Project teamsKamal, Joshi 1Jones, Mary Ann 1Yeh, Ijen 1Raghu, Anand 2Wang, Yu 2Keane, Gene 2Sathyanarayana, Seshadri 3Legesse, Mehari 3McMurray, Thomas 3Pangarkar, Amruta 4Kim, Dohyun 4Newlin, Cynthia 4Li, Jia 5Sheeba , John 5Manjula Miryalkar 5Rajasekaran, Indumathi 6Ranade, Tejas 6Kishore, Kothinti Rajendra 6Xu, Xizhen 7Zulfiqar, Aeysha 7Atluri, Sasi 7

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Projects● E-Cell – cell simulation

Phylip – 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

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

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

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!

E-cell

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

Phylip

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

Sage

http://www.sagenet.org/

Teiresias

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

Blast

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

GenThreader

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

Clustal-W

http://www.ebi.ac.uk/clustalw/

GeneQuiz

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

HMMGene

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

ProteinExplorer

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

BioSpice

https://community.biospice.org/