Mots-Clés

Genomic Data Index Database Search

Description

This two years position is offered within the framework of the OmicFinder project, which aims to create a search engine to index and query sequences across numerous genomic databases. Genomic data enable crucial advances in medicine, ecology, agronomy, and ocean monitoring. A major limitation is the inability to query all these data comprehensively. The OmicFinder project's objective is to remove this barrier and allow complete and global exploitation of the generated sequences, enabling users to perform queries on raw sequencing data on the fly to make the best use of available resources in life sciences.

The recruited person will work in Montpellier with Zenith team at Inria (the French National Institute for Research in Digital Science and Technology). Several Inria teams are participating in the project, contributing expertise in algorithms, indexing, and more. There are also external partners involved in algorithmic development and result validation.

2. Main Activities

The mission assigned to the recruited person is the design and development of a distributed index. This will build on an existing centralized index, distribution approaches developed within the Zenith team, and new joint developments by the teams involved in the OmicFinder project to define the principles of a distributed index for genomic data.

The main activities of the recruited postdoc are as follows:

• Studying the state of the art on indexes for genomic data, including the approaches developed by the partners of the project.

• Designing a distributed index for large volumes of genomic data.

• Developing the designed index in collaboration with project partners.

• Creating a query system that leverages the index for efficient query answering.

• Participating in writing scientific papers to disseminate research results.

3. Requirements

- Experience in bio-informatics applied to genomic data

- Knowledge of distributed systems and indexing algorithms

- Good programming skills

4. Languages

French or English

5. Contact

- Reza Akbarinia <reza.akbarinia@inria.fr>

- Florent Masseglia <florent.masseglia@inria.fr>