Connecting TOPSAN to Computational Analysis<br />Christian M Zmasek<br />
Overview<br />About me<br />Software projects<br />What is TOPSAN?<br />TOPSAN and the semantic web<br />2<br />
About me<br />Work<br />Currently work at the Sanford-Burnham Medical Research Institute<br />Previously worked at Genomic...
Software projects<br />forester<br />Open source libraries ofJava andRuby software for Comparative Genomics and Evolutiona...
TOPSAN<br />5<br />
What is TOPSAN?<br />TOPSAN: The Open Protein Structure Annotation Network <br />http://www.topsan.org/<br />Ten-thousands...
What is TOPSAN?<br />TOPSAN contains collaborative  annotations of protein structures<br />Combines automated with human e...
“Semantic” TOPSAN<br />Using the principles of the semantic web to turn TOPSAN into a database that can be:<br />Searched<...
Acknowledgements<br />Kyle Ellrott<br />Dana Weekes<br />ConstantinaBakolitsa<br />John Wooley<br />Adam Godzik<br />Joint...
Thank You!!<br />10<br />Biohackathon organizers<br />JST – Japanese funding agency for Science and Technology <br />NBDC ...
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Zmasek TOPSAN Biohackathon 2011

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Zmasek TOPSAN Biohackathon 2011

  1. 1. Connecting TOPSAN to Computational Analysis<br />Christian M Zmasek<br />
  2. 2. Overview<br />About me<br />Software projects<br />What is TOPSAN?<br />TOPSAN and the semantic web<br />2<br />
  3. 3. About me<br />Work<br />Currently work at the Sanford-Burnham Medical Research Institute<br />Previously worked at Genomics Institute of the Novartis Research Foundation (GNF)<br />PhD in Prof. Sean Eddy’s lab at Washington University Medical School <br />Research Interests<br />Regulatory pathway evolution<br />Comparative functional genomics <br />Sequence function analysis and prediction<br />Phylogenetic inference<br />Genome evolution<br />Protein structure evolution<br />Evo-devo<br />Computer<br />Java<br />Ruby (BioRuby)<br />Learning Scala (http://www.scala-lang.org/) and re-learning C++ <br />Graphics, Visualization, Linked Data <br />Website: http://www.cmzmasek.net/<br />3<br />
  4. 4. Software projects<br />forester<br />Open source libraries ofJava andRuby software for Comparative Genomics and Evolutionary Biology research<br />http://www.phylosoft.org/forester/<br />phyloXML<br />XML for evolutionary biology and comparative genomics<br />http://www.phyloxml.org/<br />4<br />
  5. 5. TOPSAN<br />5<br />
  6. 6. What is TOPSAN?<br />TOPSAN: The Open Protein Structure Annotation Network <br />http://www.topsan.org/<br />Ten-thousands of protein structures have been determined by structural genomics (SG) centers and many more are expected<br />While these structures are available in PDB (Protein Data Bank)…<br />… annotations for most of them a limited to one-line PDB titles<br />TOPSAN is the first database that specifically focuses on proving extensive annotations for almost 10,000 structures solved by the SG centers<br />6<br />
  7. 7. What is TOPSAN?<br />TOPSAN contains collaborative annotations of protein structures<br />Combines automated with human edited elements <br />Spans the range of analysis of <br />single proteins<br />characterization of protein families<br />reconstruction of entire genomes<br />Created by SG staff and over 400 external users<br />Containing over 7,250 proteins<br />Collaborating with PFAM to use JCSG structures to refine and create PFAM families<br />7<br />
  8. 8. “Semantic” TOPSAN<br />Using the principles of the semantic web to turn TOPSAN into a database that can be:<br />Searched<br />Exported<br />Thus – by linking curated and automatic annotations to the semantic web, TOPSAN content can be connected to a larger set of analysis tools and databases<br />8<br />
  9. 9. Acknowledgements<br />Kyle Ellrott<br />Dana Weekes<br />ConstantinaBakolitsa<br />John Wooley<br />Adam Godzik<br />Joint Center for Structural Genomics<br />Sanford-Burnham Medical Research Institute, La Jolla, California, USA<br />University of California, San Diego, La Jolla, California, USA<br />Joint Center for Molecular Modeling<br />9<br />
  10. 10. Thank You!!<br />10<br />Biohackathon organizers<br />JST – Japanese funding agency for Science and Technology <br />NBDC – National Bioscience Database Center<br />DBCLS – Database Center for Life Science<br />

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