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 |