Getting Started in the Piccolo Lab

To get started as a student in the lab, please do the following:

  • Send me your BYU ID. I will use that to give you to access the bioinformatics lab in 4134 LSB.

  • Request an account with the Fulton Supercomputing Laboratory. Go to https://marylou.byu.edu and click on "Request an Account." Read the information on the following page. Then go through the process to request an account. When it asks what you plan to do with your account, tell them briefly about the research project(s) you will be doing. Tell them that you will be executing custom Python and/or R scripts, that you expect to execute only single-node jobs, and that you expect to install bioinformatics software and execute it. Mention that you anticipate executing jobs that typically require between 1 and 64 GB memory per job and 1-16 processing cores per job, depending on the specific needs of your project.

  • Watch a few videos on this channel to become familiar with using the Fulton Supercomputing Laboratory. Also read these tips. Then submit a simple test job to make sure you are comfortable with it.

  • Go to https://orca.byu.edu/irb/irbtutorial.php and follow the instructions to complete the online CITI training. The purpose of this training is to help you understand implications for doing research with humans or with data that have been collected from humans. Some of the material will be applicable to your research, while other material will seem less applicable. But it is important to learn these concepts to make sure we are doing research responsibly. The training takes a few hours to complete. Please complete the required quizzes and send me a certificate of completion when you are done.

  • Create an account on Bitbucket and learn the basics of using Git. Add me (srp33) as a collaborator.

  • Decide on a strategy for backing up all files that require intellectual effort to create during the research process. This includes computer code files and scripts, writeups related to your research, presentations, etc. You might also include data files, depending on the source of the data.

  • Go to this page and read the following tutorials:
    1. Thirty-percent feedback
    2. The surprisingly large cost of telling small lies
    3. Ten simple rules for effective computational research
    4. A quick guide to organizing computational biology projects
    5. Command-line bootcamp
    6. How to get a great letter of recommendation
    7. Any of the other tutorials that you think would be useful

  • Take the 1-minute typing test on Aesop's fables at www.typingtest.com. You must be able to type at a minimum rate of 40 words per minute (take a screenshot of your score and send it to me). To be effective at coding or writing (two important skills in a bioinformatics research lab), you must be able to type proficiently. If you cannot type that well yet, keep working on it until you can. If you look online, you can find some typing games that can help you with this.

  • Become proficient with a text editor (if you are not already). My favorite is vim. I believe it has increased my productivity considerably by using various shortcuts that it provides. Another benefit is that it can be used on any Unix-based server. Whatever tool you prefer, spend some time learning shortcuts and setting it up according to your preferences.

  • Send me an email with a Word document that lists each of these tasks and whether you have completed them.