Software engineer web development in bioinformatics

 CDD · IE  · 18 mois    Bac+5 / Master   Laboratoire de Recherche en Sciences Végétales, Equipe GBF · Auzeville-Tolosan (France)  Selon expérience

 Date de prise de poste : 15 septembre 2021

Mots-Clés

Developpement web données omiques base de données

Description

Context:

For the last 20 years, EU-researchers and EU-funded projects have made important contributions in characterizing genetic resources of relevance for the EU economy/agriculture. This contribution has been even more dramatic in the case of the genetic resources related to the Solanaceae crop tomato. The time is now ripe for building on previous successes and attain the benefits by first collecting and organizing the scattered results from previous projects on tomato, after which researchers will tackle scientific questions by exploring the integrated and unified data based on those previous results. The recently funded EU project HARNESSTOM (http://harnesstom.eu/) is an Innovation Action that aims to improve the accessibility and to consolidate the use and knowledge of tomato genetic resources in order to tackle the new challenges imposed by consumers and global change threats by fostering the interaction between the different stakeholders in the tomato production chain.

The GBF is part of the HARNESSTOM consortium involving 22 partners from different countries and will take in charge the bioinformatics activities to develop tools and a web platform based in Europe. We aim to provide partners with a curated and integrated web-based relational database including data mining tools and publicly available genomics, genetics and breeding data for tomato accessible via an academia URL in a one-stop-shop configuration.

Missions:

In this context, we are seeking a software engineer that will be involved in the improvement of the Genomic Resources (GenRes) user interface to make the search of information and visualization of the genotypic, metabolomic and phenotypic information readily available for all stakeholders. The user interface will be developed with a series of visual elements, thus allowing a user to interact with specific services and applications to display information based on the user experience. To this end, an RIA (Rich Internet Application) using web services such as REST (Representational State Transfer) will be developed to provide users with a quick, yet simple and comprehensive interface.

The engineer will work in the bioinformatics team of the GBF team that includes a mathematician/statistician and a bioinformatician specialized in web development. The engineer will also work with an international consortium to develop the HARNESSTOM gateway. The GBF team is recently become part of the LRSV lab (https://www.lrsv.ups-tlse.fr/) that is situated at the INRAe Occitanie center near Toulouse (https://www.inrae.fr/centres/occitanie-toulouse) and benefits from the Bioinformatics infrastructure of the Genotoul-Bioinfo platform (http://bioinfo.genotoul.fr/).

Profile:

Experience in some or all of the following areas is appreciated:

• server-side web frameworks such as Symfony

• client-side frameworks including Vue.js

• relational databases

• API development


References:

Zouine M, Maza E, Djari A, Lauvernier M, Frasse P, Smouni A, Pirrello J, Bouzayen M. TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks. Plant J. 2017 Nov;92(4):727-735. doi: 10.1111/tpj.13711

Web portal: http://tomexpress.gbfwebtools.fr/ Shusei S. et al. (Including M. Zouine).

The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012 May 30;485(7400):635 ‐41. « The Tomato Genome book» co-édité par Mathilde Causse, Jim Giovannoni, Mondher Bouzayen & Mohamed Zouine. Springer, January 2017. DOI10.1007/978-3-662-53389-5.

Web links related to the project:

• http://harnesstom.eu/ 

• http://www.traditom.eu/

• https://genophenoenvo.github.io/

• https://solgenomics.net/

• https://brapi.org/

Candidature

Procédure : A CV and letter of motivation are to be sent to Dr. Mohamed Zouine before July 15th

Date limite : 30 juillet 2021

Contacts

Mohamed Zouine

 moNOSPAMhamed.zouine@ensat.fr

Offre publiée le 9 juin 2021, affichage jusqu'au 30 juillet 2021