[BBC] [Gtpb] GTPB Bioinformatics Training Course Announcement/Reminder

[Pedro Fernandes]

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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