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Project teams

Project teams. 5. 3. Projects.

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Project teams

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  1. Project teams 5 3

  2. Projects • E-Cell – cell simulationPhylip – infer phylogeniesSAGE Serial Analysis of Gene ExpressionTeiresias – sequence pattern discoveryBlast – local alignment toolClustalW – multiple sequence alignmentGenThreader – Protein Structure PredictionGeneQuiz – automated sequence analysisHMMgene – Prediction of genesProtein Explorer – visualizing molecular interactionsBioSpice – modeling dynamic cellular network functions

  3. Project specs • Utilize a piece of bioinformatics software • Generate a 'mass' of data • Tweak the parameters • Apply to 'mass' of raw data • Possibly automate the generation of the data • Analyze the data • Cluster • Compare • Evaluate • Look 'behind the curtain' at the methods

  4. Project schedule • April 6 • 1-page detailed outline of project • April 13 • Data generation complete • 'Behind the curtain' in parallel • April 20 • Data analysis completed • April 27, May 4 • Class reports

  5. Class reports • Each team member does a segment • Prepare slides • 3 10-minute presentations, 5 minutes q/a • What you got done • Problems as well as findings • Things left undone • Hand in slides and written report • Due April 27 – no extensions!

  6. E-cell • Cell simulation • http://www.e-cell.org/

  7. Phylip http://evolution.genetics.washington.edu/phylip.html

  8. Sage http://www.sagenet.org/

  9. Teiresias http://cbcsrv.watson.ibm.com/Tspd.html

  10. Blast http://www.ncbi.nlm.nih.gov/BLAST/

  11. GenThreader http://bioinf.cs.ucl.ac.uk/psipred/

  12. Clustal-W http://www.ebi.ac.uk/clustalw/

  13. GeneQuiz http://jura.ebi.ac.uk:8765/ext-genequiz/

  14. HMMGene http://www.cbs.dtu.dk/services/HMMgene/

  15. ProteinExplorer http://molvis.sdsc.edu/protexpl/frntdoor.htm

  16. BioSpice https://community.biospice.org/

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