BIOINFORMATICS SCIENTIST: H2020-­INFRADEV-­4 PROJECT CORBEL | EMBRC

BIOINFORMATICS SCIENTIST: H2020-­INFRADEV-­4 PROJECT CORBEL

2015.09.22

BIOINFORMATICS SCIENTIST: H2020-­INFRADEV-­4 PROJECT CORBEL

Develop pipelines to establish harmonised databases integrating genomic, transcriptomic and morphological data for selected marine metazoan developmental model species

Context:

The H2020-­‐INFRADEV-­‐4 project CORBEL (Coordinated Research Infrastructures Building Enduring Life-­‐ science services), just started in September 2015, will establish a collaborative framework of shared services between the ESFRI Biological and Medical Research Infrastructures. CORBEL will build on existing efforts to develop the tools, services and data management required by cutting-­‐edge European research projects.

Within WP4 of CORBEL, the EMBRC (European Marine Biological Resource Centre) is coordinating the “use case” Marine Metazoan Developmental Models for Biomedical research – from predictive integrated databases to functional testing (Use Case 4). This Use Case 4 will develop pipelines to establish harmonised databases integrating genomic, transcriptomic and morphological data for selected marine metazoan developmental model species. This will be achieved by researchers at five EMBRC marine station sites in Scotland, Italy and France, as well as close interactions with other European Research Infrastructures, notably ELIXIR and Euro-­‐BioImaging.

Use Case 4 will be coordinated at the Villefranche sur mer Developmental Biology Laboratory (France), and we are seeking a bioinformatician to lead the data integration.

The LDBV is a CNRS/ Université Pierre & Marie Curie research laboratory with 7 scientific teams exploiting marine organisms for research in cell and developmental biology, genomics and evolution.

 

Job outline:

The successful candidate will integrate sequence (genome and transcriptome) and imaging data from the major marine metazoan model organisms of the EMBRC, making them accessible the wider research community through the development of model organism databases such as ANiSEED. The initial database suite will cover ascidians (Phallusia, Ciona) through collaboration with the ANiSEED project, as well as amphioxus (Branchiostoma), sea urchin (Paracentrotus) and jellyfish (Clytia). The role will involve extensive liaison to establish interchange standards and protocols with project partners within EMBRC and the wider CORBEL programme.

 

Main activities :

-­‐      Lead the development of model organism databases for CORBEL WP4, Use Case 4

-­‐      Interact with the contributing research groups to define the essential features and structure of the database

-­‐      Integrate sequence (genome and transcriptome) data into the databases

-­‐      Develop protocols for integrating image data (In situ hybridisation expression patterns and morphology ), and functional data.

-­‐      Liaise  with  partners  in  ELIXIR  and  Euro-­‐BioImaging  concerning    standards  and  protocols  for  data integration

 

Qualifications and experience:

  • Demonstrable interest in molecular, developmental and/or evolutionary biology.
  • Masters Level qualification or higher in a relevant discipline.
  • Familiarity with analysis methods for genomic and transcriptomic sequence data.
  • Competence with Unix computer environments.
  • Proficiency in computer programming, ideally in Perl and/or Python.
  • Knowledge of web development with PHP5 would be an asset.
  • Good spoken and written English essential.

 

Start date: as soon as possible; Deadline for application: until position is filled.

Activity  rate:  100%;  Duration  of  contract:  1  year,  renewable.  Funding  available  for  3-­‐4  years.

Take-‐home salary on the CNRS “Ingénieur d'Étude“ pay-­‐scale: 1600-­‐1850€ per month, depending on experience.

 

Contact : Richard Copley (LBDV Group leader in Genome and Protein evolution)  copley@obs-vlfr.fr

Nicolas, Pade | MBA

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