Kartzinel:Computing Resources

From OpenWetWare
Jump to navigationJump to search

Useful web links


  • Getting started with sequencing data.. This GoogleDoc was originally prepared by Lindsay McCulloch in 2020, with input from lab members. It is a 'living document' that includes notes on formatting metabarcoding data for use in R, working with the Phyloseq package, using GitHub, and more. As of late 2020, it is under active development and input is appreciated.
  • SLIM looks like a useful WebAp for metabarcoding workflows.

GIS resources


Rhode Island

Coding resources

Lab code repositories


Comments... PTF?

Computing at Brown


Setting up a new CCV account for students/lab members: https://web1.ccv.brown.edu/start/account
Documentation for new CCV users, including how to change passwords: https://www.ccv.brown.edu/doc
Once logged in, our lab's shared data directory is at /gpfs/data/tkartzin


To gain access to the "Lab Server" through IBES, get permission from the PI and then talk to Henry.
Use your Brown username and password, (or if you are using a computer within Active Directory which you are already logged into), you should have access to our shared files and your private directory with a 100 GB quota.

On a Mac, you get to these using the following paths:
1. Shared: smb://files.brown.edu/Research/IBES_KartzinelLab
2. Your home: smb://files.brown.edu/Home/username (where username is your Brown username)
If you aren't using a Mac, check with Henry.


To connect to the lab server and other resources from off campus: https://www.brown.edu/information-technology/software/catalog/vpn-f5-desktop-client


The lab has a floating license for Geneious.

Useful commands

Command line

  • rsync: sync or backup data
rsync -rav [source location]:path [destination path]
rsync {options} {source} {destination}
rsync --help
  • ls: list files and folders in a directory
ls -lrth [directory]