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EBITrainingEBI User Training ProgrammeHands-onEMBO Practical Course On In Silico Systems BiologyProgramme

Hands-on training at EBI - EMBO Practical Course 'In silico systems biology: network reconstruction, analysis and network based modelling'

Course Summary
Course Details Title: EMBO Practical Course 'In silico systems biology: network reconstruction, analysis and network based modelling'
Date: 10-13 April 2010
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organisers: Vicky Schneider, Nicolas le Novere
Admin Support: Holly Foster & Alison Barker
Registration Deadline: 26 February 2010 - 12 noon (GMT)


The course materials are now available to download. You will need a username and password to access these files. This is only available to people who attended the course (contact courses@ebi.ac.uk for details). Please take note of any materials licensing notices in these documents.

To download a zip folder of each day's course materials click on the relevant link:

Programme



Time Topic
Day 1 (Sat 10th April) - Introduction-State of the art, Getting to know each other. Chair: Dr. Javier De Las Rivas
09:00 - 09:15 Welcome and safety briefing
09:15 - 09:45 Dr. Nicolas le Novere Scientific Lecture: Introduction to Systems Biology and this course
09:45 - 10:30 Your Systems Biology research
10:30 - 11:15 Dr. Laurence Calzone Scientific Lecture: Computational Systems Biology workflow for modelling cell fate decision process
11:15 - 11:30 Coffee break
11:30 - 12:15 Dr. Javier De Las Rivas Scientific Lecture: T.B.A.
12:15 - 13:00 Dr. Rune Linding Scientific Lecture: Cancer Related Network Dynamics and Cellular Information Processing
13:00 - 14:00 Lunch + posters
14:00 - 14:45 Dr. Jasmin Fisher Scientific Lecture: Executable Biology
14:45 - 15:30 Dr. Julio Saez-Rodriguez Scientific Lecture: Uncovering signaling differences between normal and transformed cells using cell-specific pathway models
15:30 - 16:00 Tea break
16:00 - 16:45/td> Dr. Laura Ines Furlong Scientific Lecture: Integration of genomic data with biological networks – state of the art and future challenges
16:45 - 17:15 Wrap up and summary of main learning objectives
17:15 - 17:30 Short break
17:30 - 18:30 Evening discussion. Chair:Dr. Javier De Las Rivas
20:00 Course dinner at Arundel House Hotel
Day 2 (Sun 11th April) - Reconstructing Networks. Chair: Dr. Laura Ines Furlong
09:15 - 09:30 Concept and Objectives of the Day- Dr Nicolas Le Novere
09:30 - 10:15

Methodological Lecture: Construction of human gene expression map using large-scale integration of public microarray data - Margus Lukk
10:15 - 11:15 Hands on: Mining the data in human gene expression map - Margus Lukk
11:15 - 11:30 Coffee break
11:30 - 12:15 Methodological Lecture and Hands on: Samuel Kerrien - Primary data resource: IntAct. How to retrieve, download and process protein interaction data in a form suitable to reconstruct protein networks.
12:15 - 13:00 Methodological Lecture: Dr. Julio Saez-Rodriguez - Construction of context-specific maps of signalling networks using high-throughput proteomics data and literature-derived networks
13:00 - 14:00 Lunch and demos
14:00 - 15:30 Hands on exercises: Dr. Julio Saez-Rodriguez - From high-throughput protein activity data to cell-specific logic models using DataRail and CellNetOptimizer
15:30 - 16:00 Tea break
16:00 - 16:30 Methodological Lecture: Dr. Javier De Las Rivas - Protein-Protein interaction networks, first steps towards the human interactomes
16:30 - 18:00 Hands on exercises: Dr. Javier De Las Rivas - Protein-protein interaction networks: build and explore them with Cytoscape, APID2NET and other tools.
20:00 Course Dinner at Jesus College, Cambridge
Day 3 (Mon 12th April) - Analysing Networks. Chair: Dr. Rune Linding
09:15 - 09:30 Concept and Objectives of the Day- Dr Nicolas Le Novere
09:30 - 11:15 Methodological Lecture/Hands on exercises: Dr. Thomas Schlitt - Approaches to Modelling Gene Regulatory Networks
11:15 - 11:30 Coffee Break
11:30- 12:15 Methodological Lecture: Dr. Laurence Calzone - RB/E2F Pathway: A Biological and a Mathematical Perspective
12:15- 13:00 Hands on exercises: Dr. Laurence Calzone - Disentangling RB/E2F pathway with BiNoM
13:00 - 14:00 Lunch and demos
14:00 - 14:45 Methodological Lecture and Hands on: Dr. Rune Linding - Modelling of Phosphorylation Networks
14:00 - 15:30 Methodological Lecture: Dr.Laura Ines Furlong and Anna Bauer-Mehren - Integration of biological annotations and networks using Cytoscape
15:30 - 16:00 Tea Break
16:00 - 18:00 Hands on exercises: Anna Bauer-Mehren - Integration of biological annotations and networks using Cytoscape
18:00 - 18:45 Evening discussion session. Chair: Dr. Rune Linding
20:00 Course dinner at Arundel House Hotel
Day 4 (Tue 13th April) - Modelling Networks. Chair: Dr. Nicolas Le Novere
09:15 - 09:30 Concept and Objectives of the Day- Dr Nicolas Le Novere
09:30 - 10:00 Methodological Lecture: Dr. Nicolas Le Novere - Introduction to modeling chemical kinetics
10:30 - 11:00 Methodological Lecture: Dr. Sven Sahle - The COmplex PAthway SImulator
11:00 - 11:15 Coffee break
11:15 - 13:00 Hands on Tutorial: Dr. Viji Chelliah - Modelling signalling pathways
13:00 - 14:00 Lunch and demos
14:00 - 15:00 Methodological Lecture: Dr. Sarah Keating - The Systems Biology Markup Language (SBML)
15:00 - 15:30 Methodological Lecture: Dr Viji Chelliah - BioModels Database, a public model-sharing resource
15:30 - 16:00 Tea Break
16:00 - 16:30 Methodological Lecture: Dr. Nick Juty - Controlled annotations for Systems Biology models
16:30 - 18:00 Methodological Lecture and Hands on: Dr Wolfram Liebermeister - SemanticSBML: Model analysis and merging
18:00 Course wrap up and survey


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