In Silico Systems Biology

Date:

 Sunday 3 Friday 8 July 2016

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application deadline: 

Friday March 11 2016

Participation: 

Open application with selection

Contact: 

Yvonne Thornton

Registration fee: 

£595

Registration closed

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Overview

Systems biology is now an established and fundamental field in life sciences. It has facilitated the move from the identification of molecular ‘parts lists’ for living organisms towards integrating information from different ‘omics’-based approaches with our knowledge on the underlying biochemical mechanisms, to generate and test new hypotheses about how biological systems work.

Run jointly with Wellcome Genome Campus Advanced Courses and Scientific Conferences, this course will provide participants with an overview of modelling approaches and an introduction to network analysis. The course will combine lectures, practical sessions and group activities, and there will be opportunity for discussion of current trends in the field.

Audience

This workshop is aimed at PhD students and researchers with a minimum of one year experience in the field of systems biology modelling, and who are using systems-based modelling approaches to understand biological and biomedical problems.

Syllabus, tools and resources

During this course you will learn about:

  • Qualitative Modelling: modelling and simulation of networks using logic approaches, and analysis of their dynamical properties
  • Quantitiative Modelling: Chemical kinetics, constraint-based modelling and stochastic simulations, including spatial respresentations
  • Network analysis and Pathway Enrichment
  • Model sharing: how to encode and annotate models

Outcomes

After this workshop, you should be able to:

  • Identify strengths and weaknesses in a variety of systems biology modelling approaches
  • Use a range of bioinformatics and modelling software to develop predictive and mechanistic models
  • Access, query and retrieve models from public repositories for systems biology
  • Use data standards in your work
  • Identify an appropriate modelling approach for a given biological question and dataset

Programme

Time Topic Trainer
Day 1 - Sunday 3 July 2016
14:00 - 14:30  Registration 
14:30 - 15:00 Welcome and introduction Laura Emery
15:00 - 16:00

Systems Biology: overview of modelling approaches approaches 

Nicolas Le Novere 
16:00 - 17:30 Flash presentations All Participants 
17:30 - 19:00 Poster Session  All Participants
19:00 - 20:00 Dinner Hinxton Hall Restaurant
Day 2 - Monday 4 July 2016
08:45 - 09:00 Introduction 
09:00 - 10:00 Network inference Javier De Las Rivas 
10:00 - 10:30 Hands on session Javier De Las Rivas  
10:30 - 11:00  Tea/Coffee Break 
11:00 - 12:00 Build and explore protein-protein interaction network Javier De Las Rivas  
12:00 - 13:00 Hands-on session Javier De Las Rivas 
13:00 -14:00 Lunch 
14:00 - 15:00 Cytoscape Pablo Porras 
15:00 - 15:30 Hands on session Pablo Porras 
15:30 - 16:00 Tea/Coffee break 
16:00 - 17:00 BiNoM Laurence Calzone
17:00 - 17:30 Hands on session Laurence Calzone
17:30 - 19:00 Expectation  
19:00 - 20:00 Dinner Hinxton Hall Restaurant
Day 3 - Tuesday 5 July 2016
08:45 - 09:00  Introduction  
09:00 - 09:30  Standards in systems biology Nicolas Le Novere 
09:30 - 10:30  Introduction to Logic models 

Julio Saez-Rodriguez

Laurence Calzone

10:30 - 11:00 Tea/Coffee Break 
11:00 - 12:00 From data analysis to logic modeling Julio Saez-Rodriguez 
12:00 - 13:00 CellNOpt/CytoCopter Julio Saez-Rodriguez 
13:00 - 14:00 Lunch  
14:00 - 14:30 Hands on session

Thomas Cokelaer

Emanuel Goncalves

14:30 - 15:30 GinSim Laurence Calzone 
15:30 - 16:00 Tea/Coffee Break
16:00 - 17:30 Hands on session  
17:30 - 19:00 Introduce group project All participants
19:00 - 20:00 Dinner  Hinxton Hall Restaurant
Day 4 - Wednesday 6 July 2016
08:45 - 09:00 Introduction  
09:00 - 09:30 Introduction to Kinetics  Nicolas Le Novere 
09:30 - 10:30 Introduction to COPASI Sven Sahle 
10:30 - 11:00 Tea/Coffee break  
11:00 - 12:30 Hands on session  Vijayalakshmi Chelliah
12:30 - 13:30 Lunch 
13:30 - 14:30 Parameter estimation Sven Sahle 
14:30 - 15:30 Hands on session Sven Sahle
15:30 - 16:00 Tea/Cofffee Break
16:00 - 17:00 Stochastic simulations Joerg Stelling
17:00 - 18:00 Robustness and Sensitivity Joerg Stelling
18:00 -19:00 1 to 1 quantitative All Participants
19:00 - 19:30 Pre dinner drinks Hall Foyer
19:30 - 22:00 Dinner Hinxton Hall Restaurant
Day 5 - Thursday 7 July 2016
08:45 - 09:00  Introductions 
09:00 - 10:30 Spatial Models Smolydn  Karen Lipkow  
10:30 - 11:00 Tea/Coffee brek  
11:00 - 13:00

Smolydn Hands on session 

Karen Lipkow 
13:00 - 14:00 Lunch 
14:00 - 15:00 Tours All Participants 
15:00 - 16:00 Constraint based models  Kiran Patil 
16:00 - 16:30 Tea/Coffee break 
16:30 - 17:00 Hands on session  Kiran Patil
17:00 - 19:00 Group Project All Participants
19:00 - 20:00 Dinner Hixton Hall restaurant
Day 6 - Friday 8 July 2016
08:30 - 08:45 Check Out 
08:45 - 09:00 Introductions 
09:00 - 09:30 SBML

Sarah Keating

09:30 - 10:30 LibSBML/JSBML

Sarah Keating

Nicolas Rodriguez

10:30 - 11:00 BioModels database Vijayalakshmi Chelliah 
11:00 - 11:30 Tea/Coffee break
11:30 - 12:30 Annotations Beyond Chemical Kinetics Camille Laibe
12:30 - 13:30 Interactive Q & A

Julio Saez-Rodriguez

Nicolas Le Novere

13:30 - 14:30 Lunch
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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In association with

How to apply

Applications for this course are managed by Wellcome Genome Campus Advanced Courses and Scientific Conferences. Clicking on the "apply now" button will take you to their webpage for this event.

Cost
The course tuition fees are subsidised by the Wellcome Trust for scientists based anywhere in the world. This is a residential workshop, without exception, and there is a fee of £595 towards accommodation and food for the duration of the workshop.

Bursaries
Limited bursaries are available for non-commercial applicants (up to 50 per cent of fee) and are subject to open competition.

Please note
Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.

Application deadline

11 March 2016

Registration closed

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Organisers

Annalisa Mupo

Julio Saez-Rodriguez

Nicolas Le Novère

Karin Sasaki

Trainers

Nicolas Le Novère - European Bioinformatics Institute

Julio Saez-Rodriguez - EMBL-EBI, UK

Kiran Raosaheb Patil - EMBL, Heidelberg, Germany

Karin Sasaki - European Molecular Biology Laboratory

Pablo Porras Millan - EMBL-EBI, UK

Javier De Las Rivas - Cancer Research Center (CiC-IBMCC, CSIC/USAL) Salamanca

Sven Sahle - University of Heidelberg, Germany

Jörg Stelling - ETH Zurich, Switzerland

Sarah Keating - EMBL-EBI, UK

Laurence Calzone - Institut Curie, France

Vijayalakshmi Chelliah - EMBL-EBI, UK

Emanuel Gonçalves - EMBL-EBI, UK

Karen Lipkow - Babraham Institute, UK

Nicolas Rodriguez - EMBL-EBI, UK

Bhupinder Virk - Babraham Institute

Materials & attachments