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Hands-on training at EBI - EMBO Practical Course 'In silico systems biology: network reconstruction, analysis and network based modelling'
Course Summary
Title: EMBO Practical Course ' In silico systems biology: network reconstruction, analysis and network based modelling'
Date: 10-13 April 2010
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organisers: Vicky Schneider, Nicolas le Novere
Admin Support: Holly Foster & Alison Barker
Registration Deadline: 26 February 2010 - 12 noon (GMT)
Main Sponsor
Additional Sponsor
Scientific Committee
- Dr. Vicky Schneider (EMBL-EBI, Wellcome Trust Genome Campus, UK)
- Dr. Nicolas Le Novère (EMBL-EBI, Wellcome Trust Genome Campus, UK)
- Dr. Rune Linding (Institute of Cancer Research, Chester-Beatty Laboratories, London, UK)
- Dr. Javier de las Rivas (Grupo de Investigación Bioinformática y Genómica Funcional, Universidad de Salamanca, Spain)
- Dr. Sandra Orchard (EMBL-EBI, Wellcome Trust Genome Campus, UK)
Course Overview
Is it right for me?
Over the past few years, systems biology has become a fundamental field in molecular biology. Neither experimental nor computational biology alone will be sufficient to uncover a systems-level understanding of biology. This course addresses the need to train new generation of life scientists to become equally comfortable at the lab bench and at the computer screen. The ability to analyse large datasets from transcriptomics, proteomics, protein-interaction studies, pathway and networks analysis, to infer how molecules function within systems in ways that are not predictable from their individual properties, are therefore becoming required skills for experimental biologists.
- This course is aimed at advanced PhD students and post-doctoral researchers who are using or planning to use a systems-based approach to understanding a biological problem.
- This course will bring together lead researchers in the field of systems biology, experts in biological data resources, and you: a highly motivated group of early-stage experimental researchers.
- The course will combine lectures and led discussions to identify the key challenges, opportunities and bottlenecks, with practical sessions on network reconstruction, network analysis and network-based modelling.
What will I learn?
- This course specifically aims to enable early-stage experimental researcher to bridge the gap between data exploration in individual domains (genomics, transcriptomics, proteomics, etc.) and allow them to synthesise the data to gain a whole systems perspective.
- The hands-on sessions will allow the participants to gain practical experience of handling, analysing and integrating a wide range of different data types.
- The lecture-based sessions will provide the conceptual framework on which to base the students’ own analyses, and led discussions will allow participants to discuss key challenges to progress.
- The participants will present their own research through poster sessions.
- Each day will be concluded by an evening discussion led by the chair (invited speaker) of the day.
What will it cover?
- In “Silico” Systems Biology: Overview and State of the Art
- Reconstruction of networks: Lectures on reconstruction of networks from information coming from experimental datasets, such as interactomes and gene expression data, databases and scientific literature. Practical session based on Hands on tutorials, giving the attendees the opportunity to practice the concepts, resources and tools presented in the morning Hands on session on.
- Analysing Networks: A full day revolving around the analysis of networks to gain knowledge about complex biological processes and dysfunctions. The course will cover integration of networks and genomics data (e.g. SNPs), analysis of network structure, moving from network to pathways etc.
- Modelling Networks: Introduction to qualitative and quantitative modelling of genetic, metabolic and signalling networks.
- By holding this training course at the EMBL-EBI, we will provide a unique opportunity for all those participating to benefit not only from the scientific programme of the course, but also to interact with the curators and programmers behind some of Europe’s major biological databases and tools particularly relevant to this course (e.g. IntAct, Reactome, BioModels, OLS, PICR, PRIDE) through demo session schedules along the breaks.
Programme
The hands-on course programme, material and related information is available below.
Registration and Payment
Important Information
We can accommodate a maximum 30 participants. Participant’s will be selected by the scientific committee in consultation with EMBO. There is no fee for this course; registration, accommodation and meals are subsidised by the sponsors. All places on the course will be distributed according a selection process based on information collected upon registration covering the following areas:
- Relevance of the candidate’s research interests and current work to the course objectives.
- Scientific excellence of the previous research
- Letter of support from the candidate’s supervisor or another senior co-worker.
- Geographical distribution
- Recommendations from EMBO
Participants at early stages of their career will be accepted if they can demonstrate the relevance of their work to the objectives of the course. Participants who have used a systems-based approach to understanding a biological problem will be preferred. The last Hands on session will concentrate on the participants specific research cases, so participants are encouraged to bring data from their own research. However, in order to make these feasible, participants will be asked upon acceptance to prepare their data in specific format (and to a specified maximum size).
Applicants from industry will not be considered (similar courses for industry are provided by the EBI separately, without EMBO funding). Additionally, staff from the host institutions (EBI and Sanger Institute) will not be accepted and students from the UK will not be given any preference.
Please complete the registration/application form in order for you to be considered as an attendee for this course. Items marked * are mandatory. Incomplete registrations will not be processed.
Registration:
Is now closed
Invited Speakers and Trainers
- Dr. Nicolas Le Novère, EMBL-EBI
- Dr. Rune Linding, Institute of Cancer Research (ICR), UK
- Dr. Laura Inés Furlong, Research Unit on Biomedical Informatics (GRIB) IMIM/UPF, Spain
- Dr. Anna Bauer-Mehren, Research Unit on Biomedical Informatics (GRIB) IMIM/UPF, Spain
- Dr. Javier de las Rivas, Grupo de Investigación Bioinformática y Genómica Funcional
- Dr Laurence Calzone, Computational Systems Biology of Cancer, Institut Curie, France
- Julio Saez-Rodriguez, Ph. D., Department of Systems Biology, Harvard Medical School, U.S.A.
- Jasmin Fisher, Microsoft Research Cambridge, UK
- Dr. Sven Sahle, Bioinformatics and Computational Biochemistry, EML, Germany
- Dr. Wolfram Liebermeister, Humboldt-Universität zu Berlin, Institut für Biologie, Germany
- Dr.Thomas Schlitt, Kings College London, UK (t.b.c.)
- Dr. Gabriella Rustici, EMBL-EBI, UK
- Samuel Kerrien, EMBL-EBI, UK
- Margus Lukk, EMBL-EBI, UK
- Dr. Viji Chelliah, EMBL-EBI, UK
- Dr. Sarah Keating, EMBL-EBI, UK
- Dr. Nick Juty, EMBL-EBI, UK
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