This course focuses on computational skills for processing data using programming language Python and UNIX environment. No prior programming experience is required, but some basic computer skills will be useful.
With the advancement of high throughput data generation methods, a major challenge that graduate students in life sciences have to face today is to analyze large amount of biological data. The objective of this course is to provide an opportunity for graduate students with no computer science background to learn the basic skills of handling high throughput biological data. It covers the Linux/Unix environment and the importance of the command line interface; the Python programming language; program design, implementation, and testing; BioPython; Strategies for analyzing genome resequencing, RNASeq, sequencing data. Students build hands-on skills by analyzing real high throughput biological data through homework assignments and team projects.
Units: 3
Instructor: Jason Stajich (jason.stajich@ucr.edu)
Time and location: W 2:10-4:00PM, F 2:10-3:00PM, ULB104
Office Hours: By Appointment, 1207K Genomics
None of these texts are required for completion of the course but they will provide a great deal of helpful background and examples that will improve your ability to master UNIX or Programming in Python.
Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Vince Buffalo. 2015 O’Reilly & Associates. Available from O’Reilly and Associates, Amazon
Unix and Perl to the Rescue: A Primer. Keith Bradnam and Ian Korf. Unix and Perl Primer for Biologists
Unix and Perl to the rescue! Bradnam and Korf. Amazon
Rosalind - An online platform to learn bioinformatics and programming in Python.
Software Carpentry - https://software-carpentry.org/ and Data Carpentry - http://www.datacarpentry.org/.
Berk Ekmekci, Charles E. McAnany, Cameron Mura. An Introduction to Programming for Bioscientists: A Python-Based Primer. PLoS Comp Bio. DOI: 10.1371/journal.pcbi.1004867
Programming Homework assignments (5 in total): 50%
Team project: 50%
There will be a programming assignment every two weeks. Programming assignments must be prepared along with any necessary input files or documentation to demonstrate program usage.
Code should be runnable as turned in. You will deposit your code in your github repository or if not possible, by iLearn. You can make one private personal repository to deposit and should organize a folder for each homework assignment (e.g. hw1, hw2, hw3).
Homework is due BEFORE class on the Wednesdays it is due. The next homework will be posted on Friday at latest.
Topics to be selected from a set of choices or the team’s choosing (with approval from instructor). Selection of topics will occur by end of October.
Project teams will be 2-3 individuals working together.
A presentation will be made by each team - last day(s) of class.
A final report with the details will be turned in by the group.
The report needs to detail what each person’s contribution is to the project.
| Date | Day | Lecture Topic | Notes |
|---|---|---|---|
| Sep-29 | F | Course Outline / UNIX I: Introduction | |
| Oct-4 | W | UNIX II: Running programs, capturing output | |
| Oct-6 | F | UNIX III: Tools for data processing | |
| Oct-11 | W | Logging into Biocluster. Running Jobs | Guest Lecture: Charles Forsyth Lecturer |
| Oct-13 | F | Python 1 - Variables, running, cmdline, strings, math | |
| Oct-18 | W | Python 2 - Logic, loops, lists, iterator | Guest Lecture: TBD |
| Oct-20 | F | Python 3 - I/O reading/writing files, directories | |
| Oct-25 | W | Python 4 - Dictionaries, Arrays, functions | |
| Oct-27 | F | Python 5 - Libraries, packages, BioPython | |
| Nov-1 | W | Python 6 - Structured data (CSV, XML, GFF, BED) | |
| Nov-3 | F | Data Plotting and R graphics | |
| Nov-8 | W | Bioinformatics 1 - BLAST, cmdline & automation | |
| Nov-10 | F | Veteran’s Day Holiday: No class | |
| Nov-15 | W | Bioinformatics 2 - short reads, alignment, stats, SNPs | |
| Nov-17 | F | Bioinformatics 3 - Genome Assembly | |
| Nov-22 | W | Project Workshop / No class? | |
| Nov-24 | F | Thanksgiving Holiday - No class | |
| Nov-29 | W | Bioinformatics 4 - Orthologs and Domain finding | |
| Dec-1 | F | Bioinformatics 5 - Phylogenetics | |
| Dec-6 | W | Bioinformatics 6 - SNP and variant discovery | Guest Lecture: Daniel Koening |
| Dec-8 | F | Presentations | |
| Exam week | TBD | Additional presentations TBD |