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 https://uabworkshop.googlecode.com.
*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.
Location
The workshop takes place every Wednesday from 9 am to noon at one of these two locations (current room is highlighted):
Online participation
Some introductory reading material:
- http://www.data.gov/semantic.
- 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].
People
- 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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 Updating... Jonas Almeida, Apr 27, 2011, 8:18 AM
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