project teams 5 3 projects ● e-cell – cell simulation phylip – infer phylogenies sage serial...

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

5

3

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/