IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF

IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT®, the international ImMunoGenetics information system® that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) proteins, antigen receptor/antigen complexes (IG/Ag, TR/peptide/MHC) of vertebrates; 3D structures of related proteins of the immune system (RPI) of vertebrates and invertebrates, belonging to the immunoglobulin and MHC superfamilies (IgSF and MhcSF, respectively) and found in complexes with IG, TR or MHC. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY concepts and axioms. IMGT/3Dstructure-DB provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), amino acid positions according to the IMGT unique numbering (NUMEROTATION) that are used in IMGT/3Dstructure-DB cards, results of contact analysis and renumbered flat files. In its Web version, the IMGT/DomainGapAlign tool analyses amino acid sequences, per domain. Coupled to the IMGT/Collier-de-Perles tool, it provides an invaluable help for antibody engineering and humanization design based on complementarity determining region (CDR) grafting as it precisely defines the standardized framework regions (FR-IMGT) and CDR-IMGT. IMGT/3Dstructure-DB and IMGT/DomainGapAlign are freely available at http://www.imgt.org

Adaptive and plastic responses of Quercus petraea populations to climate across Europe

How temperate forests will respond to climate change is uncertain; projections range from severe decline to increased growth. We conducted field tests of sessile oak (Quercus petraea), a widespread keystone European forest tree species, including more than 150,000 trees sourced from 116 geographically diverse populations. The tests were planted on 23 field sites in six European countries, in order to expose them to a wide range of climates, including sites reflecting future warmer and drier climates. By assessing tree height and survival, our objectives were twofold: (1) to identify the source of differential population responses to climate (genetic differentiation due to past divergent climatic selection versus plastic responses to ongoing climate change), (2) to explore which climatic variables (temperature or precipitation) trigger the population responses. Tree growth and survival were modeled for contemporary climate and then projected using data from four regional climate models for years 2071-2100, using two greenhouse gas concentration trajectory scenarios each. Overall results indicated a moderate response of tree height and survival to climate variation, with changes in dryness (either annual or during the growing season) explaining the major part of the response. Whilst, on average, populations exhibited local adaptation, there was significant clinal population differentiation for height growth with winter temperature at the site of origin. The most moderate climate model (HIRHAM5-EC; rcp4.5) predicted minor decreases in height and survival, whilst the most extreme model (CCLM4-GEM2-ES; rcp8.5) predicted large decreases in survival and growth for southern and southeastern edge populations. Other non-marginal populations with continental climates were predicted to be severely and negatively affected, while populations at the contemporary northern limit (colder and humid maritime regions) will probably not show large changes in growth and survival in response to climate change

An electronic laboratory notebook at INRAE

Suite à la publication du rapport du groupe de travail du CoSo sur les Cahiers de Laboratoire Electronique (CLE), INRAE s’est engagé dans son adoption et son intégration dans ses processus de recherche. Le groupe de pilotage «Produire, partager et réutiliser des données pour une recherche ouverte et reproductible» du plan Données pour la Science a missionné un groupe afin de fournir des recommandations dans le déploiement des CLE et d’en définir les cadres. INRAE a choisi de supporter l'utilisation d’eLabFTW.Following the publication of the CoSo working group's report on Electronic Laboratory Notebooks (ELK), INRAE is committed to adopting and integrating them into its research processes. The "Produce, share and reuse data for open and reproducible research" steering group of the Data for Science plan has commissioned a group to provide recommendations for the deployment of CLEs and to define their framework. INRAE has chosen to support the use of eLabFTW

eLabFTW@INRAE

INRAE envisage de proposer un service de cahiers de laboratoire électroniques pour ses communautés scientifiques. Le projet de INRAE tient compte des conclusions du groupe de travail du comité pour la science ouverte (CoSO)[1] et s'inspire de la démarche du CNRS[2], notamment dans le choix de l'outil (eLabFTW).Dans cette perspective, nous avons, entre autres, travaillé sur une preuve de concept de eLabFTW à la demande. Cette communication relate l'état d'avancement de ce projet d'adoption de eLabFTW@INRAE et des actions en cours dans le domaine.[1] https://www.ouvrirlascience.fr/cahiers-de-laboratoire-electronique-un-guide-pour-vous-aider-a-en-choisir-un/[2] https://www.datacc.org/wp-content/uploads/2021/02/analyse_enquete_cle_cnrs_2020.pdfINRAE plans to offer an electronic laboratory notebook service for its scientific communities. INRAE's project takes account of the conclusions of the working group of the Committee for Open Science (CoSO)[1] and is inspired by the CNRS[2] approach, particularly in the choice of the tool (eLabFTW).With this in mind, we have, among other things, worked on a proof of concept for eLabFTW on demand. This paper reports on the progress of this project to adopt eLabFTW@INRAE and on the actions underway in this area

IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF).

International audienc

Maggot : Designed to foster good data management, with « data sharing » in mind.

Sharing descriptive metadata is the first essential step towards the so-called “Open Data” approach. With this in mind, the Maggot tool was specially designed to allow users to easily add descriptive metadata to datasets produced within a collective (research unit, platform, multi-partner project, etc.), thus promoting the sharing of metadata within this same collective and beyond

Maggot

Les métadonnées descriptives sont cruciales pour la découverte et le reporting des données 23 et la résolution de tous les problèmes liés aux métadonnées dans le cadre du plan de gestion des données24, défi pour les producteurs de données et pour l\u27Organisation des données dans le stockage des données25 afin de créer diverses métadonnées descriptives. Par la suite, le partage des données implique d’assurer la métadata26 en vue de l’interopérabilité conformément aux principes de FAIR. Compte tenu de la nature tangible de ces défis, il faut répondre à un besoin réel d’outils de gestion pour aider les gestionnaires de données au maximum 28. De plus, ces outils doivent répondre aux exigences des producteurs de données et être conviviaux (données 29)

Gestion de métadonnées pour les espaces de stockages de données

Gestion de métadonnées pour les espaces de stockages de données. Comment mettre en oeuvre de bonnes pratiques de gestion des données qui ne soient pas trop restrictives (simplicité, flexibilité, robustesse, évolutivité)