New "Mini-projets" started in 2024
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Ephemer microbiome | C. Jeanthon | procaryote microbiome, metabarcoding, community comparison | UMR7144 | Bioanalysis (UMR7144) |
| OnDemand | G. Le Corguillé | SLURM, R, IFB | FR2424 | E-infra |
| ATLASea - portal | E. Corre | ATLASea, portal, genome, marine organisms, French EEZ | FR2424 | Dev / E-infra |
| ATLASea - Marine Genome Portal | E. Corre | ATLASea, portal, genome, marine organisms, visualisation, analysis | FR2424 | Dev / E-infra |
| ATLASea - get public data | E. Corre | ATLASea, genome, marine organisms, public data | FR2424 | Data management / E-infra |
| ATLASea - get data | E. Corre | ATLASea, genome, marine organisms, ATLASea species, French EEZ | FR2424 | Data management / E-infra |
| ATLASea-DB | E. Corre | ATLASea, genome, marine organisms, database | FR2424 | Dev |
| Adaptsearch v3 | D. Jollivet | Analysis pipeline, python, phylogeny, transcriptomes | UMR7144 | Bioanalysis (UMR7144) |
| CryptoPE | C. Six | Microalgae cryptophytes, Phycoérythrine, environmental genomics | UMR7144 | Bioanalysis (UMR7144) |
| Genome browser urchin | J. Morales | Urchin, RNASeq, genome browser, BLAST | UMR8227 | E-infra |
| TREC Benchmark | C. De Vargas | Metabarcoding | UMR7144 | Bioanalysis (TARA) |
| Tara microbiome metabarcoding data 1st release | C. De Vargas | Metabarcoding | UMR7144 | Bioanalysis (TARA) |
| Dashboard FUTURE-OBS | M. Hoebeke | Development of a monitoring tool for FUTURE-OBS research products | FR2424 | Dev |
| ANR BONUS | A.-C. Baudoux,N. Simon | Viral fraction analysis | UMR7144 | Bioanalysis |
| ANR TaxCY | L. Garczarek | Cyanorak devlopment | UMR7144 | Bioanalysis / Dev |
| ANR Sexisol | T. Broquet | Jaera, genome assembly and comparative analysis | UMR7144 | Bioanalysis / E-infra |
"Mini-projets" started in 2023
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Parada euk | C. Jeanthon, C. de Vargas | metabarcoding, methodology | UMR7144 / FR Tara GOSEE | Bioanalysis (TARA) |
| Rosko Naples diatoms paper revisions | N. Simon | metabarcoding, diatoms, microscopy, time-series, intercomparison | UMR7144 | Bioanalysis (TARA) |
| ANF MetaBioDiv 2023 | F. Armougom | metabarcoding, formation | IRD MIO | Bioanalysis (TARA) |
| Time-series sampling effort core | C. de Vargas, A. Soccodato | metabarcoding, plankton, time-series, europe | UMR7144 / EMBRC | Bioanalysis (TARA) |
| Metabarcoding analyses mesocosms Tvärminne part 2 | C. Hall | metabarcoding, mesocosm | Tvärminne Zoological Station (TZS) | Bioanalysis (TARA) |
| SNO data visualisation | M. Hoebeke | ILICO, BenthOBS, PHYTOBS, Dashboard, Visualisation, API | FR2424 | Dev |
| Marfungi | L. Meslet-Cladiere | Marine Fungi, Genome Browser | ESIAB | Bioanalysis/E-infra |
| MARCO BOLO | N. Pade | interert ADNe environmental analysis | EMBRC-ERIC | Bioanalysis |
| Genome RCC3390 | P. Gourvil | genome assembly RCC3390 | FR2424/Univ. espagne | Bioanalysis |
| AO embrc WP5 | E. Corre | Management of local infrastructures for project AO EMBR | FR2424 | E-infra |
| AO embrc WP6 | E. Corre | Management of AO EMBRC marine data, FAIR data | FR2424 | Data |
| mudis4ls IS2 | E. Corre | Management of IFB marine data, FAIR data | FR2424 | Data |
| webaplat | E. Corre | Migrate, update, secure or close all ABiMS websites | FR2424 | E-infra |
| Ventflux | D. Jollivet | demo-genetics model, hydrothermal sources, mining threat | UMR7144 | Bioanalysis (UMR7144) |
| Phytonoise | F. Not | transcriptomics, coccolitophore, sound stress | UMR7144 | Bioanalysis (UMR7144) |
| Eskemm POC | G. Le Corguillé | Datacenter | FR2424 | E-infra |
| Amplicon nanopore Coralie | C. Rousseau | Nanopore, metabarcoding, nextflow | UMR8227 | Bioanalysis (TARA) |
| diatoms adhesion museum | M. L. Bourguet | RNAseq Diatomes | MNHN | Bioanalysis |
| Eskemm meta | G. Le Corguillé | Datacenter | FR2424 | E-infra |
| RNAseq moule | C. Gaudin | RNAseq, training | Univ. Caen | Bioanalyse |
| Fungal plastisphere metabarcoding | G. Burgaud | Plastisphere, diversity, fungal communities, earth-sea continuum, impacts | UBO / UR3882 | Bioanalyse (TARA) |
| SAD genomalg | M. Cock, G. Markov, S. Dittami | Metabolic networks and comparative genomics Phaeomicus | UMR8227 | Bioanalyse |
| Tara Pacific metabarcoding data 2nd release | C. De Vargas | Production and provision of ASV tables of Tara Pacific data | UMR7144 | Bioanalysis /Data management (TARA) |
| SOMLIT-Astan metaB | N. Simon | organization of metabarcoding data obtained from SOMLIT-Astan samples | UMR7144 | Bioanalysis /Data management (TARA) |
"Mini-projets" started in 2022
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| r-shiny ecto v2 | M. Cock | r-shiny, ectocarpus, phaeoexplorer | UMR8227 | E-infra |
| ANR Brownsugar | C. Hervé | Polysacharides algae | UMR8227 | Bioanalyse/E-infra |
| Heterotis_V2 | J. Henry | RNAseq | BOREA | Bioanalyse |
| Phaeo_virus_v2 | M. Cock | virus : EVE detection | UMR8227 | Bioanalyse |
| Phaeo_virus_v3 | M.Cock | Virus : detection in metaviromes | UMR8227 | Bioanalyse |
| EOSC Life MGnify pipeline | N. Pades | pipeline dev et deployement | EMBRC -ERIC | Bioanalyse/E-infra |
| ARCTOS | A. Lebrun | RNAseq brown algae | LOV | Bioanalyse |
| Rimicaris | J. Henry | RNAseq | BOREA | Bioanalyse |
| Carcinus v2 | C. Gaudy | RNAseq parasites | BOREA | Bioanalyse |
| RNAseq Lupinv2 | G. Dubrulle | RNAseq | Univ. Toulouse | Bioanalyse |
| RNAseq Hermetia | J. Henry | RNAseq | BOREA | Bioanalyse |
| Sacculine_Taiwan_v2 | JY.Toullec / CY Chi | RNAseq parasites | UMR7144/Taiwan | Bioanalyse |
| Ventchitin | F. Thomas | metabarcoding, chitin degradation, GH18 | UMR8227 | Bioanalyse |
| Tonga MetaB Virus | A.C. Baudoux | Metabarcoding, Virus | UMR7144 | Bioanalyse (UMR7144) |
| DisKordia | C. Jeanthon | RNAseq | UMR7144 | Bioanalyse (UMR7144) |
| TongaMetaB_V2 | L. Garczarek | Metab bacteria plancton volcano | UMR7144 | Bioanalyse (UMR7144) |
| Glomicon | C. Jeanthon | Metab standardisation | UMR7144 | Bioanalyse (UMR7144) |
| Data Organisation ASTAN | N. Simon | PGD - ASTAN- Genomic observatory | UMR7144 | Data (UMR7144) |
| Carcinus_V1 | C. Gaudy | RNASeq | BOREA | Bioanalyse |
| RNAseq_swarmer | I. Rizos | RNAseq sc | UMR7144 | Bioanalyse (ABiMS/UMR7144) |
| RUMISBAC | M. Lafond | RNAseq C. perfringens | Univ. Marseille | Bioanalyse |
| SNC Sepia | J. Henry | RNAseq SNC Sepia | BOREA | Bioanalyse |
| SA3 | M. Valero / ML Guillemin | ADN Ancien | UMI/UNIChi | Bioanalyse |
| MSCA Si-ORHIGENS | N. Liopis Monferrer | diatoms silificaion | MBARI | Bioanalyse |
| Metabarcoding analyses mesocosms Tvärminne part 1 | C. Hall | metabarcoding, mesocosm | Tvärminne Zoological Station (TZS) | Bioanalyse (TARA) |
| beauris_func_annot | L. Guéguen, E. Corre | functional annotation nextflow orson beauris atlasea | FR2424 | E-infra |
| Tara single cell pilot | C. de Vargas | metabarcoding, single-cell | UMR7144 / FR Tara GOSEEA | Bioanalyse (TARA) |
| Rhodoexplorer public genomes | A. Lipinska, E. Corre | Add public genomes to the Rhodoexplorer web portal | Max Planck, Tübingen | E-infra |
"Mini-projets" started in 2021
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| KrillDB | JY Toullec | KRill transcriptome database | UMR7144 | Bioanalyse/IL |
| MetDBv2 | E.Corre.; E. Pelletier | MetDB transcriptome database | FR2424/CEA | Bioanalyse/IL |
| AOZAN | Genomer | LIMS for the Genomer PF | FR2424 | E-infra |
| VDGOB | ABiMS + BGO collaborators | Genomic observatories interface | FR2424+ BGO | IL |
| Zobellia MetaG v2 | F. Thomas | Metagenome, recruitement, MAGs | UMR8227 | Bioanalyse |
| DuBii ATACseq amphioxus | L. Subirana | ATACseq | OOB | Bioanalyse |
| Gracilaria database | A. Lipinska, S. Krueger, S. Dittami | Red algae, Genome browser | UMR8227, Tubinguen | Bioanalyse/E-infra |
| Migration Webtools | L. Guéguen/ G. L Corguillé | Galaxy | FR2424 | E-infra |
| Migration Galaxy MetaB | L. Guéguen / G. L Corguillé | useGalaxy.fr | FR2424 | E-infra |
| Jupyterhub | G. Le Corguillé | E-environnement | FR2424 | E-infra |
| Migration Banko | G. Le Corguillé | E-environnement/Storage | FR2424 | E-infra |
| Migration GitLab | G. Le Corguillé | E-environnement | FR2424 | E-infra |
| Evolution GPU | G. Le Corguillé | E-environnement/Infrastructure | FR2424 | E-infra |
| Phaeoexplorer_microsattelites | M. Valero | Brown algae, Phaeoexplorer, microsattelites | UMI3614 | Bioanalyse |
| PGD_SMQ | E. Corre | ISO9001, process, data management and FAIR data | FR2424 | Management |
| DiatomsDMSP | E. Bucciarelli/ F. Not | RNAseq, Transcriptome/Fe-DMSP | Univ. Brest /UMR7144 | Bioanalyse (UMR7144) |
| MetaB Mollusque | I. Boutet | Metabarcoding Oyster | UMR7144 | Bioanalyse (UMR7144) |
| TongaMetaB_V1 | L. Garczarek | Metab bacteria plancton volcano | UMR7144 | Bioanalyse (UMR7144) |
| Roskokeys | L. Garczarek | RoskoBase curation pipeline | UMR7144 | Bioanalyse/IL (UMR7144) |
| Adapsearch_V2 | D. Jollivet | Adaptive evolution pipeline | UMR7144 | Bioanalyse/IL (UMR7144) |
| TARA_16S | C. De Vargas | TARA Ocean 16S analysis | FR-GO-SEE | Bioanalyse (TARA) |
| EukBank | C. Berney | Metab Ref Data processing | FR-GO-SEE | Bioanalyse (TARA) |
| Indigene | N. Simon, C. Jeanthon | Metabarcoding data to study changes in marine microbial communities: ASV tables | UMR7144 | Bioanalyse (TARA) |
| Phenomap | I. Probert | Identify in silico potential new phytoplankton lineages | FR2424 | Bioanalyse (TARA) |
| Plancton ASTAN: analysis | N. Simon | Astan data analysis | UMR7144 | Bioanalyse (TARA) |
| Plancton ASTAN: Planctonic species temporal dynamics | N. Simon | Planctonic species temporal dynamics on the SOMLIT ASTAN point | UMR7144 | Bioanalyse (TARA) |
| Plancton ASTAN: Naples | N. Simon | Comparison of diatoms communities between Roscoff and Naples | UMR7144 | Bioanalyse (TARA) |
"Mini-projets" started in 2020
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Phaeoexplorer data integration second wave | M. Cock, S. Coelho | brown algae, data integration, JBrowse, blast | UMR8227 | E-infra |
| Phaeoexplorer reseau metabolique | G. Markov | brown algae, metabolic networks | UMR8227 | Bio |
| Phaeoexplorer functionnale annotation | M. Cock, S. Coehlo | brown algae, annotation | UMR8227 | Bio |
| Phaeoexplorer web portal | M. Cock, S. Coelho | brown algae, web portal | UMR8227 | E-infra |
| Metagenome Corail | C. Clerissi | Metagenome / genome assemblies Coral symbionts | Univ. Perpignan | Bio |
| SNO Benthobs | C. Houbin | databases, in situ data, biodiversity | FR2424 | Dev |
| CyanorakFast Edit | L. Garczarek F. Partensky | Genome annotation environment | UMR8227 | Dev |
| ASTAN-EVO | T. Cariou, E. Mace | Database evolution | FR2424 | Dev |
| Roskobaz IO | C. Jeanthon et al. | Database development | UMR8227 | Dev |
| RNAseq Heterotis | J. Henry | Rnaseq, annotation | BOREA Caen | Bio |
| RNAseq Arapaima | J. Henry | RNaseq, annotation | BOREA Caen | Bio |
| Metagenome Venise | E. Bianchi | Metagenome | INOGS Italy | Bio |
| RNAseq Acantharia | F. Not J. Mansour | Metatranscriptome | UMR7144 | Bio |
| RNAseq Alviniconcha | T. Broquet. J.Castel | RNAseq assembly, evolution, genes selection | UMR7144 | Bio |
| RNAseq Pseudoalteromonas | H. Cuny | RNAseq , DEG | UBS | Bio |
| Genasex | D. Roze, S. Glemin | Storage | Univ. Rennes | E-infra |
| LDAPAPLAT | G. Le Corguillé | user account, LDAP, MY, NUM | FR2424 | E-infra |
| e-infra++ | G. Le Corguillé | SLURM, ANsible, IFB | FR2424 | E-infra |
| BLUE CLOUD | P. Debeljak | Storage | Sorbonne Université | E-infra |
| BBMOSE | C. Hochart, P. Galand | Storage | Banyuls | E-infra |
| SulfAtlas - HMMWeb | G. Michel | HMM, database | UMR8227 | Dev |
| Cristallo-Singularity | M. Czjzek | Cristallographie, Singularity, Ansible | UMR8227 | E-infra |
| EOSC-Life – GGA on Cloud | J.K Hériché | GGA, Galaxy, Cloud, Docker | EOSC-Life WP2 | E-infra |
| MetaG OCP | C. Six | MEtaG reads recruitement | UMR7144 | Bio |
| CBM-Supplementary Material | N. Guyard | CBM – supplementary material – book review | FR2424 | Dev |
"Mini-projets" 2019
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| IMPEKAB _ reseau | C. Trottier | Assembalge meta Transcriptomes Symbionts | COMBI LS2E | Bio |
| Micrococus | C. Gaudin | Metabarcoding bacterien , Sepia officinalis | BOREA Caen | Bio |
| jbrowse_hapar | E. Kayal, L. Guillou | genome browser, JBrowse, Amoebophrya | UMR7144 | E-infra |
| traductome_v3 | J. Morales | traductome, sea urchin | UMR8227 | Bio |
| Reseau metabolique Amoebophrya | L. Guillou | parasite metabolic network | UMR7144 | Bio |
| idealg virus | M. Cock | virus, brown algae | UMR8227 | Bio |
| idealg organelles | M. Cock | organelar genome, brown algea | UMR8227 | Bio |
| phaeo reseau metabolique | G. Markov | metabolic network reconstruction, brown algea | UMR8227 | Bio |
| reseau metabolique E. subulatus and epibiontes | S. Dittami | metabolic network , brown algea, epibiont | UMR8227 | Bio |
| Sabellaria transcriptome | F. Nunes | RNAseq meta transcriptome | IFREMER | Bio |
| marine metagenome Zobellia recruitment | F. Thomas | metagenome recruitement, MAGs | UMR8227 | Bio |
| RNAseq Zobellia | F. Thomas | RNAseq Bacteria | UMR8227 | Bio |
| kordia | C. Jeanthon | genome, bacteria, assembly | UMR7144 | Bio |
| convergAnt | F. Delsuc | genome assembly | CNRS Montpellier | E-infra |
| Alvinella annotation | C. Thomas Bulle | RNAseq annotation | UMR7144 | Bio |
| ADNenv_Poisson | F. Viard | environmental DNA, fish | UMR7144 | Bio |
| ESPRITS | A. Leduc | RNAseq, protontherapy | Caen University | Bio |
| Lupin | G. Dubrulle | RNAseq pathogens | LUBEM UBO | Bio |
| Roskobaz | L. Garczarek, C. Jeanthon, L. Guillou | Marqueurs, Cyanobase, PR2, Micrhode, PhytoRef | UMR7144 | Dev |
| Phytobs data services | M. Lemoine, P. Claquin | long-term follow-up, phytoplankton, data portal, national observation service | IFREMER / CNRS / Universities | Dev |
| Phaeoexplorer data integration ecto | M. Cock | Brown algae, data integration, JBrowse, blast | UMR8227 | E-infra |
| Phaeoexplorer metabolic networks | M. Cock, G. Markov | Brown algae, metbolic network | UMR8227 | Bio |
| SequenceServer | E. Corre | BLAST, SequenceServer tool | FR2424 | E-infra |
| EOSC-Life D4 | J.K Hériché | Galaxy, Conda, Docker | EOSC-Life WP2 | E-infra |
"Mini-projets" 2018
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| w4m_xcms3 | G. Le Corguillé | W4M | ABiMS | E-infra |
| virus_guinardia | L. Arsenieff | assemblage, génome, virus | UMR7144 | Bio |
| w4m_vizu | G. Le Corguillé | W4M, visualisation, interactivité | ABiMS | E-infra |
| endokelp | C. Leblanc | RNAseq, assemblage, annotation, DE | UMR8227 | Bio |
| SarDiv | F. Viard | Sargassum, diversité, RNAseq, assemblages, annotation, polymorphisme | UMR7144 | Bio |
| Shiny-ecto | M. Cock | Shiny R visualisation | UMR8227 | E-infra |
| Shiny-Vaulot | D. Vaulot | Shiny R visualisation | UMR7144 | E-infra |
| génome Alvinella | D. Jollivet | assemblage, génome | UMR7144 | Bio |
| génome Loripes | A. Tanguy | assemblage, génome | UMR7144 | Bio |
| sacculine Taïwan | J-Y. Toullec | assemblage, transcriptome | UMR7144 | Bio |
| phylotunicata | P. Simion | phylogeny | NAMUR LEGE | E-infra |
| MetDB | E.Corre / E.Pelletier | BAse de référence de transcriptome de micro eucaryotes marins | FR2424/CEA | Bio |
"Mini-projets" 2017
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Inventaires v3 | C. Houbin | observation, inventaires | FR2424 | Dev |
| Chondrus_annot_v2 | J. Collen | IdeAlg, Genome, Chondrus, Genomique | UMR7139 | Bio |
| ChondrusDB_v2 | J. Collen | IdeAlg, Genome, Chondrus, Jbrowse/Apollo | UMR7139 | E-infra |
| Quercus | J.-P. Mevy | RNAseq de novo, Quercus, adaptation | IMBE | Bio |
| DuckLiver | C. Diot | RNAseq de novo, Canard, hybrides, adaptation | INRA Saint Gilles | Bio |
| Transition du système de management de la qualité en ISO9001 v2015 | E. Corre | ISO 9001:2015, qualité, certification | ABiMS | Mngt |
| Galaxy4MetaB | E. Corre | Frogs, obitool, qiime, mothur | ABiMS | E-infra |
| CBM V4 | N. Guyard | Cahiers de Biologie Marine, informatique documentaire | COMEDIS | Dev |
| Sepia_v6 | J. Henry | RNAseq de novo | Univ. de Caen | Bio |
| Codivir | J.-M. Escoubas | Virome de l’hémolymphe, Métagénomique, Microbiologie environnementale, Taxonomie virale | Univ. Montpellier | Bio |
| Vibalgo | A.Rahmani | meta transcriptome, palourde, vibrio | LEMAR (Brest) | Bio |
| Aquanis | F. Viard | metabarcoding, plancton | UMR7144 | Bio |
| Sepia_v7 | J. Henry | sepia officinalis rnaseq | Univ. de Caen | Bio |
| Algabact | S. Dittami, F. Thomas | IdeAlg, Genome assembly, Alga-associated bacteria, MiSeq | UMR8227 | Bio |
| Branchinecta | M. Gonzalez | RnaSeq, branchinecta | Chilean Antarctic Institute | Bio |
| Pterois v2 | C. Gaudin | Transcripome, Pterois | UMR Borea Caen | Bio |
| aLFF | S. Dittami | E. subulatus metagenome and transcriptome | UMR8227 | Bio |
| Wolbachia | C. Daguin, T. Broquet | Wolbachia, jaera | UMR7144 | Bio |
| Metabarcode Microbiome | S. Buffet-Bataillon | Barecoding, microbiome humain | CHU Rennes | E-infra |
| BioMaj3 | G. Le Corguillé | Galaxy, base de données de référence, BioMAJ | ABiMS | E-infra |
| Benthobs | C. Houbin | Bases de données, observation, suivis de peuplement, abondances, mesures complémentaires | FR2424 | Dev |
| ASTAN-IP | T. Cariou | Bases de données, observation, instrumentation, paramètres physico-chimiques | FR2424 | Dev |
"Mini-projets" 2016
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Site Web Formation | C. Cabresin | enseignement, site web, formulaire, drupal | FR2424 | E-infra |
| PhaeoNO | E. Marechal | RNA-seq | CEA/UMR 5168 | Bio |
| AM1 | M. Jebhar | assemblage genome archaea | IUEM | Bio |
| Artemia | C. Lejeusne | RNA-seq | UMR7144 | Bio |
| SIP-LIEC | F. Thomas | RNA-seq | UMR8227 | Bio |
| Heterotis | J. Henry | RNA-seq | BOREA Caen | Bio |
| Sacculine | J. Henry | RNA-seq | BOREA Caen | Bio |
| Meta-transcriptome Mucus Truite | V. Cornet | RNA-seq | Univ. Namur | Bio |
| CBM-DOI | N. Guyard | DOI, CBM | FR2424 | Dev |
| MucorDB2 | J.L. Jany, L. Meslet | Apollo, annotation experte, Mucor, champignon, fromage | LUBEM (UBO) | E-infra |
| Posidonie | Y. Ferandin | RNA-seq | Banyuls | Bio |
| AdaptSearch | D. Jollivet | Orthologues, detection, Galaxy | UMR7144 | E-infra |
| W4M_IPO | Y. Guitton | W4M,Galaxy | LABERCA | E-infra |
"Mini-projets" 2015
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Caractérisation du biofilm formé dans les serres de production de tomates | Roby | Metabarcoding, MiSeq | Vegenov | Bio |
| SBEMET : Extraction et visualisation des données météo en temps réel | Cariou | hf, meteo, bdd, observation, web | FR2424 | Dev |
| Galaxy4SNiPlay V2 | A. Dereeper | SNP, diversity genetic, visualization, haplotypes, Galaxy | CIRAD - Southgreen platform | E-Infra |
| REPET Galaxy V2 | O. Inizan | transposable elements, REPET, Galaxy, IFB | URGI Versailles - Genome Analysis | E-infra |
| Oasearch V2 | D. Jollivet | Orthologues, detection | UMR7144 | E-infra |
| SEPIOM | L.Bonnaud | Transcripome Sepia | UMR Borea Paris | Bio |
| Sepia V4 | J. Henry C. Gaudin | Transcripome Sepia | UMR Borea Caen | Bio |
| Labrax | J. Henry C. Gaudin | Transcripome Labrax | UMR Borea Caen | Bio |
| Pecten | J. Henry C. Gaudin | Transcripome Pecten | UMR Borea Caen | Bio |
| Pterois | J. Henry C. Gaudin | Transcripome Pterois | UMR Borea Caen | Bio |
| CALYpSO | A.C. Baudoux | Metavirome | UMR7144 | Bio |
| Polar Poux | J.Y. Toullec M. Gonzalez | Transcripome isopde | UMR7144 - INACH Chili | Bio |
| Polar Urchin | J.Y. Toullec M. Gonzalez | Transcripome urchin | UMR7144 - INACH Chili | Bio |
| Mucor | J.L.Jany L.Cladiere | Genome Mucor | ESIAB-UBO | Bio |
| MicroMar | C. Jeanthon | Transcriptome diatome | UMR7144 | Bio |
| Radiolaria | F. Not | Transcriptome radiolaire | UMR7144 | Bio |
| Tr_C.virginica | B.Allam | Transcriptome | Stony Brook University, NY | Bio |
| Tr_Diatom | F. Vincent | Transcriptome | ENS Paris | Bio |
| ectocarpus epibiont | P. Potin | Metabarcode | UMR8227 | Bio |
| StartCorrector | L. Garczarek F. Partensky | Cyanorak | UMR7144 | Dev |
| synProDB | L. Garczarek F. Partensky | jbrowse, synechococcus | UMR7144 | E-infra |
| Assemblage de génomes d'Archea | S. Lharidon | Assembly, ION Torrent, Illumina | Univ Brest | Bio |
| STAR | F. Nunes | rnaseq, met transcriptomique | LEBAM/IFREMER | Bio |
"Mini-projets" 2014
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Renkan V2 | F. Not | UMR7144 | Dev | |
| Inventaires V2 | C. Houbin | FR2424 | Dev | |
| Wisca Galaxy | G.Farrant | Galaxy, scaffolding, genome | UMR7144 | E-infra |
| Galaxy4SNiPlay | A. Dereeper | SNP, diversity genetic, visualization, haplotypes, Galaxy | CIRAD - Southgreen platform | E-infra |
| Galaxy4Blast | E. Corre | Blast, workflow, uniq acces, authentification, visualization, automatisation | FR2424 | E-infra |
| Galaxy4Genomer | G. Le Corguillé | Archive, client link, Galaxy, data traitement, exportation | FR2424 | E-infra |
| SClims | G. Michel | Tool, web, history, gene, sequence | UMR8227 | Dev |
| Assemblage de génomes de Flavobactéries marines | G. Michel | Flavobactéries, MiSeq | UMR8227 | Bio |
| Tr_bivalves | J. Henry | Univ Caen | Bio | |
| Tr_Tilapia | J. Henry | Univ Caen | Bio | |
| REPET Galaxy | O. Inizan | transposable elements, REPET, Galaxy, IFB | URGI Versailles - Genome Analysis | E-infra |
| COLMAR | P.J. Lopez | Bio-constructions, Polychaetes, Annélides, Espèce ingénieur, Evolution | UMR BOREA | Bio |
| TransAlg V2 | S. Dittami | URM8227 | Bio | |
| Workflow4Metabo_ThalassOMICS | Y. Guitton | Galaxy, Metabolomique, Workflow | MMS EA2160 - ThalassOMICS | E-infra |
| Galaxy4NMR | G. Le Corguillé | RMN / métabolomique / Analyse Statistique / Worflow / Galaxy | CEISAM - UMR 6230 / SPCMIB - UMR 5068 | E-infra |
| Oasearch | D. Jollivet | Orthologues, detection | UMR7144 | E-infra |
| Traductome V2 | J. Morales | polysomes, traductome, RNA-binding proteins, RNA-seq DE, Paracentrotus lividus | UMR 8227 | Bio |
| Photothèque SMO | W. Thomas | Photos, Vidéos, Diffusion, Organisation et Sécurité | FR2424 | E-infra |
| Poursuite de l’intégration des données HF dans le « HF data repository » | Cariou | Meteo data | UMR7144 | Dev |
| Mucoroscope | J.L. Jany L. Meslet | Analyse RNAseq | LUBEM | Bio |
| MucorDB | J.L. Jany L. Meslet | annotation, mucor, blast | LUBEM | E-infra |
| Radiolaria-symbiose | F. Not - L. Bitner | Transcriptome holobionte radiolaire | UMR7144 - UPMC | Bio |
"Mini-projets" 2013
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| Hectar V3 | B. Gschloessl | CBGP INRA | E-infra | |
| GISM V2 | L. Leveque | sea trip, planning, workflows | FR2424 | Dev |
| galaxy4resomar | I. Ghaillard | galaxy, statistics, R | RESOMAR | E-infra |
| galaxy4metabarcoding | S. Audic | galaxy, metabarcoding, tara | UMR7144 | E-infra |
| InterEsil | T. Tonon | ectocarpus, transcriptomic, analysis, pipeline, galaxy | UMR7139 | E-infra |
| Ccarn | J. collen | chrondrus statistic analysis, red seaweeds, EST | UMR7139 | Bio |
| chondrusDB | J. Collen | chrondrus, data integration, RNA-seq, annotation | UMR7139 | E-infra |
| ectocarpusDB | M. Cock | ectocarpus, data integration, RNA-seq, annotation | UMR7139 | E-infra |
| Marine Model Organism DB | C. Caron | data integration, EMBRC, galaxy, marine genome | EMBRC-France | Dev |
| PhaeBact | T. Tonon | abiotic stress, functional genomic, macroseaweeds | UMR7139 | Bio |
| SulfAtlas | G. Michel | polysaccharides, sulfatases, bacteria, seaweeds | UMR7139 | Dev |
| Ectocarpus shoremap | S. Coelho | Bio | ||
| Ectocarpus sexseaweed | S. Coelho | Bio | ||
| Proteome discover | Delage | Analyse, protéomique | UMR8227 | Bio |
| Sepia theb | J. Henry | Univ Caen | Bio | |
| Pleurodèles | J.Y. Sire | Univ Caen | Bio | |
| WiseScaffolder | G. Farrant | UMR7144 | Dev | |
| SALGENE | P.J. Lopez | UMR BOREA | Bio | |
| Workflow4MetaboCorsaire | A. Gravot | Galaxy, Métabolomique, workflow, xcms, statistiques, Drupal | Univ Rennes - P2M2 | E-infra |
| Mercenaria RNAseq | B. Allam | Stony Brook University, NY | Bio | |
| Analyse seq ADN | S. Dumanoir | modèles pré-cliniques, mutations, sélection | IRCM - INSERM U896 | E-infra |
| myTrash | C. Caron | FR2424 | E-infra |
"Mini-projets" 2012
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| CBM V2 | D. Davoult / N. Guyard | marine biological notebook, publications, archiving | FR2424 | Dev |
| ectoTilling | M. Cock | mapping, SNP, | UMR7139 | Bio |
| RmetaT | MJ Delmas | (meta)-transcriptomic, pico eukaryotes, cocolithophore, assembly, Tara. | UMR7144/ EPPO | Bio |
| TransAlg | T. Tonon | UMR 7139 / IDEALG | Bio | |
| Reprosep | J. Henry | Sepia, Penaeus vannamei , RNASeq, main nervous system, reproduction | CNRS INEE FRE 3484 BioMEA / Université de Caen | Bio |
| Esil SNP | Mark Cock | Ectocarpus, SNP | UMR 7139 | Bio |
| uORF2 | Julia Morales | UMR 7150 | Bio | |
| IsochrysisI | M. Garnier, B. Saint-Jean | transcriptomic , RNAseq | IFREMER Nantes | Bio |
| IsochrysisK | M. Garnier, B. Saint-Jean | transcriptomic , RNAseq | IFREMER Nantes | Bio |
| Etude de la flore totale de l’éponge Asbestopluma hypogea | S. Dupont | metagenomic | MNHN | Bio |
| Comparaison des séquences et des activités enzymatiques des désaturases FADS1 et FADS2 | S. Mazan | pipeline, protein, family | UMR 7150 / UMR 7139 / IFREMER | Bio |
| Scyliorhinus canicula genome project | S. Mazan | Annotation, genome, transcriptome | UMR7150 consortium GenoShark | Bio |
| Annotation d'un transcriptome de mâchoire de crocodile | Jean-Yves Sire | annotation, transcriptome | UMR7138 / UPMC | Bio |
| Analyses Phylogénétiques des familles de protéines CDK et Cyclines | P. Colas | phylogeny | USR3151 | Bio |
| ARRAYSyn | L. Garczarek | picocyanobacteria, "puce à ADN", Bioconductor | UMR7144 | Bio |
| e-infrastructure metrology | C. Caron | metrology, flow analysis, optimization | FR 2424 | Dev |
| Cahiers de Biologie Marine V2 | D. Davoult | marine biological notebook, publications | FR 2424 | Dev |
| Renkan | F. Not | collection, plancton, protist | UMR7144 | Dev |
| GISM V1 | L. Leveque | sea trip, planification, workflows | FR2424 | Dev |
| Inventaire | C. Houbin | FR2424 | Dev |
"Mini-projets" 2011
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| RNA Seq Laminaria Lessonia | Catherine Leblanc | RNAseq, brown algae, L. digitata, L. nigressens, Herbivory | UMR 7139 | Bio |
| RNAseq Bathymodiolus azoricus | Arnaud Tanguy | RNAseq, mollus | UMR 7144 | Bio |
| Criblage du facteur de régulation 4E-interacting protein chez les cnidaires | Julia Morales | Sea urchin, cnidaires, regulation,transcription | UMR 7150 | Bio |
| ATK - Polysomes P. lividus | Julia Morales | Sea urchin ,traductome | UMR 7150 | Bio |
| Analyse transcriptomique virus vs Emiliana huxleyi | Colomban de Vargas | Viral infection, micro-arrays, coccolithophores foraminifers | UMR 7144 | Bio |
| Ectobacter | Thierry Tonon | phylogeny, blast, Ectocarpus | UMR 7139 | Bio |
| IMM-ORO array experiment | Mark Cock | Life cycle regulation, brown algae, mutant, transcriptomic, micro-arrays | UMR 7139 | Bio |
| RNASeq Ectocarpus | Susana Coehlo | RNAseq, brown algae, transcriptomic, sexual differentiation | UMR 7139 | Bio |
| Euphausia | Jean-Yves Toullec | RNAseq, Euphosia crystallorophias, temperature effect, kril | UMR 7144 | Bio |
| Upstream ORF search on urchin genome | Julia Morales | µORF, screening, Expression regulation, | UMR 7150 | Bio |
| RNAseq Perkinsus marinus | B. Allam, Stony Brook | RNAseq , parasite , oyster, Perkinsus marinus | UMR 7144 University. NY. USA | Bio |
| SSR Serpula lacrymans | Gaetan Le Floch | SSR screening, biodiversity, microbial ecology | ESMISAB Brest | Bio |
| I² (Inventaires x Images) | Céline Houbin | flore et faune marine, inventaire, bases de données, images | FR 2424 | Dev |
| RENKAN | Fabrice Not | sample database, images, web interface | UMR 7144 | Dev |
| Portail outils | Christophe Caron | tools, platform, directory, database | FR 2424 | Dev |
| Cahiers de Biologie Marine | D. Davoult | marine biology, web, database, review | FR 2424 | Dev |
| Formulaire accueil scientifique | Cécile Cabresin | workflow, accueil scientifique, ASSEMBLE | FR 2424 | Dev |
"Mini-projets" 2010
| Project | Scientific supervisor | Key words | Collaborator | Type |
|---|---|---|---|---|
| P. lividus polysome transcriptome | Julia Morales | RNAseq, sea urchin | UMR 7150 | Bio |
| FerryBox Database | Pascal Morin | ferry, transect, database, physical/chemical parameters | UMR 7144 | Dev |
| Chondrus crispus genome annotation | Catherine Boyen / Jonas Collen | Full genome , genetic model, annotation,.red algae | UMR 7139 & consortium | Bio |
| Picoeucaryotes | Daniel Vaulot | diversity analysis, metagenome, NGS, flow cytometry sorting, picoplancton | UMR 7144 | Bio |
Accomplished projects
- CapExBio (2008-2010)
- MIGADI (2008-2010)
- This project aims at developping an innovating bioinformatic environment dedicated to genome annotation and microbial proteom. It is based on current resources from both ABiMS and MIGALE platforms, and on several research programs from the MIG (MOSAIC) and MIA-J (PARIS) units. The integration process is based on the deployment of web service technologies. This project was financed by the ANR PTFV 2007. An oral presentation (Web Services for MIcrobial Genome Annotation using Data Integration) was given in 2010 at the JOBIM convention.
