2. Project teams 5 3

3. Projects ● E-Cell – cell simulation Phylip – infer phylogenies SAGE Serial Analysis of Gene Expression Teiresias – sequence pattern discovery Blast – local alignment tool ClustalW – multiple sequence alignment GenThreader – Protein Structure Prediction GeneQuiz – automated sequence analysis HMMgene – Prediction of genes Protein Explorer – visualizing molecular interactions BioSpice – modeling dynamic cellular network functions

4. 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

5. 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

6. 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!

7. E-cell ● Cell simulation ● http://www.e-cell.org/ http://www.e-cell.org/

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

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

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

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

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

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

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

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

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

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