Joint EMBL-EBI and Wellcome Trust In Silico Systems Biology 2012
Is it right for me?
This joint EMBL-EBI-Wellcome Trust Advanced Course will combine lectures and led discussions to identify the key challenges, opportunities and bottlenecks, with practical sessions on network analysis and network- based modelling. The course is aimed at advanced PhD students and post-doctoral researchers who are using or planning to use a systems-based approach to understanding biomedical problems.
Please note: Previous experience in computational and/or systems biology approaches is required to attend this course.
What will I learn and what will it cover?
- Overview of the field of Systems Biology: past, present and future
- Network Analysis
- Qualitative Modelling: modelling and simulation of interesting networks and pathways, as well as analysis of dynamical systems
- Quantitative Modelling, in particular discrete modelling and stochastic simulations
- Network and Pathway Enrichment
- Importance of semantics in systems biology: how to annotate models, and how to use those annotations to understand, merge and reason on models
- Programmatic approaches (e.g. libSBML)
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.
Scientific Committee
- Nicolas Le Novere (EMBL-EBI, UK)
- Julio Saez-Rodriguez (EMBL-EBI, UK)
- Vicky Schneider (EMBL-EBI, UK)
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - 23 April 2012 | ||
| 11:30 | Registration & Lunch | |
| 12:30 | Introduction | |
| 13:00 | Systems Biology Lecture | Nicolas Le Novere |
| 13:30 | Flash Presentations | Participants |
| 15:00 | Tea/Coffee | |
| 15:30 | Approaches to modelling GRNs - Lecture | Thomas Schlitt |
| 16:30 | Hands on session | |
| 17:00 | Poster Session inc. wine and cheese | Participants |
| 18:30 | Free time | |
| 19:30 | Welcome Drinks and Dinner | |
| Day 2 - 24 April 2012 | ||
| 08:45 | Introduction | |
| 09:00 | Build and explore protein - Protein interaction network - Lecture | Javier De Las Rivas |
| 10:00 | Hands on session | |
| 11:00 | Tea/Coffee | |
| 11:30 | Integration of genomic data with biological networks using Cytoscape | Anna Bauer-Mehren |
| 13:00 | Lunch | |
| 14:00 | Standard formats - Lecture | Nicolas Le Novere |
| 14:30 | Working with pathways - Lecture | Martijn van Iersel |
| 15:00 | Hands on session | |
| 15:30 | Tea/Coffee | |
| 16;00 | BiNoM - Lecture | Laurence Calzone |
| 16:30 | Hands on session | |
| 17:30 | Q & A/post-its based session | |
| 18:30 | Free time | |
| 19:15 | Dinner | |
| Day 3 - 25 April 2012 | ||
| 08:45 | Introduction | |
| 09:00 | GinSIM - Lecture | Laurence Calzone |
| 09:30 | Hands on session | |
| 10:30 | Tea/Coffee | |
| 11:00 | CNO - Lecture | Julio Saez-Rodriguez |
| 11:30 | Hands on session | |
| 12:30 | Lunch | |
| 13:30 | Introduction to Kinetics - Lecture | Nicolas Le Novere |
| 14:00 | Introduction to COPASI - Lecture | Sven Sahle |
| 15:00 | Tea/Coffee | |
| 15:30 | Building and Simulating Models - Hands on session | Sven Sahle & Nicolas Le Novere Group |
| 17:00 | Free time | |
| 18:00 | Dinner | |
| 19:00 | Free time in Cambridge | |
| Day 4 - 26 April 2012 | ||
| 08:45 | Introduction | |
| 09:00 | Stochastic simulations - Lecture | Joerg Stelling |
| 09:45 | Robustness and Sensitivity - Lecture | Joerg Stelling |
| 11:00 | Tea/Coffee | |
| 11:30 | Constraint based models | |
| 12:30 | Hands on session | |
| 13:00 | Lunch | |
| 14:00 | Parameter estimation - Lecture & Hands on | Sven Sahle |
| 15:30 | Tea/Coffee | |
| 16:00 | Visit sequencing facilities | |
| 16:30 | Visit to data center | |
| 17:00 | Poster Session inc. wine and cheese | Participants |
| 18:30 | Free time | |
| 19:30 | Dinner | |
| Day 5 - 27 April 2012 | ||
| 08:45 | Introduction | |
| 09:00 | SBML - Lecture | Sarah Keating |
| 09:30 | LibSBML & JSBML Hands on | Sarah Keating |
| 11:00 | Tea/Coffee | |
| 11:30 | BioModels Db - Lecture | Vijayalakshmi Chelliah |
| 12:00 | Controlled annotations - Lecture | Nick Juty |
| 12:30 | Lunch | |
| 13:30 | One to One | |
| 15:00 | Tea/Coffee | |
| 15:30 | One to One | |
| 17:00 | Close of Workshop | |
The course tuition fees are subsidised by the Wellcome Trust for scientists based in non-commercial institutions anywhere in the world. This is a residential course, without exception, and there is a fee of £500 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.
For further details on the course and to register please follow this link.