Computational Molecular Biology Unit -
                University of Alabama at Birmingham


CB2-101: Bioinformatics computing (Introduction to Scientific Computing)

Best course at UAB. Period. - Anonymous student review



  • CB2-101 is our flagship course. This is a very highly-rated, fast paced, intensive and demanding, workshop-style course designed after NSF immersion learning proposal. The goal is not to make you an expert in bioinformatics, but to make you competent in carrying out bioinformatics research. The emphasis in on skills, not on theoretical expertise. The course is a registered graduate course with full 3 credits, but taught in just 12 working days. The course is designed in such a way so that the participants should be immersed in the material and dedicate full time in the duration of the course.

    The 2020 course is going to start soon. The course is free for everyone. No computing experience necessary. Contact malay@uab.edu for more information.

    Dates: Nov 5 - 20, 2020
    Time: 9:00 AM - 1:00 PM every working day.
    Note: the course has a soft start. I strongly urge you enroll in Slack as soon as possible. This year the course will be delivered online via Zoom.

  • Registration
  • Registration form *Registration is now closed*.
    Slack workspace. Course info and discussion forum. We also use this platform for all communications inside and outside of the class. If you have not joined already, join by clicking here. Make sure that you have subscribed to cb2-101-2020 channel.

  • General resources
  • Syllabus A general outline of the course. Note that this is just an outline, the actual materials generally get adjusted based on participant learning pace and interest.
    Anthem of CB2-101 Computer Love, Album: Computer World, Kraftwerk (1981).
    Github repository Course materials source code and binaries.
    Course disk image CentOS 7 (64bit) VirtualBox disk image, compressed with xz. Unzip the file using 7zip. Download the latest version of VirtualBox for your OS here. Install the image in VirtualBox using instructions here.
    Github repository Course materials source code and binaries.


  • Materials
    Introduction to Linux and practicals Jupyter notebook November 5-6, 2020.
    Introduction to R handout. Practicals RMD file. November 9-10, 2020.
    Reproducible research in R slides and handout November 10, 2020.
    Important data formats: talk and handout. November 11-12, 2020
    Sequence search slides and handout and practicals notebook November 11-12, 2020
    Molecular Evolution slides and handout November 12-13, 2020.
    Introduction to NGS talk, handout, and practicals November 16-17, 2020.
    Alignment and variant calling. notebook. November 17-18, 2020
    Variant annotation tabix and vcftools. November 18, 2020
    Introduction to RNASeq: talk & notebook. November 19, 2020
    Introduction to Single Cell RNASeq notebook. November 20, 2020


  • Previous Editions
    Nov 2019 Held November 1-15, 2019.
    Nov 2018 Held November 1-16, 2018.
    Nov 2017 Held November 2-17, 2017.
    Nov 2016 Held November 3-18, 2016.
    Nov 2015 Held November 5-20, 2015.
    Nov 2014 Held November 6-21, 2014.
    Feb 2014 Held February 17-28, 2014.


  • University of Alabama at Birmingham. 619 19th St. South, WP220. Birmingham (AL), 35249 (USA).
    Computational Molecular Biology Unit -
   University of Alabama at Birmingham