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Hands-on training at EBI - FEBS: In Silico Systems Biology: Network Reconstruction, Analysis and Network-based Modelling

Course Summary
LogoTitle: FEBS: In Silico Systems Biology: Network Reconstruction, Analysis and Network-based Modelling
Date: 23-26 May 2011
Venue: EMBL-EBI, Hinxton, Nr Cambridge, CB10 1SD, UK
Organisers: Vicky Schneider, Nicolas Le Novère and Julio Saez-Rodriguez
Admin Support: Alison Barker
Registration Opens: 1st October 2010
Registration Deadline: 1st March 2011





Co-sponsored by ENFIN

Course Overview

Is it right for me?

This course is aimed at advanced PhD students and post-doctoral researchers who are using or planning to use a systems-based approach to understanding a biological problem.
  • Will bring together lead researchers in the field of systems biology, experts in biological data resources, and you: a highly motivated group of early-stage experimental researchers through a common theme centred on human complex disease.
  • Highlights the latest advances in the field by tackling the bridge from functional effects of sequence variations (SNPs) into pathways, as well as from networks to pathways.
  • Combine lectures and led discussions to identify the key challenges, opportunities and bottlenecks, with practical sessions on network reconstruction, network analysis and network-based modelling.

What will I learn?

This course specifically aims to enable early-stage experimental researcher to bridge the gap between data exploration in individual domains (genomics, transcriptomics, proteomics, etc.) and allow them to synthesise the data to gain a whole systems perspective.
  • Hands-on sessions will allow the participants to gain practical experience of handling, analysing and integrating a wide range of different data types.
  • Lecture-based sessions will provide the conceptual framework on which to base the students’ own analyses, and led discussions will allow participants to discuss key challenges to progress.
  • Participants will present their own research through poster sessions.

What will it cover?

  • In “Silico” Systems Biology: Overview and State of the Art
  • Reconstruction of networks
  • Analysing Networks
  • Modelling Networks

Programme

Course materials are available as zip folders for each day. Click on each link to access the day's materials:

Day1.zip         Day2.zip         Day3.zip         Day4.zip

 

Time Topic

Day 1 -Monday 23 May 2011 Network Reconstruction and Analysis

08:45 Coach from accommodation Holiday Inn Express Duxford, Cambridge to EBI (this will be in a 16 seater coach and you will not all fit in at once so there will be two trips)
09:15 - 09:30 Introduction and Welcome (Nicolas Le Novere)
09:30 - 11:00 Approaches to modelling gene regulatory networks (Thomas Schlitt)
11:00 - 11:30 Tea/Coffee Break
11:30 - 13:00 Build and explore protein-protein interaction networks (Javier De Las Rivas)
13:00 - 14:00 Lunch
14:00 - 15:00 Flash presentations
15:00 - 16:00 Poster session and Tea/Coffee Break
16:00 - 17:30 Integration of genomic data with biological networks using cytoscape (Anna Bauer-Mehren)
18:30 - 20:30 Dinner at the Red Lion HInxton
20:30 Coach back to accommodation (this will be in a 16 seater coach and you will not all fit in at once so there will be two trips)

Day 2 - Tuesday 24th May 2011 

Network R & A Logical Modelling 

08:45 Coach from accommodation Holiday Inn Express Duxford Cambridge to EBI (this will be in a 16 seater coach and you will not all fit in at once so there will be two trips)
09:15 - 11:00 Modelling of cell signaling networks (Rune Linding)
11:00 - 11:30 Tea/Coffee Break
11:30 - 13:00 BINoM (Laurence Calzone)
13:00 - 14:00 Lunch
14:00 - 15:30 GinSim (Laurence Calzone)
15:30 - 16:00 Tea/Coffee Break
16:00 - 17:30 CNO (Julio Saez-Rodriguez)
18:30 - 20:30 Dinner at the Red Lion HInxton
20:30 Coach back to accommodation (this will be in a 16 seater coach and you will not all fit in at once so there will be two trips)

Day 3 - Wednesday 25th May 2011

Mechanistic Modelling

08:45 Coach from accommodation Holiday Inn Express Duxford Cambridge to EBI (this will be in a 16 seater coach and you will not all fit in at once so there will be two trips)
09:15 - 10:15 Introduction to chemical kinetics (Nicolas Le Novere)
10:15 - 11:00 COPASI introduction (Sven Sahle)
11:00 - 11:30 Tea/Coffee Break
11:30 - 13:00 Tutorial building models and running simulations (Sven Sahle and Le Novere Group)
13:00 - 14:00 Lunch
14:00 - 15:30 Your data
15:30 - 16:00 Tea/Coffee Break
16:00 - 17:30 1 to 1 continues (all)
17:30 Coach back to accommodation (this will be in a 16 seater coach and you will not all fit in at once so there will be two trips)
19:00 Coach pick-up from accommodation to Cambridge for dinner at Newnham College
22:30 Coach back to Holiday Inn Expres, Duxford, Cambridge

Day 4 - Thursday 26th May 2011

Stochastic Simulations & Encoding Sintax & Semantics

08:45 Coach from accommodation Holiday Inn Express Duxford Cambridge to EBI (this will be in a 16 seater coach and you will not all fit in at once so there will be two trips)
09:15 - 11:00 Stochastic simulations (Andrew Golightly)
11:00 - 11:30 Tea/Coffee Break
11:30 - 13:00 Supporting SBML as a model exchange format in software applications (Sarah Keating)
13:00 - 14:00 Lunch
14:00 - 15:00 BioModels database, a public model *database* (Lukas Endler)
15:00 - 15:30 MIRIAM controlled annotations for Systems Biology (Nick Juty)
15:30 - 16:00 Tea/Coffee Break
16:00 - 17:30 Using metadata to develop and integrate models (Neil Swainston)
17:33 Farwell and hope you have all enjoyed the course

Participant Survey


Registration and Payment

The cost for this course will be £695 which will include all accommodation and meals for the duration of the course.

For members of a FEBS Constituent Society there will be a limited number of Young Travel Fellowships for students within FEBS Countries and Trans Youth Travel Funds for non-FEBS Countries (USA/Canada, Asia, Africa, South America, which will be awarded only after acceptance onto the course.

If you are a PhD student or within the 5 years of your PhD and you are not already a member of the FEBS Constituent Society, you can join now and still be considered for one of the funded awards. Here is a link to the members list http://www.febs.org/index.php?id=74

Information for commercial applicants
Our course funders request that we charge a higher registration fee to commercial delegates, and may also set some limits on the number of commercial delegates at each course. Please see the section on costs below for details.

Academic Registration Fee = £695
Commercial/SME Registration Fee = £900.00
EBI Industry Programme Member Registration Fee = £340.00 (accommodation costs)

Registration

Click here to register


Trainers

 

Nicolas Le Novere (EBI)

Thomas Schlitt (KCL)
Javier De Las Rivas (USAL)
Anna Bauer-Mehren (IMIM)
Rune Linding (DTU)
Laurence Calzone (Institut Curie)
Julio Saez-Rodriguez (EBI)
Sven Sahle (University of Heidelberg)
Andrew Golightly (NCL)
Sarah Keating (EBI)
Lukas Endler (EBI)
Nick Juty (EBI)
Neil Swainston (University of Manchester)

 

 

 

 

 

 

 

 

 

 




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