ESTOOLS - Advances with human embryonic stem cells - New Project Partner call for ESTOOLS consortium

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New Project Partner call for ESTOOLS consortium

THIS CALL CLOSED 12 MARCH 2008

Background

During initial contract negotiation with the Commission, ESTOOLS reserved a portion of the project budget for tasks that may be carried out by a new contractor joining the consortium at a later date to be selected by means of a competitive call. ESTOOLS has now received and is evaluating several proposals. No new proposals can be accepted.

THE CALL 

ESTOOLS aims to advance the fundamental knowledge that will underpin biomedical application of human embryonic stem cells by developing tools and procedures to facilitate (1) unlimited expansion of hESCs (2) creation of techniques for the efficient, regulatable expression and ablation of hESC gene function (3) directed differentiation of hESCs into mature neural cell types exhibiting full phenotypic fidelity.
ESTOOLS wishes to enhance data storage and data analysis in the consortium with links to external datasets. A substantial amount of gene expression data will be generated and collated, primarily from Illumina gene chips but also from other microarray platforms and sequencing based approaches.

TASKS REQUESTED

The role in the project of the new partner, which may be an SME, will be to undertake the following tasks:

1. Design and implement an accessible database for ESTOOLS that accommodates gene expression data from various sources.  This database should also allow inclusion of transcription factor binding data from various sources, such as ChIP on Chip analyses, starting in 2008.
2. Undertake basic statistical analysis of different forms of gene expression or array data including normalisation, identification of differential genes, gene ontologies and clustering.
3. Implement a system for the integration of a variety of different data formats/types enabling depth 'mining' (or network production) with a capacity to integrate data from established gene expression repositories, Chip-chip data, cis-regulatory information and protein interaction maps.
4. Train staff in ESTOOLS laboratories in the above techniques through an effective combination of protocol dissemination via the consortium website and video/face-to-face workshops.
5. Maintain oversight of the suitability of bioinformatics and statistical methods deployed across the consortium.

Based on the above tasks ESTOOLS will negotiate with the successful proposer the detailed milestones and deliverables that will form part of the revised contract with the Commission.

The following expertise and experience would qualify the proposer as a potential new participant in the ESTOOLS consortium:

• Designing and implementing of databases, statistical analyses and data integration approaches using human genetic information.
• Management of database hosting (either in-house or by contract).
• Designing and promulgating (a) bioinformatic investigation protocols (b) training programmes.
• Holding lead responsibility for bioinformatics work within a European multi-country research consortium.

Funding available is up to Euro 300,000.

Information about the ESTOOLS project partners is available on this page. 

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