In Silico Systems Biology

Date:

 Sunday 3 Friday 8 June 2018

Venue: 

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

Application opens: 

Monday November 27 2017

Application deadline: 

Tuesday February 27 2018

Participation: 

Open application with selection

Registration fee: 

£625

Overview

The use of dynamical mathematical models to understand the function of biological systems is at the core of systems biology. Such models have facilitated the move from mere identification of molecular ‘parts lists’ for living organisms towards a more integrated view, based on the integration of ‘omics’-based data with our knowledge on the underlying biochemical mechanisms. This in turn allows us to generate and test new hypotheses about how biological systems work.

Run jointly with EMBL-EBI, this course will provide participants with an introduction to network analysis and in-depth training in the main modelling approaches used in systems biology. The course will combine lectures, hands-on computational practical sessions and group activities, and there will be opportunity for discussion of current trends in the field.

Audience

This course is aimed at PhD students and researchers who already have some experience of using systems-based modelling approaches to understand biological and biomedical problems. This is an advanced course and participants are expected to have:

  • A familiarity with the use of bioinformatics tools and data resources
  • A working knowledge of using Linux commands and experience of using a programming language (e.g. Python)
  • An undergraduate level knowledge of molecular and cellular biology

Syllabus, tools and resources

  • Network Analysis and Pathway Enrichment
  • Qualitative Modelling: reconstruction, modelling and simulation of systems using logic approaches, and analysis of their dynamical properties
  • Quantitative Modelling: chemical kinetics, constraint-based modelling and stochastic simulations, including spatial representations
  • Model Sharing: how to encode, annotate and distribute models

Several tools will be used during the course, including Cytoscape, OmniPath , GINsim, CellNOpt, COPASI, COBRApy, Smoldyn and BioModels.

Outcomes

After the course, participants 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
  • Identify an appropriate modelling approach for a given biological question and dataset

Programme

Time Topic Trainer
Day 1 - Sunday 3th June
15:00 - 15:30 Registration (CC Foyer)  
15:30 -16:00 An introduction to the EBI Alexandra Holinski
16:00 - 16:30 Expectation activity  
16:30 - 18:30 Systems Biology - overview of modelling approaches Nicolas Le Novère
19:00 Dinner at tbc
Day 2 - Monday 4th June
08:45 - 09:00 Introduction  
09:00 - 10:30 Network inference  with hands-on session Javier De Las Rivas
10:30 - 11:00 Tea/coffee break 
11:00 - 13:00 Build and explore protein-protein interaction networks with practical Javier De Las Rivas
13:00 - 14:00 Lunch 
14:00 - 15:30 Cytoscape with practical Pablo Porras
15:30 - 16:00 Tea/coffee break 
16:00 - 18:00 OmniPath with hands-on session Denes Turei
18:00 - 19:30 Poster session with cheese and wine
19:30 - 20:30 Dinner at tbc  
Day 3 - Tuesday 5th June 
08:45 - 09:00 Introduction  
09:00 - 09:30 Standards in systems biology Nicolas Le Novère
09:30 - 10:30 Introduction to logic models Julio Saez-Rodriguez
10:30 - 11:00 Tea/coffee break 
11:00 - 12:30 From data analysis to logic modelling Julio Saez-Rodriguez
12:30 - 13:30 Lunch 
13:30 - 15:30 CellNOpt/CytoCopter with hands-on session Julio Saez-Rodriguez, Emanuel Goncalves
15:30 - 16:00 Tea/coffee break 
16:00 - 17:00 Logic modelling tools: GINsim & MaBoSS Laurence Calzone
17:00 - 18:30 Logic modelling and systems pharmacology  tbc
19:00 - 20:00 Dinner at tbc
Day 4 - Wednesday 6th June 
08:45 - 09:00 Introduction  
09:00 - 09:30 Introduction to Kinetics Nicolas Le Novère
09:30 - 10:30 Introduction to COPASI Sven Sahle
10:30 - 11:00 Tea/Coffee break  
11:00 - 12:30 COPASI hands-on session tbc
12:30 - 13:30 Lunch   
13:30 - 15:30 Parameter estimation with hands-on session Sven Sahle
15:30 - 16:00 Tea/coffee break  
16:00 - 18:30 Stochastic simulation with hands-on session Joerg Stelling, Nicolas Le Novère
19:00 - 20:00 Dinner at tbc  
Day 5 - Thursday 7th June
08:45 - 09:00 Introduction  
09:00 - 10:30 Spacial Modles Smolydn  
10:30 - 11:00 Tea/coffee break  
11:00 - 13:00 Smolydn hands-on session
13:00 - 14:00 Lunch  
14:00 - 15:00 Sequencing centre tours
15:00 - 16:00 Constraint based models Aleksej Zelezniak
16:00 - 16:30 Tea/coffee break 
16:30 - 18:30 Hands-on session  Aleksej Zelezniak
19:00 - 20:00 Dinner at tbc  
Day 6 - Friday 8th June
08:30 Check out  
08:45 - 09:00 Introduction  
09:00 - 09:30 SBML Sarah Keating
09:30 - 10:30 LibSBML/JSBML Sarah Keating, Nicolas Rodriguez
10:30 - 11:00 BioModels database Rahuman Sheriff
11:00 - 11:30 Tea/coffee break
11:30 - 12:30 Annotations Beyond Chemical Kinetics Sarala Wimalaratne
12:30 - 13:30 Interactive Q&A  Nicolas Le Novère, Julio Saez-Rodriguez
13:25 Course wrap up and feedback Alexandra Holinski
13:30 - 14:30 Lunch