tfcb_2021

MCB 536

Tools for Computational Biology

Today’s objectives

Locate information relevant to the course (lecture materials, assessment, communication streams)
Identify range of skills and concepts covered in this course
Learn basics of VSCode, Git, Markdown

Zoom logistics

Same Zoom link for duration of class
Separate Zoom link for TA office hours

Zoom link pinned on #lectures-homework Slack channel

Etiquette

Stay muted
Highly encouraged: Unmute yourself and ask questions at any point
Use Slack for detailed questions (next slide)

Communication

Slack Workspace: TFCB2021

#general: course announcements (please turn on notifications for this channel)
#lectures-homework: questions about course content and help for homework
see pinned posts in each channel for quick links and reminders

Today’s instructor

Rasi Subramaniam
Associate Professor in Basic Sciences & Computational Biology @FredHutch
Research Area: mRNA Translation

Teaching assistants & office hours



Ty Bottorff	Timothy Yu
Mon 1-2PM	Wed 1-2 PM

Other instructors

Herbold Computational Biology Program
Fred Hutch

Introduce yourself!

Name (including preferred form of address)
Research interests (type of data, model organism, research questions, etc)

Course objectives

By the end of the course, you should be able to: - Use VSCode to program in R, Python, and Unix/bash shell using appropriate syntax and code convention - Apply good practices for computational research including project and data organization - Select appropriate tools to perform specific programming and data analysis tasks - Analyze common forms of data generated by molecular biology experiments including flow cytometry, 96-well plate readers, and high throughput sequencing.

What you won’t be able to do

- Use ALL of the computational tools your research will require - Know the best algorithm or analysis method for a specific research question - Code with expert-level skills ... but you should be equipped to work towards these goals on your own.

Course website

Syllabus, lectures, homeworks

Rendered materials (prettier/easier to view):
https://fredhutch.github.io/tfcb_2021/

Original GitHub repository: https://github.com/fredhutch/tfcb_2021

Homeworks

Submit through Canvas
MCB 536 A Au 21
Tools For Computational Biology

Eight assignments (10% each) + [participation](/tfcb_2021/lectures/lecture01/participation_rubric.html) (20%) --- ## Play time - GitHub - VSCode - Markdown --- ## Helpful resources - [VSCode Intro Video Series](https://code.visualstudio.com/docs/getstarted/introvideos) - [Crash Course on Git and GitHub Video](https://www.youtube.com/watch?v=RGOj5yH7evk) - [Markdown Syntax Guide](https://guides.github.com/features/mastering-markdown/) --- ## Before next class - Compete the pre-class survey - Install all required [software](/tfcb_2021/software/) - Ensure your paperwork has been submitted to the Hutch so you can obtain a HutchNetID!