Diego S Penha (penhaeds at uab dot edu) - Div Informatics, Dept Pathology.
  • etc - sorry people, we need this list and will keep harassing you to fill it :-)

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Jonas Almeida,
Apr 27, 2011, 8:18 AM