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1st network progress meeting in EMBL

Training Course: Bioinformatics tools to study PPI (September 26 - September 29)

Day Time Plan
1 09:00 - 09:30 Coffee/Introduction to the course
1 09:30 - 11:00 Practical session/Marc Gouw, Malvika Sharan, Jelena Calyseva/Linux commandline course - I
1 11:00 - 11:30 Coffee break
1 11:30 - 12:30 Practical session/Malvika Sharan, Marc Gouw, Jelena Calyseva/Linux commandline course - II
1 12:30 - 14:00 Lunch
1 14:00 - 15:30 Practical session and demonstration/Jelena Calyseva/Protein databases and related annotation resources
1 15:30 - 16:00 Coffee break
1 16:00 - 17:00 Practical session and demonstration/Malvika Sharan/Studying similar sequences (BLAST, MSA etc.) and EBI-EMBOSS toolkits
1 17:00 End
2 09:30 - 10:30 Lecture/Toby Gibson/Complexity of PPIs
2 10:00 - 10:30 Coffee break
2 10:30 - 11:30 Practical session and demonstration/Jelena Calyseva, Malvika Sharan/Tools and resources for the analysis of the structural architecture of a protein (PDB, InterPro, TMHMM etc.)
2 11:30 - 12:30 Practical activity and demonstration/Marc Gouw, Malvika Sharan/Understanding linear motifs & intrinsically disordered region-1 (ELM, SLiMSearch, ProViz)
2 12:30 - 13:30 Lunch break
2 13:30 - 15:00 Practical activity and demonstration/Marc Gouw, Malvika Sharan/Understanding linear motifs & intrinsically disordered region-2 (JPred, IUPRED, Anchor)
2 15:00 - 15:30 Coffee break
2 15:30 - 17:00 Practical activity/Toby Gibson/Revealing interactive features in protein multiple sequence alignments with Jalview
2 17:00 end
3 09:00 - 11:00 Practical activity and demonstration/Matt Rogon/Network analysis using Cytoscape - I
3 11:00 - 11:30 Coffee break
3 11:30 - 12:30 Practical session and demonstration/Toby Gibson/Visualizing protein structures and interaction interfaces with UCSF Chimera
3 12:30 - 13:30 Lunch
3 13:30 - 15:00 Practical activity and demonstration/Jelena Calyseva/Sequence/structure alignment based study of PDZ domains
3 15:00 – 15:30 Coffee
3 15:30 - 17:00 Practical session and demonstration/Michael Kuhn/Protein association networks with STRING
3 17:00 end
4 09:00 - 10:30 Practical activity and demonstration/Matt Rogon/Network analysis using Cytoscape to integrate experimental datasets (e.g. BIO-ID) 1
4 10:30 - 11:00 Coffee break
4 11:00 - 12:30 Practical activity and demonstration/Matt Rogon/Network analysis using Cytoscape to integrate experimental datasets (e.g. BIO-ID) 2
4 12:30 – 13:30 Lunch
4 13:30 – 15:00 Practical activity/Group tasks: Work on your protein(s) of interest and prepare group presentations
4 15:00 – 15:30 Coffee
4 15:30 - 17:00 Practical activity/Group tasks: Group presentations and final feedback
4 17:00 end