Welcome to the Capra Lab! Here's some introductory information that you'll need. Feel free to ask me or other people in the lab as you have questions. We also have a GitHub repository with tutorials and resources: https://github.com/CapraLab/resources
Our lab space is on the second floor of the Valley Tower in the Bakar Computational Health Sciences Institute. For card acces to the building and our space, email Andrew Jan and Edna Rodas. The space is new and, with most of working remotely, the assignment of desks is somewhat in flux. Ask Tony or another lab member about where to sit when you arrive.
We use slack to share information, jokes, and chat. I will send you an invite.
We use a program called Notion (https://www.notion.so/) to keep track of progress on projects in the lab. You'll need to download Notion and setup an account. Academic accounts can get the Personal Pro Plan for free. Please create a note and share it with me (my first name dot last name AT vanderbilt.edu).
We use UCSF’s Wynton compute cluster (https://wynton.ucsf.edu/) for many of our projects. If you don’t already have a Wynton account, please set one up by following the instructions here: https://wynton.ucsf.edu/hpc/about/join.html. Let them know that you'll need to be in the capra group.
We have lab storage and data available here:
/wynton/group/capra/
Also, check out the database of bioinformatics datasets here:
/wynton/group/databases/
It is also important to keep your filesystem organized. See the project directory tutorial for the Capra Lab standard directory structure, and have a look at these tips for coding workflows.
If you would like to be listed on the lab web page, please send me a photo and a brief description of your background and interests.
I will add you to the lab's shared google calendar. This calendar is for meetings involving multiple members of the group and events potentially of interest to others. This calendar is not for events that only involve you. However, if you are going to be away for more than a day, please list that on the lab calendar. We also have a “Capra Lab Relevant Seminars” calendar where we post seminars that might be of interest to the group.
We have lab meeting from 3:30-5 Pacific on Thursdays in VCV206. We start with a round of quick updates from each person in the group. Following the updates, someone gives a longer update on their research project. If you are doing a temporary internship or rotation, you will give a summary presentation on your work the last week of your program.
We also have a weekly meeting to discuss recent research papers or other issues that we call Science Discussion Time every Tuesday from 3:30-4:30 Pacific in VCV206. I will send out the paper or other relevant materials by email before the meeting.
Each week I make hours of "Tony Open Meeting Time" available. This can be booked by creating an event with your name and a zoom link. If you need less than the full time window, please leave the remaining open time available. If you need to discuss something and no meeting times are available, just email me to schedule a meeting about it. In general, I'm happy for you to stop by my office if the door is open, but there's a chance I may not be able to chat.
People in the lab are very friendly and eager to help, but please be respectful of their time when you are starting out and have lots of questions. Try to solve any problems you are having before asking for help. Googling the problem first will often yield a solution. If not, email me or the lab member you think can help to ask if they have a moment.
We are looking forward to working with you!
Tony