The homepage of the Bio-IT project, the portal provides.
- information on the project, EMBL Centres, and Bio-IT initiatives
- links to the course materials curated for various topics, including programming, working on the command line, and cluster usage
- course and event listings and registration
- profiles of members of the Bio-IT community
- unified list of links to sites, pages, and resources related to computational biology at EMBL
Most information regarding general computing resources and procedures at EMBL can be found on the intranet pages of the IT Services Group. See intranet.embl.de/it_services/ for links to pages covering
- getting IT support
- a quick-start guide to EMBL systems for newcomers
- user accounts
- network access
- data sharing
- using the EMBL calendar
- data storage and filesystems
- compute resources and the HPC cluster
- policies and best practice
We particularly recommend that newcomers to computational biology at EMBL make themselves familiar with the sections on compute resources and data storage.
Unit-Specific Computational Support
SCB, GB, and CBB unit members enjoy the services of dedicated support staff. The type of support that they provide may vary depend on the presence/absence of dedicated hardware and software. For further information, please check the IT services intranet.
GBCS provides a webpage of information for newcomers to GB (New@GB), which contains information and advice relevent to all EMBL members, regardless of their unit.
EMBL Chat: chat.embl.org
Members of the Bio-IT community developed a workplace chat system, chat.embl.org, which can be used for instant messaging one-to-one, in groups/teams, and in wider channels. The system is accessible inside the EMBL network. Join the Bio-IT channel for updates on project activities and events, and to ask questions of Bio-IT community members. Some of the other channels of interest to the Bio-IT community are:
- Python - For general discussions around Python Programming and EPUG sessions
- R & Statistics - Discussion of anything related to R programming and emblr
- Coding Club - a great place to learn and discuss programming stuff
- Cluster - useful for anyone using EMBL's HPC facilities
- GBCS - for questions/discussion regarding GBCS resources & services
Git at EMBL: git.embl.de
Version Control with
git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. A version control application keeps track of all the changes that you do in the files of your project. Every time you make changes to files of a project, you can push those changes to a repository. Other developers can pull your changes from the repository and continue to work with the improvements that you added to the project files.
If you are going to write your own programs/scripts, we strongly recommend that you use
git to enhance reproducible research. Specifically, we recommend that you add a repository for your scripts in a project-specific manner.
The Bio-IT community maintains a GitLab system, git.embl.de, for remotely hosting projects that are under version control with
git. This system is served and stored from a local VM, which helps to ensure security and privacy of data and intellectual property. GitLab has many powerful features to help manage your projects and collaborate with other developers. You can log in with your standard EMBL credentials, and accounts can be created for external users on request from a EMBL member.
Bio-IT runs courses and maintains training materials for effective use of
git and GitLab. We also recommend the Software Carpentry training materials (software-carpentry.org/lessons/) for an introduction to version control. For common practices and further help, ask Bio-IT or other people in your group who work with it!
Bio-IT also maintains a continuous integration server, incorporated with
git.embl.de, which provides an environment for setting up automated builds and tests of software projects managed through the GitLab system. For more information, check out the GitLabCI documentation (about.gitlab.com/gitlab-ci/) and speak to the Git Admins.
Collaborative notes: pad.bio-it.embl.de
Conduct your surveys on this platform hosted at EMBL and ran by Bio-IT, based on the Open Source project LimeSurvey. To use it, you need only to login with your EMBL credentials.
EMBL cluster system
The EMBL HPC Cluster is a shared resource which provides access to more than 4000 CPUs (in total more than 8000 job slots) for scientific computing at EMBL.
EMBL IT Services provide a number of software packages to EMBL users via site-wide or EMBL- wide license agreements with the software providers. For a list, see intranet.embl.de/it_services/services/software. Find out more about how to use the system by reading the cluster wiki at wiki.embl.de/cluster/ looking at the training materials available on the Bio-IT portal.
If you need specific software, first check if it is already available, the most commonly used software for our purposes is already installed. Importantly, always include the specific version when executing a particular program to increase reproducibility. If the tool that you would like to use is not available in the modules system, follow this useful guide from GBCS.
Useful computational resources for newcomers
- RStudio: rstudio.embl.de - RStudio Server Pro maintained by GBCS. An RStudio FAQ can be found here and a support channel exists in the EMBL Chat.
- Jupyter Hub: jupyterhub.embl.de - JupyterHub server maintained by IT and Bio-IT (with CPU and GPU access).
- Bioimage ANalysis Desktop: band.embl.de - A Virtual Desktop packed with a broad selection of image analysis tools.
- Galaxy: galaxy.embl.de - Local Galaxy server maintained by GBCS. The Galaxy FAQ can be found here.
- Shiny server - Work in progress project to host Shiny applications. Shiny is an R package that makes it easy to build interactive web apps straight from R.