GTPB Bioinformatics Training Course Announcement/reminder

Dear all,

The Applications for the PHSMCP15 course, "Promoter hunting and
systems modelling of cellular pathways", are now OPEN.


IMPORTANT DATES for this Course
Deadline for applications: April 2nd 2015
Latest notification of acceptance: April 3rd 2015
Course date: April 22nd - April 24th 2015

With Alexander Kel
Details are available here:
http://gtpb.igc.gulbenkian.pt/bicourses/PHSMCP15/

In short:
Learn how to find promoters in NGS data an how to use genes and
promoters to produce inferences at the pathway and system levels.



Full description:

Overview
This course starts by reviewing basic principles of gene regulation
and how information is encoded in the huge part of genome - it's so
called "non-coding" part. Bioinformatics plays a huge role in
exploring how gene regulation works. We will introduce mathematical
modelling of cellular pathways and address the interplay between
feedback and feed-forward loops of regulation. We will see how a range
of modelling techniques can help us to:

- find master regulators
- understand disease mechanisms
- build models for use in precision medicine
- design novel systems for biotechnology

Starting from techniques for the computational prediction of promoters
and distant enhancers, we will deal with the analysis of the structure
of regulatory regions by identifying binding sites for transcription
factors. A complete annotation of a newly sequenced genome has to
address the identification of these regions in addition to the
classical task of finding genes in terms of coding regions. Regulatory
regions determine where, under which conditions and when genes become
active. Thus, they are a fundamental part of the definition of the
function of a gene. We will have a chance to introduce and acquire
*hands-on* practice in next generation sequencing (NGS) techniques for
genome-wide epigenetic analyses such as ChIP-seq.

Then we will approach the analysis and modelling of biological systems
from several practical angles. Systems biology and modelling are
approched here from the interaction and network-based perspectives. We
will introduce several pathway databases, such as Reactome, KEGG,
TRANSPATH, TRANSFAC, ConsensusPathDB and use these information
resources to perform pathway analysis. Next, we will use modelling of
biological systems to look at different mathematical modelling
strategies, such as Boolean networks and ordinary differential
equation systems (ODEs). We will describe computational tools, like
Cytoscape and CellDesigner, for the set-up and development of model
prototypes and show further tools, such as Copasi, BioUML and PyBioS
that can be used for parameter-fitting and sensitivity analysis.

We will follow-on by looking at methods for reconstructing gene
regulatory networks from gene expression data. The application of such
methods can reveal key nodes in networks as potential biomarkers or
drug targets. Dynamic systems modelling will be used to check the
consistency of target and biomarker predictions. We will show real
examples of application of these methods for identification of disease
related biomarkers, drug discovery and personalized medicine.

Special attention will be given to the application of the above
mentioned methods in designing novel biological systems, in the
growing field of Synthetic Biology.

Methods
Participants will learn about several techniques of finding promoters
and enhancers and the principles on which these methods are based on.
In the hands-on exercises, several analytical tools will be introduced
and the results critically evaluated to assess their reliability. The
course sessions will consist of lectures that lay out the conceptual
framework as needed, and hands-on exercises, which will provide the
practical insight on the use of the methods, gradually, in order to
produce skills that can be used with a relatively high degree of
independence. Participants will learn how to set-up some of the
programs, and use publicly available servers for more complex
analytical jobs, in an informed fashion, so that they fully understand
the output generated and how their quality can be assessed.
Participants will also learn the novel principles of organization of
gene regulatory regions, which will help them to interpret their
results of genomic and transcriptomic studies.

The course will provide sufficient skills for the participants to
address problems using open source software and freely accessible data
resources. It will also be a chance to use commercially licensed
resources such as TRANSFAC or the geneXplain integrated analytic
platform for specific purposes.

Target Audience
The course was designed for researchers in biology, bioinformatics,
biochemistry and medicine that have an interest in gene regulation and
related topics.

Course Pre-requisites
Basic biochemistry. Elementary computing skills. Background knowledge
in bioinformatics is not absolutely necessary, but may be
instrumentally useful.



Best wishes
Pedro Fernandes
GTPB Coordinator



--
Pedro Fernandes
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt





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