Joint EMBL-EBI-Wellcome Trust Course: In Silico Systems Biology
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. This joint EMBL-EBI-Wellcome Trust course will combine lectures on modelling approaches, led discussions to identify the key challenges, opportunities and bottlenecks, and practical sessions on network analysis and network-based modelling.
Please note: This course will not cover high-throughput ‘omics’ data analysis methods, e.g. statistical models, GWAS analysis, etc. We will touch on protein networks and data integration, but the focus is more on building predictive and mechanistic models. If you are interested in protein networks, please consider the Interaction and Pathways course instead.
Topics
• Overview of the field of Systems Biology: past, present and future
• Analysis of Gene Regulatory Networks
• Qualitative Modelling: modelling and simulation of interesting networks and pathways, as well as analysis of dynamical systems
• Quantitative Modelling: Chemical kinetics, constraint-based modelling and stochastic simulations
• Network and Pathway Enrichment
• Model sharing: how to encode and annotate models
• Programmatic approaches (e.g. libSBML)
Target audience
The course is aimed at advanced PhD students, post-doctoral and more senior researchers who are using or planning to use systems-based approaches to understand biomedical problems.
Please note: Previous experience in computational and/or systems biology approaches is required to attend this course.
After this course you should be able to…
- Know how the field of systems biology has developed
- Understand some of the challenges that we face in the field of systems biology today
- Develop your presentation skills
- Understand a range of approaches for modeling gene regulatory networks
- Learn approaches to build and explore protein-protein interactions networks
- Analyze and annotate interaction networks using Cytoscape and BiNGO
- Learn the standard formats used to express models in the life sciences
- Explore pathways using Cytoscape
- Analyze networks using R and GinSiM
- Learn general principles for chemical kinetic modeling
- Use simulation based approaches to model complex pathways using COPASI
- Understand some general principles of stochastic simulations
- Understand the terms ‘robustness’ and ‘sensitivity’ in the context of parameter estimation
- Understand some general principles of constraint based models and their implementation
- Learn the general principles, and gain hand-on experience of parameter estimation
- Learn about the structure and syntax of systems biology markup language (SBML) and relevant resources available
- Implement systems biology markup language with Python
- Access and explore the BioModels database
- Develop an awareness of the minimum controlled annotations for systems biology models (MIRIAM) guidelines
- Develop an awareness of a variety of other types of model including spatial models
Participants will be encouraged to bring their own data for one-to-one sessions. However, specific size limits and formats will be specified in order to ensure data is usable in the available time. Participants will also be requested to provide a poster for the poster session.
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - 25 June 2013 | ||
| 11:30 | Registration & Lunch | |
| 12:30 | Welcome and introduction to the EBI | Laura Emery |
| 13:00 | Systems Biology (lecture) | Nicolas Le Novère |
| 13:30 | Flash Presentations Participants | |
| 15:00 | Coffee break | |
| 15:30 | Approaches to modelling GRNs (lecture) | Thomas Schlitt |
| 16:30 | Approaches to modelling GRNs (hands-on) | Thomas Schlitt |
| 17:00 | Poster Session with wine and cheese | Participants |
| 18:30 | Free time | |
| 19:00 | Welcome Drinks and Dinner | |
| 20:00 | Close | |
| Day 2 - 26 June 2013 | ||
| 08:45 | Introduction | |
| 09:00 | Build and explore protein-protein interaction network (lecture) | Javier De Las Rivas |
| 10:00 | Build and explore protein-protein interaction network (hands-on) | Javier De Las Rivas |
| 11:00 | Coffee break | |
| 11:30 | Network Functional Annotation and Analysis using Cytoscape (hands-on) | Pablo Porras Millán |
| 13:00 | Lunch | |
| 14:00 | From data analysis to modelling with Cytoscape (lecture) | Julio Saez-Rodriguez |
| 14:30 | CyRface hands-on) | Julio Saez-Rodriguez |
| 15:30 | Coffee break | |
| 16:00 | CNO to GinSiM (lecture) | Julio Saez-Rodriguez |
| 16:30 | CNO to GinSiM (hands-on) | Julio Saez-Rodriguez |
| 17:30 | Interactive Q&A Session | Julio Saez-Rodriguez & Nicolas Le Novère |
| 18:30 | Free time | |
| 19:00 | Dinner | |
| 20:00 | Close | |
| Day 3 - 27 June 2013 | ||
| 08:45 | Introduction | |
| 09:00 | Introduction to Kinetics (lecture) | Nicolas Le Novère |
| 09:30 | Introduction to COPASI (lecture | Sven Sahle |
| 10:30 | Coffee break | |
| 11:00 | hands-on session | |
| 12:30 | Lunch | |
| 13:30 | Spatial Models Smolydy (lecture) | |
| 15:00 | Coffee break | |
| 15:30 | Smolydn (hands-on) | |
| 17.00 | Free time | |
| 19:00 | Dinner | |
| 20:00 | Close | |
| Day 4 - 28 June 2013 | ||
| 08:45 | Introduction | |
| 09:00 | Stochastic Simulations (lecture) | Joerg Stelling |
| 09:45 | Robustness and Sensitivity (lecture) | Joerg Stelling |
| 11:00 | Coffee break | |
| 11:30 | Constraint Based Models (lecture) | Kiran Patil |
| 12:30 | Constraint Based Models (hands-on) | Kiran Patil |
| 13:00 | Lunch | |
| 14:00 | Parameter Estimation (lecture) | Sven Sahle |
| 14:30 | Parameter Estimation (hands-on) | Sven Sahle |
| 15:30 | Coffee break | |
| 16:00 | Visit sequencing facilities | Nicolas Le Novère / Julio Saez-Rodriguez |
| 16:30 | Visit to data centre | Nicolas Le Novère / Julio Saez-Rodriguez |
| 17:00 | Poster Session with cheese and wine | Participants |
| 18:30 | Free time | |
| 19:00 | Onsite Course Dinner | |
| 21:00 | Close | |
| Day 5 - 29 June 2013 | ||
| 08:45 | Introduction | |
| 09:00 | SMBL (lecture) | Sarah Keating |
| 09:30 | LibSBML/JSBML (hands-on) | Sarah Keating/Nicolas Rodriguez |
| 10:30 | BioModels Database (lecture) | Viji Chelliah |
| 11:00 | Coffee break | |
| 11:30 | Annotations Beyond chemical Kinetics (lecture) | |
| 12:30 | Lunch | |
| 13:30 | 1 to 1 session | |
| 15:00 | Coffee break | |
| 15:30 | Roundtable Q&A | |
| 17:00 | End of course | |
For further details on the course and to register please follow this link.
Prerequisites
The course is aimed at advanced PhD students and post-doctoral researchers who are using or planning to use a systems-based approach to understand biomedical problems.
Please note: Previous experience in computational and/or systems biology approaches is required to attend this course.
Cost
The course tuition fees are subsidised by the Wellcome Trust for scientists based anywhere in the world. This is a residential course, without exception, and there is a fee of £550 towards accommodation and food for the duration of the course.
Bursaries
Limited bursaries are available for non-commercial applicants (50 per cent of fee) and are subject to open competition.
Bursary application information, plus terms and conditions
Applications
Application is now closed.
Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your 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.
F +44 (0) 1223 495130
E advancedcourses@hinxton.wellcome.ac.uk
Deadlines
Application deadline: 8 March 2013