Welcome on Biosphere, IFB Cloud for Life Sciences

French Institute of Bioinformatics (IFB) provides life scientists with a federation of clouds, Biosphere, and bioinformatics cloud services to analyze life science data. Biosphere is used for scientific production in the life sciences, developments, and to support events like scientific training sessions, university courses, hackathons or workshops.

Biosphere Features

  • A unified user portal (Biosphere portal) to deploy all bioinformatics environments on all clouds

    • Single sign-on, with your academic credentials (Sign in).
  • Pre-defined bioinformatics environments, ready to deploy in one-click from the RAINBio catalogue

    • Infrastructure as Code: most configurations rely on public git repositories available in Biosphere Commons.
  • 8 cloud sites with 8,400 vCPU and 40 TB RAM (System status)

    • High-availability provided by the 8 sites available and usable equally.
  • Modular cloud environments:

    • Single virtual machine (VM) to bunch of VMs.
    • Usual VMs of up to 64 vCPUs-250 GB RAM.
    • BigMemory VMs with up to 3 TB RAM.
    • HighFrequency VMs with up to 3.8GHz vCPU.
    • ManyCores VMs with up to 255 vCPUs in a VM
  • Bring-Your-Own-Tools

    • You have the admin rights in your VM (all apps).
    • You can deploy your own container image (RtudioWeb/Shiny, JupyterLab).
    • You can configure your app with your own git repository (Infrastructure as Code).
  • Useful public biological reference databases

  • On-demand resources (CPU, RAM, storage, IFB experts) to support:

Biosphere Portal

The Biosphere portal provides high-level cloud interfaces:

  • The RAINBio catalogue to select the bioinformatics cloud appliances for your analysis.
  • The dashboard to manage your cloud deployments with single virtual machines (VM) or complex applications with multiple VMs.
  • The data center showing the public reference databases available in the IFB's clouds.

Bioinformatics Virtual Research Environments

The Biosphere bioinformatics apps are referenced in the RAINBio catalogue and provide scientists with pre-defined bioinformatics environments, base appliances, web-based and desktop appliances. In case none of the available apps is fully satisfying your needs, you have the administration rights (sudo) in your environment to tune the installation of bioinformatics tools and configurations. You can also deploy some apps with your own container image or configure the deployment with your own git repository (Infrastructure as Code).

Domain-specific environments:

  • Genomics (assembly, mapping, regulation, expression profiling, annotation, visualization, etc).
  • Bioimaging (ImageJ-Fiji, Icy, OMERO).
  • Metabolic pathway, metabolomics.
  • Microbial ecology.
  • etc

Generic apps:

  • Linux distributions (Ubuntu, Debian, CentOS, Rocky Linux):
    • including python-pip, docker (docker-compose & swarm), ansible, conda/mamba (bioconda and R channels).
  • Workflow environments (BioPipes):
    • including Nextflow, SnakeMake, CWLtool, conda + Bioconda, Docker + Docker-compose.
  • Rstudio web server (incl. Bioconductor).
  • R Shiny apps (Bring your own Rshiny app).
  • Jupyter notebooks (with standard kernels Julia, Python & R).
  • Graphical Remote Linux Desktop (XFCE4 + X2Go).
    • App Bioimage (Fiji/Icy), Cytoscape, ETBII.

Cloud Sites

Biosphere relies on interconnected IT infrastructures of IFB’s platforms (details):

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