Welcome to the Fall 2024 and Spring 2025 Bioinformatics (BFX) Workshop! It can be taken for credit under the WUSTL course titles: Applied Bioinformatics for Genomics I and II.
This workshop series is designed for people who want to:
- learn the fundamentals of computational genomics
- use this information to improve and expedite their research
- expand their knowledge by hearing from experts in other subject areas
By the end of this series, participants will be able to:
- Demonstrate basic competency in running key bioinformatics software
- Analyze sequencing data, going from raw data to biologically interpretable results
- Draw upon a diverse set of genomic technologies to answer specific research questions
- Apply critical thinking and analytic competencies to genomics research
You are welcome to join at any time by registering on this form. After registering, you'll be added to an email distribution list and slack channel for the course. See the Communications section below for details. There is no obligation to complete the course if you register, but it helps us with planning and securing appropriate resources.
Weekly workshops are held on Mondays @ 10am in Mid-Campus Center (MCC) 11th floor Main Conference Room (Room #11504)
The BFX Workshop schedule, subject to change, is available below. Previous years' course materials can still be accessed in the archive folder. We strongly encourage in-person participation, but a Zoom recording of each Workshop session will also be made available shortly after each session. See Participation for more details about external or remote participation.
Time will be set aside before and after lectures for "office hours", where you can get help with assignments, or ask for advice about your own projects.
| Date | Time | Topic | Presenter |
|---|---|---|---|
| 08/26/24 | 10:00am | Workshop Intro + setting up your laptop for bioinformatics | Chris Miller |
| 11:00am | Extra hands-on help with setup | ||
| 09/02/24 | NO SEMINAR - LABOR DAY | ||
| 09/09/24 | 9:00am | Extra hands-on help with setup | |
| 10:00am | Introduction to Unix and the command line | Chris Miller | |
| 11:00am | Extra hands-on help with setup/unix | ||
| 09/16/24 | 10:00am | Sequence data generation/manipulation | Chris Miller |
| 09/23/24 | 10:00am | DNA Alignment Fundamentals | Jason Walker |
| 09/30/24 | 10:00am | Sequence data visualization/IGV | Chris Miller |
| 10/07/24 | 10:00am | Data manipulation and basic plotting with R | Chris Miller |
| 10/14/24 | 10:00am | NO SEMINAR – FALL BREAK | |
| 10/21/24 | 10:00am | RNA sequencing I – Data and Alignment | Kartik Singhal |
| 10/28/24 | 10:00am | RNA sequencing II – Transcript Quantification | My Hoang |
| 11/04/24 | 10:00am | RNA sequencing III – Differential Expression | Mariam Khanfar |
| 11/11/24 | 10:00am | NO SEMINAR | |
| 11/18/24 | 10:00am | Germline and Somatic Variant Calling | Chris Miller |
| 11/25/24 | 10:00am | Parsing, Filtering, and Annotating VCFs | Susanna Kiwala, John Garza |
| 12/02/24 | 10:00am | Troubleshooting bioinformatics, Semester wrap-up | Chris Miller |
Spring presenters and topics are still tentative
| Date | Topic | Presenter |
|---|---|---|
| 01/13/25 | 10:00am | Intro/prereqs, Genomic Intervals and Bedtools |
| 01/20/25 | NO SEMINAR - MLK DAY | |
| 01/27/25 | 10:00am | Epigenomics, ChIP/ATAC/WGBS |
| 02/03/25 | 10:00am | Genome Assembly, Pangenome |
| 02/10/25 | 10:00am | Data visualization with R and ggplot2 - part 1 |
| 02/17/25 | 10:00am | Data visualization with R and ggplot2 - part 2 |
| 02/24/25 | 10:00am | Single-cell RNAseq part 1 |
| 03/03/25 | 10:00am | Single-cell RNAseq part 2 |
| 03/10/25 | NO SEMINAR - SPRING BREAK | |
| 03/17/25 | 10:00am | Genomic Workflows/Cloud Computing |
| 03/24/25 | 10:00am | Microbial Genomics |
| 03/31/25 | 10:00am | Machine Learning/AI in Genomics |
| 04/07/25 | NO SEMINAR | |
| 04/14/25 | 10:00am | Long Read Sequencing |
| 04/21/25 | 10:00am | Genomic Medicine, course wrap-up |
There are no requirements or qualifications to participate in the BFX Workshop. However, this course ramps up quickly and you will need to have basic competency at the unix command line within the first three weeks. We will cover some of these skills in the first two weeks of class, but if you are new to working at a terminal, we strongly recommend that you work through the command-line exercises listed on the prerequisites page ahead of the course, and/or block out some substantial time to work through them in the first two weeks.
If you are not taking the course for credit, there are no attendance requirements. There will be "assignments" given during most lectures and we strongly encourage you to complete them in order to get the most out of the course - lectures are no substitute for hands-on learning!
For external or remote asyncronous participation, we suggest watching each weekly Zoom recording (available shortly after each in-person session) and strongly encourage interaction via Slack. The #bfx_workshop Slack channel is the primary form of interaction between workshop attendees, external participants, organizers, and presenters.
This workshop is a collaborative effort between the Institute for Clinical and Translational Sciences (ICTS), the Department of Medicine, McDonnell Genome Institute (MGI), the Division of Hematology & Oncology, and the Department of Pediatrics with faculty, staff, and student representation and participation from many other Institutes, Departments, and Divisions at Washington University School of Medicine in St. Louis.
The course director is Chris Miller (c.a.miller@wustl dot edu), Jenny Mckenzie (j.mckenzie@wustl dot edu) is the course coordinator, and John Garza is our dedicated teaching assistant.
Folks giving lectures in this workshop have multi-disciplinary backgrounds in Bioinformatics, Medicine, Computational Biology, Genetics, Computer Science, Oncology, Virology, Information Systems, Microbiology, Immunology, and many other combinations of both Data and Biological Sciences. They share best practices, technology, and knowledge from decades of experience working in these fields of study. Each year, the course evolves to match the rapidly evolving landscape of tools and techniques.
The organizers would like to specifically thank the ICTS Precision Health function for supporting the Bioinformatics Workshop. (NIH CTSA Grant Number UL1TR002345)
Announcements, discussion, and homework help all take place primarily via Slack. For members of the ICTS Precision Health Slack organization ictsprecisionhealth.slack.com, please use the #bfx-workshop channel. If you do not have access to the ICTS Precision Health Slack, please email [j.mckenzie at wustl.edu]
An Office 365 email group will be created for general announcements, schedule changes, etc from those that register.
If you'd like to look back at past sessions, course info and lectures from previous academic years are available in the archives:
Banner image adapted from NHGRI (public domain)