In person — Room 34290, INMG, Faculté de Médecine Lyon Est, Rockefeller campus — September 10, 2024, 1–3 pm

Attendees

Present: 17 participants from 8 research institutions.

Apologies: 3 people.

Profile: 10 fixed-term and 7 permanent staff. The large majority works on genomic and transcriptomic data, with a clear trend towards single-cell and spatial transcriptomics.

Introduction

This first gathering starts from a shared observation: the Lyon bioinformatics community is poorly represented in national networks. The aim is to build connections, structure a local network, and provide a space for exchange and mutual support.

The three meeting organisers introduced themselves: Guillaume Marcy and Maxime Lepetit are bioinformaticians at the Profilexpert genomics platform (Labex CORTEX, Rockefeller), specialised in single-cell and spatial transcriptomics. William Jarassier is a bioinformatician within the MyoNeurALP2 project, also at Rockefeller.

Missions and perspectives

The following broad directions emerged from the discussions:

  • Facilitate collaboration among bioinformaticians in the region.
  • Share resources and expertise through a dedicated space.
  • Offer training, building on and articulating with existing programmes.
  • Structure the network in connection with national and regional initiatives.

The network is primarily oriented towards omics data.

Communication tools

A discussion took place around the value of a dedicated chat tool. The saturation of existing channels was raised: Discord Bioinfo.fr and Slack are available nationally, but have many silent users. A local space would offer a more convivial feel and help keep the network active on a day-to-day basis. Participants already use various tools depending on their institution: Element/Matrix, Rocketchat (SFR BioSciences) or Framateam (HCL). The Renater mailing list is positioned as a broadcast tool, not a discussion space. It was decided to set up and test a Matrix space in October.

Positioning with respect to existing structures

MERIT: there is no Lyon local network yet accredited within MERIT. Accreditation would give access to funding for events (lunches, coffee breaks, etc.) and to all the information, training and events of the other local networks across France.

PRABI: an initial discussion had taken place in July. PRABI, in the process of updating its scope, wished to draw up an inventory of bioinformaticians and platforms in the region. It is in favour of delegating local network coordination to the new initiative, and supports MERIT accreditation.

Spatial-Cell-ID: this EquipeX, dedicated to single-cell and spatial transcriptomics, is complementary to our initiative. Coordination with its scientific coordinator, Sergio Sarnataro, is planned.

Training

Training is identified as an essential component of the network. The emphasis is on building on existing programmes — in particular the CAN training sessions of SFR BioSciences — rather than creating new structures.

Meeting format

Participants proposed:

  • Quarterly thematic seminars (half-day), starting in 2025.
  • An annual broad-spectrum workshop (full day).

In-person attendance is considered important.

Mailing list

The first round of outreach (late July 2024) revealed several limitations: the summer period reduced the reach of the announcement, the list initially targeted mainly the single-cell community, and no representative from the La Doua campus was present at this meeting. Some participants heard about the initiative late, or somewhat by chance. A second outreach round is planned for September, via the SFBI, JeBiF and MERIT channels, to broaden the reach. Participants were in favour of opening the list to professionals from private laboratories.

Steering committee

The current committee is composed of William Jarassier, Guillaume Marcy and Maxime Lepetit. Volunteers are being sought to bring in representatives from the different sectors of the Lyon bioinformatics community. Establishing a code of conduct for the mailing list was also identified as a need.

Agenda

September:

  • Advertisement around the mailing list via SFBI, JeBiF and MERIT channels.
  • Schedule the next meeting (late November / early December).

October:

  • Circulate a directory of members’ affiliations, contacts and areas of expertise.
  • Call for volunteers for the steering committee.
  • Set up and test a Matrix discussion space.

Written by: Maxime Lepetit — Reviewed by: William Jarassier, Guillaume Marcy