Bioinformatics (BFX) Workshop
Welcome to the Fall 2021 and Spring 2022 Bioinformatics (BFX) Workshop!
Objectives
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
Schedule
Weekly Workshops on Mondays @ 10am
For the Fall 2021 Semester, we will start by holding all BFX Workshops remotely via Zoom. Please see the Communications section below for accessing the Email alias to receive a Outlook Calendar invite that includes the Zoom meeting link. It's important to use the Outlook Calendar invite to be automatically notified of cancellations or changes to scheduling.
The BFX Workshop schedule, subject to change, is available below. Last year's course materials can still be accessed in the "archive" folder.
The first 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 13 | Workshop Intro and Prerequisite Review | Chris Miller, Jason Walker |
| September 20 | Sequence Data Generation | Chris Miller |
| September 27 | RIS Infrastructure + Office Hours | |
| October 04 | DNA Alignment Fundamentals | Jason Walker |
| October 11 | NO MEETING | |
| October 18 | DNA Alignment Workflows | |
| October 25 | Exploring Data + Office Hours | |
| November 01 | Docker and Germline Variant Calling | |
| November 08 | Somatic Variant Calling | |
| November 15 | Parsing and Filtering VCFs with Python | |
| November 22 | THANKSGIVING BREAK | |
| November 29 | Annotation and R | |
| December 06 | RNAseq part 1 | |
| December 13 | RNAseq part 2 | |
| December 20 | Visualizing variants + Office Hours | |
| December 27 | WINTER BREAK |
Participation
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!
Unfortunately, we're unable to offer slack membership or cluster access to people outside of Washington University, but you are welcome to follow the recorded lectures and homework on your own.
Organizers
This workshop is a collaborative effort between the McDonnell Genome Institute, 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 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.
Communications
Slack
For members of the mgibio Slack organization, please use the #bfx_workshop channel. If you do not have access to the mgibio Slack organization please email one of the following organizers:
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