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Last update: May 2021

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Software, databases

Software

CAVISOFT (Burlett R) : Data acquisition, control and analysis software for cavitron instruments.

 

Simulation platform

METAPOP (Soularue JM et Kremer A) : A STOCHASTIC INDIVIDUAL-BASED SIMULATION PROGRAM FOR STUDYING THE EVOLUTION OF TREE POPULATIONS IN HETEROGENEOUS LANDSCAPES

Metapop simulates the evolution of meta-populations of monoecious plants across heterogeneous landscapes. Based on quantitative genetic theory, Metapop describes individuals with an explicit representation of their genetics and spatial position. Its structure comprises several interacting modules. Metapop, developed at UMR BIOGECO, is a free software under the GNU General Public License version 3. Mol. Ecol. Resour. (2019) 19(1):296-305. 

 

Programmes

Disseq, MPI-Disseq, Diskm, Diagno-Syst

Objectifs : 

1) calculer les distances entre séquences d'un échantillon environnemental (smith-waterman pour disseq, parallélisé en mpi-disseq ; distances k-mers pour diskm ; traite des grands jeux de données

2) annotation taxonomique read par read d'un échantillon environemental par apprentissage supervisé (mapping sur une base de référence, calcul des distances query  x référence, décision d'assignation)

Les programmes et plus de précisions techniques sont disponibles sur github.La démarche générale est publiée dans : Frigerio JM, Rimet F, Bouchez A, Chancerel E, Chaumeil P, Salin F, Thérond S., Kahlert M, Franc A- (2016)  diagno-syst: a tool for accurate inventories in metabarcoding. arXiv:1611.09410v1 [q-bio.QM].

 

Information systems / Databases

PINELINE (Ehrenmann F, Bouffier L, Segura R, Gion JM) : Web application/database for the storage of daily micro-variation data of maritime pine and associated environmental data (only internal Biogeco access).

Quercus Portal (Ehrenmann F) : European Information System on Oak Genetic Resources and Genomics. Web portal for access to genomic and genetic resources on Fagaceae. The portal provides access to 9 different databases (QUERCUSMAP, GD², CMap, EST, TREEPOP, OAK PROVENANCE, SSR, CANDIDATE GENES, SNP). A static section of the portal is dedicated to general information on the genus Quercus.

Pinus Portal (Ehrenmann F) : European Information System on Pine Genetic Resources and Genomics.  Web portal for access to genomic and genetic resources on Pinaceae. The portal provides access to 5 separate databases (PINUSMAP, GD², CMap, EST, TREEPOP). A static section of the portal is dedicated to general information on the genus Pinus. 

SYLVCOOP (Ehrenmann F, Meredieu C) : Web application / local database for forestry silviculture (internal Biogeco access only).

 

Websites

IN-SYLVA France (Ehrenmann F, Saint-André L, Meredieu C, Plomion C) : website of the national research infrastructure grouping all the services (in-situ, in-lab and in-silico) of the main institutions working on forest management and its adaptation.

Oakgenome.fr (Ehrenmann F, Plomion C) : website with all the oak genome data 

 treepeace.fr (Ehrenmann F) : website with all the data of the ERC TREEPEACE project

 

Decision support tools

-ForestGALES implémenté dans CAPSIS

Meredieu C, Labbé T, De Coligny F, Gardiner B (2015) ForestGALES in Capsis: a new library in JAVA. Mathematical Modelling of Wind Damage Risk to Forests, Arcachon (présentation orale)

-Impact de la plateforme Capsis sur la filière en France et dans le monde. [Vidéo] Anne Jambois, Philippe Dreyfus, François de Coligny, Céline Meredieu, Christine Deleuze, Benoît Courbaud, Thierry Sardin Mathieu Fortin, Ariane Gaunand, Laurence Colinet (2017) La plateforme de modélisation Capsis –de la recherche aux impacts. Etude Asirpa [Vidéo]. Paris, FRA : INRA