Welcome to the Fall 2022 and Spring 2023 Bioinformatics (BFX) Workshop!
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
Weekly Workshops on Mondays @ 10am in Mid-Campus Center (MCC) 11th floor Main Conference Room (Room #11504)
Please see the Communications section below for accessing the Office 365 group to find the Outlook Calendar invite. To be automatically notified of cancellations or changes to scheduling, ex. Room # changes, please accept the Outlook Calendar invite. One of the organizers listed in the Communications section can forward the Outlook Calendar invite upon request.
The BFX Workshop schedule, subject to change, is available below. Previous years' course materials can still be accessed in the "archive" folder. Additionally, a Zoom recording of each Workshop session will be made available shortly after each session. NOTE: See Participation for more details about external or remote participation.
The last Monday of each month will be a short lecture (15-30m), followed by open "office hours" to get help with assignments, or ask for advice about your own projects. Please contact the organizers if you have suggestions for additional lectures.
| Date | Topic(s) | Presenter(s) |
|---|---|---|
| September 12, 2022 | Workshop Intro and Prerequisite Review | Chris Miller, Jason Walker |
| September 19, 2022 | Sequence Data Generation and Manipulation | Chris Miller |
| September 26, 2022 | Command line tips, office hours | Chris Miller |
| October 3, 2022 | DNA Alignment Fundamentals | Jason Walker |
| October 10, 2022 | Office Hours | |
| October 17, 2022 | DNA Alignment in the Cloud | Jason Walker |
| October 24, 2022 | Germline Variant Calling | Alex Paul, Chris Miller |
| October 31, 2022 | Somatic Variant Calling | Chris Miller |
| November 7, 2022 | Exploring Data + Office Hours | |
| November 14, 2022 | Parsing and Filtering VCFs with Python | John Garza, Susanna Kiwala |
| November 21, 2022 | THANKSGIVING BREAK | |
| November 28, 2022 | R basics | Chris Miller |
| December 5, 2022 | Data visualization with R and ggplot2 | Chris Miller |
| December 19, 2022 | Data Munging/Cleaning in R | Chris Miller |
| December 26, 2022 | WINTER BREAK | |
| January 2, 2023 | WINTER BREAK | |
| January 9, 2023 | RNAseq part 1 | Kelsy Cotto |
| January 16, 2023 | MLK Day - no meeting | |
| January 23, 2023 | RNAseq part 2 | Kelsy Cotto |
| January 30, 2023 | Office Hours | |
| February 6, 2023 | ctDNA/Error-corrected sequencing | Aadel Chaudhuri |
| February 13, 2023 | Epigenomics, ChIP/ATAC/WGBS | Chris Miller |
| February 20, 2023 | President's Day - no meeting | |
| February 27, 2023 | Office Hours | |
| March 6, 2023 | Single-cell RNAseq | Jennifer Foltz |
| March 13, 2023 | Single-cell RNAseq | Jennifer Foltz |
| March 20, 2023 | Spring Break - no meeting | |
| March 27, 2023 | Long Read Sequencing/Office Hours | Chris Miller |
| April 3, 2023 | Microbial Genomics/16S seq | Brigida Rusconi |
| April 10, 2023 | Genome Assembly/Pangenome | Juan Macias-Velasco |
| April 17, 2023 | Cloud Computing - getting started | Malachi Griffith |
| April 24, 2023 | Office Hours |
There are no requirements or qualifications to participate in the BFX Workshop. All we ask is that any willing participant visit our Prerequisite tutorial to understand the computer systems, tools, and languages that will be used throughout the course. Most of the languages and tools used are common to all fields and applications of Bioinformatics. No academic credits are earned for attending the course and there no attendance requirements. There will be "assignments" given during some lectures and we strongly encourage you to complete them in order to get the most out of the course - there is 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), McDonnell Genome Institute (MGI), Department of Medicine, Division of Hematology & Oncology, and 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 organizers would like to specifically thank the ICTS Precision Health function for supporting the Bioinformatics Workshop. NIH CTSA Grant Number UL1TR002345
The organizers and presenters of 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.
This team of organizers and presenters are committed to sharing best practice methods, technology, and knowledge from decades of experience working in these fields of study. New and novel applications of genome sequencing data are constantly evolving and even more so the analytical processes and tools used to translate data to information and knowledge are ever growing and changing. The team leading this workshop will focus on standard best practices while having an eye toward the future direction of each Bioinformatics topic.
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 organization please email one of the following:
j.mckenzie at wustl.edu
jason.walker at wustl.edu
c.a.miller at wustl.edu
An Office 365 Group named Bioinformatics is used to distribute Calendar invites, announcements, and information regarding this workshop. Questions are welcome as well, but please be mindful that over 100 people subscribe to this alias. Click here to join.
The email address is:
bioinformatics at gowustl.onmicrosoft.com
If you'd like to look back at past sessions, course info and lectures from the 2020-2021 and 2021-2022 academic year are available in the archive.