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 was sponsored by the ISCD as a “junior” project-team in 2019-2022, co-led by Benoit Sarels (LJLL) and Sakina-Dorothée Ayata (LOV/LOCEAN), and as a project-team in 2023-2026, co-led by Jean-Olivier Irisson (LOV) and Sakina-Dorothée Ayata (LOCEAN).

FORMAL team

FORMAL News

2024:

  • Upcoming event: ML4Oceans school 2024: EUR-IPSL, SCAI, ISCD and the Institut de l’Océan of Sorbonne Université offer the second edition of our ML4Oceans transdisciplinary school for PhD and post-doctoral students to acquire knowledges and skills in AI applied to oceanography. 7-11 October 2024 at SCAI/ISCD, Paris. Registrations soon open.
  • Upcoming event: FORMAL scientific day 2024, Tuesday 21st of May, at ISCD, Paris. Registrations soon open.

2023:

  • Several FORMAL members attended the PISCO annual meeting in Paris on 11-12 october.
  • Welcome to our new PhD students: Lisa di Matteo joined the LOCEAN in October 2023 to work on the modelling of zooplankton’s feeding strategies in PISCES; Elsa Labourdette joined the LOCEAN in October 2023 to start the IPSL pre-doctoral programme, before starting her PhD at the LOV and LPSM next January, Alexandra Nalivaev joined the LOCEAN in fall 2023 to work on the impact of climate change on open ocean ecosystems in the Kerguelen region.
  • Congratulations to Sakina-Dorothée Ayata who has been appointed for 5 years as Junior Member of the Institut Universitaire de France (IUF) !
  • Several positions are open! PhD in biogeochemical modelling at LOCEAN (offer), PhD in Deep learning to predict plankton communities from space at LOV. Please apply if interested !
  • PhD defense: Laure Vilgrain will defend her PhD on June 13th at LOCEAN.
  • New team member: Camille Richon joined the team in April 2023 as a post-doc at the LOCEAN and LOPS to work on zooplankton modelling in PISCES.
  • The Kick-Off meeting of FORMAL-v2 will be organised at ISCD on the 21st of March 2023. More information here.
  • The new version of the FORMAL project-team has been selected by the ISCD for 2023-2026: welcome to our new members! Also note that we will recruit several master students, two PhD candidates and two post-docs in the coming years… Stay tune!

2022 :

  • Congratulations to Virginie Sonnet and Ophélie Da Silva for the publication of her first articles (here and here) !
  • Congratulations to Laure Vilgrain whose first publication obtained a price from Québec Océan ! This work was already nominated by the the Fondation de la Mer and the Institute of the Ocean in 2021. Her article is available here.
  • Upcoming event: Symposium on Machine Learning for Ecological Images: We are organising this symposium during the SFE² GfÖ EEF / Joint meeting, International Conference on Ecological Sciences that will take place in Metz, France, in November 2022.
  • Interested in deep learning and plankton imaging?Join the second edition of the imaginecology conference! This hybrid workshop on Deep Learning pour le traitement et l’analyse d’images et de sons en écologie will take place on September 29-30th 2022 in Villeurbanne. Sakina-Dorothée Ayata is part of the organizing committee.
  • Congratulations to Margaux Perhirin who got a PhD grant (2022-2025) from ISCD! Margaux will work at the LOCEAN on the impact of functional diversity of marine mesozooplankton on carbon fluxes. She will be analysing high throughput data (imaging, omics) and developing numerical models.
  • New team member: Miriam Beck joined the team in June 2022 as a post-doc at the LOV to work on plankton imaging data analysis.
  • Upcoming event: ML4Oceans summer school 2022: SCAI, ISCD and the Institut de l’Océan of Sorbonne Université offer a transdisciplinary summer school for PhD and post-doctoral students to acquire knowledges and skills in AI applied to oceanography. Registration is open here until May 31st. Detailed program here.
  • Sakina-Dorothée Ayata is currently visiting professor at UQAM and UdeM in Montreal (May-July 2022) to work with Beatrix Beisner and Timothée Poisot.
  • FORMAL mini-conference on Machine Learning for Marine Sciences (ML4MS) :The mini-conference will be organised during two afternoons at the end of March/early April 2022, just after the winter webinar series: Monday 28th March and Friday 1st April from 14h to 15h CET. It will include 7 invited international speakers on ML for Marines Sciences. Detailed program hereThe videos of the first webinars are available HERE.
  • FORMAL winter webinar series: a total of four 1-h webinars dealing with the observation and the modelling of ocean life have been organised in February and March (Feb 10th, Feb 24th, Mar 10th, Mar 24th, from 14h to 15h, CET). Detailed program here. The videos of the first webinars are available HERE.
  • A member of FORMAL is on the radio to talk about plankton! Sakina-Dorothée Ayata was invited on France Inter for “La Terre au Carré” (25 Jan. 2022: link here) and on France Culture for the “Méthode Scientifique” (10 Jan. 2022: link here). Marine plankton are under the spotlight!
  • New team member: Margaux Perhirin joined the team as a master 2 student at the LOCEAN to work on plankton imaging and metabarcoding data. Margaux is currently visiting BIOS in Bermuda for 2 months to work with Leocadio Blanco-Bercial.

2021 :

  • 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.

2020 :

  • 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 2020. 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 2020, 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 5 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 2020.
  • 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

 

Dr. Jean-Olivier Irisson, Laboratoire d’Océanographie de Villefranche-sur-mer (LOV), Sorbonne Université

Some practical information

  • Access to the archive of the member mailing list
Note that you may need to identify yourself: https://groupes.renater.fr/sympa/arc/formal/2023-03/
  • How to acknowledge FORMAL ?
You can add this sentence in the acknowledgement section of your publications: This work was performed with the support of the Institut des Sciences du Calcul et des Données (ISCD) of Sorbonne University (IDEX SUPER 11-IDEX-0004) through the support of the sponsored project-team FORMAL (From ObseRving to Modelling oceAn Life).
   

Collaborations

FORMAL gathers members from 10 laboratories at SU and 8 laboratories outside SU:

  • Laboratoire d’océanographie et du climat : expérimentations et approches numériques (LOCEAN), Sorbonne Université, Paris.
  • Laboratoire d’Océanographie de Villefranche-sur-mer (LOV), Sorbonne Université, Villefranche-sur-mer.
  • Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Paris.
  • Laboratoire de recherche en informatique de Sorbonne Université (LIP6), Paris.
  • Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Paris.
  • Laboratoire J.L. Lions (LJLL), UMR 7598,  Paris.
  • Laboratoire de Biologie des organismes et écosystèmes aquatiques (BOREA), Paris.
  • Laboratoire Adaptation et Diversité en Milieu Marin (AD2M), Roscoff.
  • Laboratoire d’Océanographie Microbienne (LOMIC), Banyuls-sur-mer.
  • Laboratoire de Biologie Intégrative des Modèles Marins (LBIM2),  Roscoff.