Formal

From ObseRving to Modelling oceAn Life

FORMAL aims to study the dynamics of life in the ocean at various spatial and temporal scales. It will build on the huge quantity of various marine data (omics, imaging, acoustics, satellite) that has been acquired by the members of the team on marine life (viruses, bacteria, plankton, fish), either at global scale (e.g. Tara Oceans) or at long-term observatories (e.g. the time-series data from the 3 marine stations of Sorbonne Université).

Our objectives are:

  1. to develop new methods to analyse and combine high throughput data in oceanography, especially imaging and omics data, but not only;
  2. to improve existing marine ecosystem models through data assimilation, and develop new statistical and mechanistic models to represent the dynamics of biological systems in the ocean; and
  3. to structure the scientific community at SU working on the analysis of marine data and on the modelling of ocean life, both in Paris and in the 3 marine stations of SU. For instance, we regularly organize online seminars.

FORMAL News

  • A member of FORMAL is on the radio! Sakina-Dorothée Ayata was interviewed on France Culture for the “Journal des Sciences” (14 Oct. 2021: link here) and she also has a weekly chronicle on the oceans on the web radio Eu!radio since Oct. 2021: Une plongée dans les Océans. Stay tuned!!
  • We are offering a post-doc position in marine ecosystem modelling at the LOCEAN! Details here
  • Next FORMAL webinar (Nov. 23rd 2021) by Laura Kanzler, FORMAL post-doc at the LJLL, and Pavla Debeljak, former BLUE-CLOUD post-doc at the ISYEB. Title of their presentations: Kinetic Modelling of Emergence Phenomena in Biological Processes; and: Carbon Fixing Unknowns: Exploring small green algae ‘dark matter’.
  • New team member: Laura Kanzler joined the team as a post-doc at the LJLL to work on applied mathematical modelling.
  • Webinaire at the LOCEAN (June 29th 2021) by Sakina-Dorothée Ayata. From plankton images to marine ecosystem functioning: a tale of high throughput imaging, machine learning, and copepod ecology.
  • Congratulations to our master students! Iris Rizos will continue as a PhD student at Roscoff.
  • Webinar for the month of marine diversity at the LOCEAN (May 4th 2021) by Sakina-Dorothée Ayata. Trait-based approaches for exploring marine plankton diversity – Chosen examples from omics and imaging.
  • New team member: Margaux Perhirin is joining the team as Master 1 student at the LOV to work on plankton imaging data with Sakina Ayata and our colleague Leocadio Blanco-Bercial from BIOS in Bermuda.
  • Online workshop: Machine learning for plankton images (March 22nd 2021).
  • Next FORMAL webinar (March 8th 2021) by Anne-Laure Dalibard, Prof. in applied mathematics at the LJLL of SU and recently nominated as Junior Member of the Institut Universitaire de France (IUF). The video of the webinar is available here. Title of the presentation (given in French): Structures multi-échelles en mécanique des fluides.
  • New team member: Iris Rizos is joining the team as Master 2 student at the ISYEB to work on the “unkown” omic sequences with Lucie Bittner.
  • Save the date! Emile Faure will defend his PhD on the 2nd of December 2020. His PhD thesis is entitled: “Apport des données méta-omiques dans la détection et la quantification des traits fonctionnels au sein des écosystèmes planctoniques”. Due to the Covid situation, the defense will append remotely.
  • Next FORMAL webinar by Eric Orenstein on plankton imaging and machine learning (Nov. 23rd 2020). Eric will soon join the LOV and FORMAL for his post-doc!
  • Interested in deep learning and plankton imaging?Join the workshop on Deep Learning pour le traitement et l’analyse d’images et de sons en écologie that will take place online on November 16th and 17th. Sakina-Dorothée Ayata is part of the organizing committee and Jean-Olivier Irisson and Frédéric Maps will present some of our work related to FORMAL!
  • If you have missed the 7th EMB Forum on Big Data in Marine Science that occured online on October 23th, the recordings of the sessions are available here on the EMB YouTube Channel, including the invited presentation of Sakina-Dorothée Ayata on the role of big data, digitalization and artificial intelligence in marine science to support of the EU 2030 Biodiversity Strategy. Sakina’s recorded presentation is also available here.
  • Benoit Sarels is currently a guest at the Wolfgang Pauli Institute in the University of Vienna.
  • Congratulations to Jean-Olivier Irisson for his HDR defense! His HDR is entitled “Towards a computational ecology of plankton”.
  • Congratulations to Lucie Bittner and Anne-Laure Dalibard who have been appointed for 4 years as Junior Member of the Institut Universitaire de France (IUF) !
  • New! The videos of the presentations of the first FORMAL Webinar on “Marine Big Data” and organised on June 18th 2020 are available on the webinar webpage.
  • The deadline for applying to our post-doc offer in applied mathematics and ecosystem modelling in Paris has been extended to May 31th.
  • Given the current pandemic situation, our activities such as our monthly seminars and our annual workshop have been postponed until further notice. Stay safe, stay home!
  • The first FORMAL workshop on “Marine data” IS POSTPONED UNTIL FURTHER NOTICE will be held on Friday 15th May 2020 at ISCD in Paris: More information will come soon.
  • Two post-doc positions at FORMAL/ISCD are open! One in applied mathematics and ecosystem modelling in Paris, the other on machine learning and plankton imaging in Villefranche-sur-Mer. Please apply if you are interested!
  • To be informed of our future activities, please register here.

Scientific Coordinators

Dr. Sakina-Dorothée Ayata, Laboratoire d’océanographie et du climat : expérimentations et approches numériques (LOCEAN), Sorbonne Université

 

Benoit Sarels
Dr. Benoît Sarels, Laboratoire J.L. Lions, Sorbonne Université

Collaborations

Main research units connected with the team:

  • Laboratoire d’Océanographie de Villefranche-sur-mer (LOV), Sorbonne Université, Villefranche-sur-mer.
  • Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Paris.
  • Laboratoire J.L. Lions (LJLL), UMR 7598, Sorbonne Université, Paris.
  • Laboratoire de Biologie Intégrative des Modèles Marins (LBIM2), Sorbonne Université, Roscoff.
  • Laboratoire d’océanographie et du climat : expérimentations et approches numériques (LOCEAN), Sorbonne Université, Paris.
  • Genoscope, CEA, Evry-sur-Seine.