Junior Web Developer (W/M)

EPFL, the Swiss Federal Institute of Technology in Lausanne, is one of the most dynamic university campuses in Europe and ranks among the top 20 universities worldwide. The EPFL employs more than 6,000 people supporting the three main missions of the institutions: education, research and innovation. The EPFL campus offers an exceptional working environment at the heart of a community of more than 16,000 people, including over 12,000 students and 4,000 researchers from more than 120 different countries.

Deplancke lab (Laboratory of Systems Blology and Genetics) at the Faculty of Life
Sciences Is currently seeking a Junior Web Developer (W/M) to strengthen its team.
The central research focus of the Laboratory of Systems Biology and Genetics (LSBG) is to understand genome organization, regulation, and variation and is broadly partitioned according to three major research pillars:

Adlpo - in the "Adipo" pillar, we are characterizing the regulatory mechanisms driving mesenchymal stromal cell heterogeneity and function in adipose biology and other metabolically relevant processes.

Geno - In the "Geno" pillar, we are examining how variation in the regulatory code affects molecular and organismal diversity.

Techno - in the "Techo" pillar, we are developing novel microfluidic, high-throughput sequencing, single cell omic, and computational approaches, which are used to address biological questions in the other two pillars.

Your mission :

In the context of a grant awarded by

SwissUniversities

, we are seeking a talented individual to actively contribute to the standardization of datasets and cell-type annotations for single-cell RNA-seq data, ultimately aiming to ensure the FAIR accessibility of this type of data and their associated metadata.

In part, this will imply the enhancement of a web portal that aims to accommodate the processing of high-throughput single-cell RNA-seq data: ASAP (asap.epfl.ch ). This project being a collaboration with UNIL and the developers of the Bgee portal (bgee.org ), will involve recurrent meetings and exchange with this team. Moreover, since the goal of this project is to establish a reference format for this type of data, the position may involve active engagement in international workshops, conferences and/or conf calls to collaborate with experts in the field.

The current ASAP website was developed in coordination with the Bioinformatics Competence Center (BICC ) at EPFL, and currently relies on a front-end using React/Plotly/Javascript, and a back-end using PostgreSQL and Ruby-on-Rails. The server is running bioinformatics jobs locally, using a queuing system relying on Ruby’s delayed_job gem. The computing is challenging since it involves very large datasets which cannot be fully loaded in RAM, and thus relies in part on the HDF5 file system using external memory algorithms.

Main duties and responsibilities include :
You will be mainly responsible for designing and implementing new visualization and data management tools in the ASAP web application, with a focus on cell-type metadata, currently handled with the UBERON ontology. You will participate in the development of the new reference format for single-cell data and metadata and implement it in ASAP. Together with an expert single-cell bioinformatician you will also benchmark, test and optimize the embedded analysis tools that run on the platform and adapt the existing tools to fit this new format.

Your profile :

The following qualifications are essential:

• You have a Bachelor and/or a Master’s degree in computer science
• You have experience in web development (front-end and/or back-end)
• You have affinity for biology/genetics/life science
• Knowledge of Ruby on Rails, Python, R, or Java would be a plus

We offer :
Excellent working conditions in a multi-cultural and stimulating environment.
Broad range of tasks and responsibilities.
Competitive remuneration.

Start date :
01.08.2023 or sooner

Term of employment :
Fixed-term (CDD)

Duration :
1-year contract, renewable once

Remark :
Only candidates who applied through EPFL website or our partner Jobup’s website will be considered. Files sent by agencies without a mandate will not be taken into account.

Reference :
Job Nb 2955

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