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Project teams

This bioinformatics project aims to utilize various software tools to generate, analyze, and interpret large datasets. By using tools like E-Cell for cell simulations, Phylip for phylogenetic analysis, and BLAST for sequence alignment, we will explore gene expression patterns and protein interactions. Key project phases include the completion of data generation by April 13, followed by data analysis and reporting. Each team member will present findings, challenges faced, and insights gained throughout the project, culminating in a comprehensive written report due on April 27.

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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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