Kartzinel:Computing Resources
Useful web links
Metabarcoding
- 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.
- Initial processing of dietary DNA metabarcoding data. This GoogleDirectory was originally prepared by Bethan Littleford-Colquhoun in 2023. It provides template documents and code that we use to download paired-end read data from our dietary metabarcoding workflows, assemble forward and reverse reads, perform initial quality controls, and evaluate sequencing success. There is also a tutorial for how to upload sample data to SRA for archiving, which we have largely started to do routinely. Some details are specific to our dietary analysis sequencing workflow and the sequencing service that we use, plus we have particular sample naming schemes, but it should be pretty straightforward to adapt for a variety of similar goals.
- SLIM looks like a useful WebAp for metabarcoding workflows.
GIS resources
R tutorials
- Map making with hillshade in R by Hannah Hoff (May 2023): detailed tutorial of how to plot maps with hill shading to help highlight terrain. It presents a worked example of 'dummy data' from Yellowstone.
- Map making with inset in R by Hannah Hoff (April 2023): detailed tutorial of how to plot maps and present sample location data when an inset is required. It presents a worked example of 'dummy data' from Yellowstone.
- Map making in R by Hannah Hoff (December 2022): detailed tutorial of how to plot maps and present sample location data. It presents a worked example of 'dummy data' from Yellowstone.
Kenya
- Kenya GIS data from World Resources Institute
- International Livestock Research Institute (ILRI) GIS data for Kenya and region
- Protected Planet
Rhode Island
Coding resources
- Google's R coding style guide Be proud of how understandable and reusable your code can be.
Graphics and communication
Some links that lab members have found helpful for preparing graphical summaries of work and conceptual figures, especially accessible images useful for communication
- https://ian.umces.edu/media-library/symbols/
- http://phylopic.org
- https://commons.wikimedia.org/wiki/Main_Page
- https://biorender.com/
- Google images: creative commons licenses is a search option
Lab code repositories
GIT
Comments... PTF?
Computing at Brown
CCV
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
IBES
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.
VPN
To connect to the lab server and other resources from off campus: https://www.brown.edu/information-technology/software/catalog/vpn-f5-desktop-client
Geneious
The lab has a floating license for Geneious. Current lab members can find instructions for access and use on this GoogleDoc. (Contact TRK for permission to access the doc.)
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]
