Getting Started in the Piccolo Lab

To get started as a student in the lab, please do the following (if you haven't already):

  1. Send me your BYU ID. I will use that to give you to access the bioinformatics lab (4134 LSB).

  2. 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 you will be doing. Tell them that you will be executing custom Python and 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.

  3. 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.

  4. 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. When you are done, please send me your certificate of completion.

  5. Fill out this biosketch form and send it to me. If you do not have software (Adobe Acrobat) that allows you to edit a PDF file, please send me the information requested in the form. When it asks about your education/training, put your estimated graduation date. On Part C, briefly describe the relevant courses you have taken and the bioinformatics skills you have gained to this point.

  6. Learn the basics of using Git. Then create an account on Bitbucket and add me (srp33) as a collaborator.

  7. Decide on a strategy for automatically backing up all code files and documents that you create during the research process. Dropbox and Google Drive offer solutions for automatically synchronizing files to the cloud. Install the software for one of these solutions and make sure it backs up your files automatically. Create a folder where you will store all your research files. Let me know which of these solutions you have set up. (In some cases, we will use BitBucket, too.)

  8. 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. Command-line bootcamp
    5. How to get a great letter of recommendation

  9. Spend a full hour (or two) learning how to use the vim text editor. This editor has shortcuts that will increase your productivity, and it can be used on any Unix-based server, including the BYU Supercomputer. Here is a helpful tutorial.

  10. Lastly, send me an email that indicates when you have completed all of these tasks.