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

With IFB-Biosphere, you get:

• 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, available with an one-click deployment from the RAINBio catalogue

  • Infrastructure as Code: most configurations rely on public git repositories available in Biosphere Commons.

• 8 cloud sites with more than 10,000 vCPU and 40 TB RAM (System status)

  • High-availability thanks to the different sites usable equally.

• Modular cloud environments:

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

• Bring-Your-Own-Tools

  • Admin rights in the VM (all apps).
  • Deploy with your own container image (some apps).
  • Configure some apps with your own git repository (Infrastructure as Code).

• Useful public biological reference databases

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

  • Training events, university courses, scientific schools, workshops, hackathons.
  • Scientific projects.

Biosphere Portal

The Biosphere portal provides high-level cloud interfaces:

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

Bioinformatics Virtual Research Environments

The Biosphere bioinformatics apps are available in the RAINBio catalogue and provide scientists with pre-defined thematics environments, base appliances, web-based and desktop appliances. In case no 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):
  • including python-pip, docker (docker-compose & swarm), ansible, conda (bioconda and R channels).
• Workflow environments (BioPipes):
  • including Nextflow, SnakeMake, CWLtool, conda + Bioconda, Docker + Docker-compose.
• Rstudio server (incl. Bioconductor).
• R Shiny apps (Bring your own Rshiny app).
• Jupyter notebooks (Kernels Julia, Python & R).
• Graphical Remote Linux Desktop (XFCE4 + X2Go).
  • Examples: Bioimage (Fiji/Icy), Cytoscape...

Cloud Sites

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