We use different computing resources depending on the job at hand.
Upon login, you will automatically land at /home/BIOTECH/jlang. This is the home directory for our lab’s VM where computing will take place. Note that this is a shared lab space, so please be respectful of others data.
BRC maintains extensive software available to all BRC server users (
BRC also maintains many reference genomes (
All data transfers on BRC VMs must be done within the data transfer server, which is a separate ssh login (same credentials):
Our BRC VM account has a total of 1TB of space allocated, and thus is only meant for active use during analysis. Our long-term data storage is on the Lang Lab RestrictedDrive (aka ResearchDrive). To move data from RestrictedDrive to the BRC VM, you must use Globus.
Note that Protected Health Identifiers (PHI) and other restricted data is not permitted on BRC VMs.
To connect RestrictedDrive > Globus:
To connect Globus > BRC VM account:
To transfer from BRC VM to your local machine, you must be in a directory on your local computer (i.e. not ssh’ed into BRC VM)
scp email@example.com:path/to/file /path/to/your/local/folder
Similarly, for BRC server installations, you may find that some software requires higher-level permissions. Contact BRC IT support.
If installing software on your computer, you may run into issues with computer permissions based on required SMPH security protocols. If so, please contact Dept of Pathology IT support.
A large amount of the software/packages we use for secondary analysis of genomic data uses R scripts and packages. These are most easily visualized in real time using the RStudio program.
Recording notes in R Markdown (.rmd) format helps to document the analysis analogous to a lab notebook entry. We strongly encourage heavy use of markdown documentation for reproducibility, troubleshooting, refining, and documentation for publication.