The Systems Biology Modelling Cycle (supported by BioPreDyn)
This course will provide a detailed overview of state-of-the-art modelling methods and tools in computational systems biology, focusing especially on dynamic (mechanistic) models. By combining lectures on modelling approaches, computer-based practicals, and organized discussions, we will identify the key challenges, opportunities, and bottlenecks in the field.
The workshop is aimed at advanced PhD students, post-doctoral, and more senior researchers who are using or planning to use systems-based dynamic modelling approaches to understand biological problems.
Syllabus, Tools and ResourcesDuring this course you will learn about:
- Databases and web services for dynamic modelling: BioModels, Bioservices
- Visualisation tools: GPy
- Tools for dynamic modelling: CellNOpt, COPASI, Meigo, AMIGO
After this course you should be able to:
- Browse and access public databases for dynamic modeling
- Use tools to visualize and analyze biological time-series data
- Comprehend the key concepts of network inference methods, dynamic modelling (including parameter estimation, optimal design of experiments, and uncertainty quantification and model selection), reverse engineering of gene regulatory networks, and computational metabolic engineering
- Discuss some applications of kinetic models to biotechnological processes involving microorganisms (E. coli, S. cerevisiae) and CHO cells
- Apply the systems biology modelling cycle and related computational workflows to biological problems
|Day 1 - Monday 12 May 2014|
|12:00||Registration and Lunch|
|13:00||An introduction to the EBI||L. Emery|
|13:30||Standards and databases for computational modelling of biological processes (TBD)||N. Le Novere|
|14:30||Logic models of signalling networks: from Boolean to differential equations||J. Saez-Rodriguez|
|16:00||Practical session: Logic modelling with CellNOpt and Cyrface.
Programmatic access to relevant web services with Bioservices
|J. Saez-Rodriguez, E. Gonçalves, T. Cokelaer|
|18:00||Networking activity||L. Emery|
|19:30||Dinner at Hinxton Hall|
|Day 2 -Tuesday 13 May 2014|
|09:00||Visualization through dimensionality reduction||N. Lawrence|
|10:00||GPy: A Gaussian process framework for dynamical biological models||N. Lawrence|
|11:30||Fourier transform analysis of dynamical differential equations for biological Models||M. Niu|
|13:30||Inference methods for biological networks||D. di Bernardo|
|14:30||Reverse engineering and modelling of metabolic networks: the case of Mendelian disorders||R. Pagliarini|
|16:00||Identifiability and parameter estimation in dynamic models||E. Balsa-Canto|
|17:00||Practical parameter estimation with COPASI||P. Mendes|
|18:00||Parameter estimation in large-scale kinetic models of microorganisms||A.F. Villaverde|
|19;00||Dinner at Hinxton Hall|
|Day 3 - Wednesday 14 May 2014|
|09:00||Optimal design of dynamic experiments||J.R. Banga|
|10:30||Practical session on parameter estimation and optimal experimental design||A.F. Villaverde|
|11:30||Uncertainty quantification analysis of biochemical models and optimal experimental design||J.G. Blom|
|13:30||Model selection and optimal experimental design||M. Navarro|
|14:30||Practical session: uncertainty quantification, model selection, and optimal experimental design||M. Navarro|
|16:00||Reverse-engineering pattern-forming gene networks in animals||Y. Jaeger, A. Crombach, J. Kaandorp (TBD)|
|17:00||Practical session: work on your own data|
|18:30||Dinner at Hinxton Hall|
|Day 4 - Thursday 15 May 2014|
|09:00||Simulation work flows in model life cycle||B. Moreau|
|10:30||BioPreDyn software practical||B. Moreau|
|13:00||Kinetic modelling and simulation of CHO cells||S. Bongard|
|14:30||Large-scale kinetic models of E. coli and yeast||P. Mendes|
|15:30||Metabolic engineering case studies||M. Schwab, J. Dyekjær (TBD)|
|16:30||Course feedback and wrap up||L. Emery|
Application will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application registration closes 14 March 2014(12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 24 March 2014 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Please note that the registration fee of £600.00 includes:
- All meals listed in the agenda (breakfast, lunch, dinner and refreshment breaks)
- Course materials on a USB
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
- Onsite single ensuite room accommodation at the Wellcome Trust Conference Centre (Check in 12 May 2014- check out 15 May 2014)
To apply for this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.
Please note successful applicants will be asked to bring a poster summarising their project/current research and asked to present during the course. Please can all posters be A2 portrait size (420mm x 594mm ~ 16.5” x 23.4”).
AllBio sponsored travel bursaries are available for applicants currently working in EU based institutions on research that is non-human / non-medical in nature. Please fill the relevant boxes within the application if you wish to be considered for a travel bursary.