In Silico Systems Biology: Dynamic Modelling of Biological Networks

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.

Target 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

Feedback from the 2017 course
“The course has been very useful to me. The instructors were easy to
reach and all the details were covered. The participants were attended
individually. I am surely looking forward to attend other suitable
courses offered by WGC. Thanks !”
“Learnt a lot here ! Very nice course. Highly recommended.”
“Thank you for bringing it up together. Thoroughly enjoyed the course and
my stay in Hinxton.”
“Thank you to all the instructors and organisers – this course has been
absolutely invaluable to me.”
“Thanks a lot for providing, organising and teaching in this course!”
“Overall the course was excellent”
“It is really nice course for all level of researchers.”
“Expert lectures and tutorials from expert presenters.”

The programme will include lecture and practical computer-based sessions
covering the following 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.

Learning 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

Scientific Organising Committee
Nicolas Le Novère Babraham Institute, UK
Julio Saez-Rodriguez RWTH-Aachen, Germany & EMBL-EBI, UK
Alexandra Holinski EMBL-EBI, UK

Instructors
Nicolas Le Novère Babraham Institute, UK
Julio Saez-Rodriguez RWTH-Aachen, Germany & EMBL-EBI, UK
Arnau Montagud Institut Curie, France
Javier De Las Rivas Cancer Research Institute of Salamanca, Spain
Emmanuel Goncalves EMBL-EBI, UK
Sarah Keating EMBL-EBI, UK
Karen Lipkow University of Cambridge, UK
Aleksej Zelezniak The Crick Institute, UK
Pablo Porras EMBL-EBI,  UK
Nicolas Rodriguez EMBL-EBI, UK
Sven Sahle University of Heidelberg, Germany
Joerg Stelling ETH Zurich, Switzerland
Rahuman Sheriff EMBL-EBI
Denes Turei EMBL-EBI
Sarala Wimalaratne EMBL-EBI
Aleksej Zelezniak The Crick Institute, UK

Prerequisites
The 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

Applications
Applications
can be submitted online. Places are limited and will be awarded on
merit. If you have any problems with the online application process,
please contact
us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical
sponsor (e.g. supervisor,
line manager, 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.

Deadlines
Deadline for Applications: Closed

Travel visas
Please contact the
event organiser if you require a letter to support a travel visa
application to the UK. Note that letters will only be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

Cost
The course is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential course and
the fee is £625, including all accommodation and meals.
This subsidised fee is available to all non-commercial applicants. Please
contact us
for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, limited bursaries are
available (up to a 50% reduction of the course fee) and are awarded on
merit. If you would like to apply for a
bursary, please complete the
bursary section of the online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Additional funding opportunities
Visit
our Funding webpage for additional funding opportunities currently
available.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.