These servers are fully paid for by the Wellcome Trust Centre for Cell Biology and are managed by the bioinformatics core facility.
Accounts are limited to members of WCB and centre collaborators. To request an account please contact the bioinformatics team.
Once your account is active, the following servers can be accessed over the university network or via the VPN service by logging in with your EASE credentials.
bifx-core2.bio.ed.ac.uk (coming soon)
bifx-core3.bio.ed.ac.uk
1Tb RAM
128 dual CPU cores
Command line usage (ssh)
R-Studio: https://bifx-rstudio.bio.ed.ac.uk/
R-Shiny: http://bifx-core3.bio.ed.ac.uk:3838/
Apache web server
For command line access, use the ssh command from a Terminal application in Windows, MacOS and Linux e.g.
ssh -Y username@bifx-core3.bio.ed.ac.ukIf you prefer to use a graphical interface the servers can be accessed via X2Go or with the Windows Remote Desktop application.
X2Go
Remote Desktop
Pre-installed on Windows
RStudio on bifx-core3 can be accessed at https://bifx-rstudio.bio.ed.ac.uk
A Shiny server is available on the university network only at http://bifx-core3.bio.ed.ac.uk:3838
Add your own Shiny Apps to a ShinyApps folder in
your home directory.
Launch these from http://bifx-core3.bio.ed.ac.uk:3838/username/
Data on the server can be accessed over the web (e.g. files, images, html documents, IGV/UCSC tracks). Please contact us for details on how to set this up.
No personal data should be stored on the bifx-* servers. All data should be related to projects associated with the Wellcome Centre unless dispensation has been given by the centre director.
All data on the bifx-* servers can be viewed by members of the bioinformatics core or the centre director.
As the bioinformatics core group has superuser permissions, we can see all data on the server. Instructions on how to access the servers are lodged with the centre director in case of emergency. Therefore they are a de-facto administrator.
Your data can be accessed by your PI on request. No request is needed if the PI has an account on the server and can view your files. The data stored on the servers should only relate to the Wellcome Centre PI grant holder for the projects and therefore it is reasonable that they can access their own data.
Users are responsible for their own data (see backup policy).
By default, when you create a new file on the server it is created with the following permissions:
This means that only you can change, delete or execute the new
file, but anyone logged in to the server can view it. If you would like
to change the permissions on a file you can use the chmod
command. Further details on how to do this can be found by reviewing our
introduction to linux course.
Users should have a data management plan for their projects. Please see this document for advice.
Users should endeavour to minimise disk usage by removing unnecessary files and compressing files where appropriate.
Completed projects should be archived with metadata and code to ensure reproducibility.
Before you leave the university, please ensure all required data is accessible to your group.
Group folders exist on the bifx servers at /groups. These can be used for shared data and for archiving old projects/accounts.
Please follow our recommended best practices for working on the bifx servers. This web page will be updated regularly.
All users must complete our introduction to linux course, either in their own time or by attending one of our workshops.
The bioinformatics servers are a shared environment and users are responsible for ensuring their jobs do not overwhelm computing resources. The servers can cope with high memory usage and multi-threading, however they will slow down when there is a high number of read/write operations.
Limit simultaneous jobs with large read/write requirements (e.g. genome alignment).
Do not set multi-threaded jobs to use the majority of CPUs.
In particular, users should be aware of Unix commands to monitor their jobs and avoid overuse of computing resources, e.g:
ps / pgreptop / htopnicekillUse the scratch space in /scratch to speed up
analyses/downloads/uploads. This is local disk space which will respond
quicker. However, it is NOT BACKED UP and should be
used as temporary storage only. All key datasets should be transferred
to your home space.
The core facility will regularly maintain software and updates. We will strive to provide adequate warning when updates may cause interruption. All communication will be broadcast via the bifx-users mailing list (see below).
Details on version control of bioinformatics software and maintaining your own packages are available in our best practices section.
Data saved in home directories is stored on the University of Edinburgh DataStore service. Two backup systems exist:
Data in /scratch directories is not backed up. This
disk space is provided to speed up analysis but output files should be
copied back to your home directory. Please remove data from /scratch
regularly to free up space for other users. Old data may be periodically
removed by the bioinformatics core facility to free up space.
We recommend that users keep additional backups of key datasets e.g:
For announcements regarding server issues and updates, please join our mailing list. To join, send an email with no subject line to the following address: sympa@mlist.is.ed.ac.uk
Include the following 2 lines of text (replacing FIRSTNAME and LASTNAME with your own first name and surname) SUBSCRIBE bifx-users@mlist.is.ed.ac.uk FIRSTNAME LASTNAME QUIT
Further information, including how to join our Slack channel and details of our Bioinformatics Live sessions, is available on our website.