RAINBio - Bioinformatics cloud appliances

Catalog of bioinformatics cloud appliances, which you can browse and filter according to the predefined keywords of the EDAM ontology or with natural language.

Askomics
 

 AskOmics
 Data integration and warehousing, Data visualisation
 olivier sallou GenOuest
Bacterial Genomics
 

 HMMER, Insygth, SGE - GridEngine, Ubuntu, Web interface
 Protein folds and structural domains, Sequence comparison, Sequence composition, complexity and repeats, Sequence sites, features and motifs, Genome annotation, Genomics, Informatics, Comparative genomics, Data visualisation, Function analysis, Gene and protein families
 Thomas Lacroix, StatInfOmics
Bioimage
 

 Bureau virtuel, Icy, ImageJ-Fiji, X2Go, XFCE
 Informatics, Data visualisation, Imaging
 Support Cloud IFB
BioPipes
 

 bioconda, cwltool, Docker, Nextflow, Snakemake
 Informatics, Bioinformatics, Workflows
 Support Cloud IFB
bistar
 

 bioconda, bowtie2, FastQC, Snakemake
 Bioinformatics, Genomics, Mapping, Sequence alignment, Data quality management, Sequencing, Workflows, Sequence analysis
 aurelien beliard ICM-ICONICS
CentOS 7
 

 Ansible, bioconda, Docker
 Informatics, Bioinformatics
 Support Cloud IFB
Cytoscape
 

 Bureau virtuel, Cytoscape, X2Go, XFCE
 Bioinformatics, Data visualisation, Molecular interactions, pathways and networks, Informatics
 Support Cloud IFB
Debian 10
 

 Ansible, bioconda, Docker
 Bioinformatics, Informatics
 Support Cloud IFB
Debian 9
 

 Ansible, bioconda, Docker
 Bioinformatics, Informatics
 Support Cloud IFB
DRomics
 

 Bioconductor, DESeq2, DRomics, R - base, Shiny
 Bioinformatics, Computational biology, Data management, Data visualisation, Data architecture, analysis and design, Transcriptomics, Statistics and probability
 Christophe Blanchet IFB-core
EBAME19-Anvio
 

 Anvi'o
 Genomics, Omics, Metagenomics, Phylogenomics, Transcriptomics
 Lois Maignien, EBAME organization
EBAME19-MarMicrobiome
 

 MMseqs2, R - base, RStudio, R - tidyverse
 Data architecture, analysis and design, Sequence analysis, Sequence assembly, Statistics and probability, Data visualisation
 Lois Maignien, EBAME organization
EBAME19-meta3C
 

 bioPython, Matplotlib, Numpy, pandas, pysam, Scipy
 Phylogenetics, Population genetics, Protein structure analysis, Sequence analysis, Informatics, Genomics, Mapping, Sequencing
 Lois Maignien, EBAME organization
formation_CIRI
 

 DESeq2, FastQC, HISAT2, RStudio, Trimmomatic
 Transcriptomics, Whole genome sequencing, Data architecture, analysis and design, Data visualisation, Data quality management, Sequencing, RNA-Seq, Genomics, Mapping, Sequence analysis
 Marie CARIOU CIRI
formation LBBE-NGS 2019
 

 ABySS, BEDTools, Bioconductor, BUSCO, FastQC, HISAT2, IGV - Integrative Genomics Viewer, KisSplice, KmerGenie, pysam, UrQt
 Bioinformatics, Computational biology, Data management, Statistics and probability, Transcriptomics, Whole genome sequencing, RNA-Seq, Sequence analysis, Data quality management, Mapping, Sequencing, Sequence assembly, Genomics
 Stephane Delmotte COURS LBBE NGS 2018
Galaxy
 

 bioconda, Docker, Galaxy portal
 Informatics, Bioinformatics, Comparative genomics, Functional genomics, Genomics, Sequence assembly, Whole genome sequencing
 Support Cloud IFB
Genopole2019 GenomeVar
 

 bcftools, BEDTools, BWA, Canvas, FastQC, GATK, IGV - Integrative Genomics Viewer, IRSOM, Matplotlib, Numpy, pandas, plotnine, SAMtools, TensorFlow
 SNP, Data quality management, Informatics, Genetic variation, Genotyping experiment, GWAS study, Mapping, Applied mathematics, Data visualisation, DNA polymorphism, Genomics, Sequencing, Machine learning, Sequence analysis
 Vincent MEYER, CNRGH, CEA
Genopole2019 Stats
 

 DESeq2, RStudio, R - tidyverse, Web interface
 Transcriptomics, Data architecture, analysis and design, Data visualisation
 Christophe AMBROISE, Université d’Evry-Val d’Essonne
integron_finder
 

 HMMER, Infernal, prodigal
 Protein folds and structural domains, Sequence comparison, Sequence composition, complexity and repeats, Sequence sites, features and motifs, Sequence analysis
 Bertrand Néron C3BI
Jupyter
 

 Julia, Jupyter, R - base
 Computer science, Mathematics, Data architecture, analysis and design, Data visualisation, Statistics and probability
 Support Cloud IFB
Kissplice-training
 

 Bioconductor, KisSplice, STAR
 Bioinformatics, Computational biology, Data management, Statistics and probability, Sequence assembly, Transcriptomics, RNA-Seq
 Stephane Delmotte stephane.delmotte@univ-lyon1.fr
lbbe-amc
 

 
 
 Stephane Delmotte LBBE
LBMC Unix 2020
 

 
 
 Laurent Modolo laurent.modolo@ens-lyon.fr
M2BINF UCBL
 

 ete3, Jupyter
 Mathematics, Statistics and probability, Data visualisation, Phylogenomics, Data architecture, analysis and design
 Guillaume Launay, Université Claude Bernard Lyon 1 (Environnement pédagogique)
Mondrian
 

 Mondrian, R - base, Shiny
 Data architecture, analysis and design, Data visualisation, Statistics and probability
 Christophe Blanchet IFB-core
NGSanalysisJupyter
 

 BEDTools, BWA, Jupyter, SAMtools
 Data architecture, analysis and design, Mathematics, Statistics and probability, Sequence analysis, Bioinformatics, DNA polymorphism, DNA structural variation, Genomics, Mapping
 Francois Sabot DIADE
NGSgenotyp
 

 bioPython, bowtie2, cap3, ete3, FastQC, Matplotlib, muscle, Numpy, phyml, pysam, python, QUAST, SAMtools, Scipy, SPAdes, sratoolkit, yass
 Phylogenetics, Protein structure analysis, Data visualisation, Phylogenomics, Phylogeny, Mapping, Sequence analysis, Genomics, Sequencing, Informatics, Bioinformatics, Genotype and phenotype, Population genomics, Population genetics, Sequence assembly
 Mathieu GENETE, EEP CNRS UMR8198
NMRProcFlow
 

 NMRProcFlow
 Metabolomics
 Daniel Jacob INRA
PlaScope
 

 Centrifuge, PlaScope, SPAdes
 Metagenomics, Sequence analysis, Genomics, Microbiology, Sequence assembly
 Mathieu Dubois email
REPET
 

 Repet
 Bioinformatics
 Hadi Quesneville URGI
Rstudio Génomique
 

 DESeq2, MMseqs2, RStudio, Web interface
 Transcriptomics, Sequence analysis, Sequence assembly, Data architecture, analysis and design, Data visualisation
 Stephane Delmotte
RStudio Server
 

 Bioconductor, HDF5, R - base, RStudio, Web interface
 Mathematics, Bioinformatics, Computational biology, Computer science, Data architecture, analysis and design, Data management, Statistics and probability, Data visualisation
 Support Cloud IFB
SGE cluster
 

 SGE - GridEngine, Ubuntu
 Informatics
 Support Cloud IFB
Shiny
 

 R - base, R - tidyverse, Shiny, Web interface
 Data architecture, analysis and design, Bioinformatics, Data visualisation, Statistics and probability
 Support Cloud IFB
Ubuntu 18.04
 

 Ansible, bioconda, Docker
 Bioinformatics, Informatics
 Support Cloud IFB
Ubuntu 18.04 Desktop
 

 Ansible, bioconda, Bureau virtuel, Docker, X2Go, XFCE
 Bioinformatics, Informatics
 Support Cloud IFB
Ubuntu 20.04
 

 Ansible, bioconda, Docker
 Bioinformatics
 Support Cloud IFB
Ubuntu 20.04 Desktop
 

 Ansible, bioconda, Bureau virtuel, Docker, X2Go, XFCE
 Informatics, Bioinformatics
 Support Cloud IFB
UE NGS-ENS Lyon
 

 BEDTools, BLAST, Bowtie, bowtie2, Clustal Omega, cmake, DESeq2, FastQC, MACS2, muscle, phyml, R - base, SAMtools, Seaview, Trinity
 Mapping, Sequence alignment, Informatics, Transcriptomics, Data quality management, ChIP-seq, Statistics and probability, Sequence comparison, Sequencing, Phylogeny, Data visualisation, RNA-Seq, Sequence analysis, Genomics
 Carine Rey, Laboratoire de Biologie et Modélisation de la Cellule
WellInverter
 

 python3, Web interface, WellInverter
 Computer science, Bioinformatics, Gene regulation, Transcription factors and regulatory sites
 Hidde de Jong
Note that the color code has no meaning other than being constant for a given appliance.

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