You're a trainer and you're looking for a solution to host your training sessions for variable durations?
IFB supports training (university courses, scientific schools, continuing education, workshops, hackathons, etc.) by providing a bioinformatics and IT infrastructure with adapted tools. Whether by setting up dedicated virtual machines on Biosphere (the IFB's federation of clouds) or by creating shared workspaces on the IFB's Core-cluster, trainers can access computing resources and specific bioinformatics environments for their students.
Applications procedures are as follows :
The IFB cluster can host training sessions for variable durations (from one-day workshops to training sessions lasting several months)
The training can be done :
We do not recommend the use of the rstudio.cluster.france-bioinformatique.fr instance for training because the resources of this server are limited. Instead, we recommend to use Rstudio from Jupyterhub, because it runs jobs on the cluster and you benefit from the computing power of the whole cluster rather than just one server.
We must have all the information related to the training (tools to install, student accounts to create, reservation to create etc..) at least 15 days before the beginning of the training.
To ensure the best possible experience, we ask instructors to contact us via email.
We then ask instructors to fill out a form, "the service request", which allows us to gather instructors' needs for tools, banks and student accounts.
Shared project folders are created to allow instructors, tutors and trainees to work in identical, private workspaces.
We follow a yynn_acromy-of-training nomenclature for training projects.
The project is then accessible on the cluster in /shared/projects/, for example /shared/projects/2301_etbii
Finally, a customized software environment is created (Conda environment), which guarantees the reproducibility of the results, the reuse of the learning material for other trainings and the portability of the whole software environment.
The service request allows you to request the installation of particular banks or tools if they are not yet available on the cluster.
We ask the trainers to have a nominative account
For student accounts we recommend:
The IFB Core Cluster team can create generic accounts for you.
For nominative accounts, students can request an account on https://my.cluster.france-bioinformatique.fr/ by specifying the name of the project used for the training. Nominal accounts also allow students to continue to use the cluster after the courses.
The trainer as owner of the project can then add the students to the project. If this solution is not possible, we can also create student accounts in batch from a list.
Note that we ask all our users to provide an academic address, not a gmail or outlook address ....
If you need particular sub-folders in the project, then you must explain your needs in the service request.
For example, you can have a data sub-folder, which will be read-only for students. Or a sub-project per student, which will be read-only for the other students but write-only for the student and the instructor.
Once your needs are explained in the service request, we will set up these subfolders for you.
We can reserve compute nodes for your training. A reservation is useful in the case of short courses such as PT, where it is crucial not to have latency or performance problems.
To use the reservation the learner will have to execute the command: `module load training/<training name>`.
The https://usegalaxy.fr instance uses its own authentication system, separate from the cluster.
It is not currently possible to create anonymous accounts but note that account openings are fast on usegalaxy.fr and do not require any validation step.
Training requests can be made directly on https://usegalaxy.fr/tiaas