Computational biology research workshops for college students

1. Linux and formatting Gene Express Omnibus data on Ebola-infected samples 

Overview: This workshop deals with basics of Linux usages, introduction of Gene Express Omnibus (GEO) and their data format, basic biology of Ebola, and practice of Linux commands to format GEO data for further statistical analysis. Therefore, you will understand how computer will enhance biomedical research in the context of Ebola. This is a first session of two-day workshops and the statistical analysis is in the second session. No prior knowledge is needed but concept of RNA expressions will be beneficialBring your laptop. For Window users, instruction of Cygwin download will be provided before the workshop.

Date: January 24, 2015             Time:10:00 am – 2:00 pm

Location: Room 2244 Undergraduate Science Building, University of Michigan

Fee: $45 (Light lunch will be provided.)

Sponsor: WISE

Registration Form  Please use your umich account to access the link.

Agenda

9:45 am – 10:00 am

Check-in

10:00 am – 10:30 am Big data in Genomics and computer

Bits and file size, genome data size


Goal: understand computer basics and need of computation power in biology

10:30 am – 11:00 am Ebola

Online resources about diseases – symptoms, treatment, genes, social impact


Goal: be able to find scientific information related to disease of interest

11:00 am- 11:30 am Linux commands and directories

Learn basic Linux commands and directory formats


Goal: understand basic Linux commands

11:30 am – noon

Linux command competition

Play games to memorize Linux commands

Goal: Become familiar with Linux

noon – 1:00 pm Intermediate Linux commands and file manipulation

Learn file manipulation commands and solve problems


Goal: manipulate file contents using Linux commands

1:00 pm – 2:00 pm Format GEO data of Ebola-infected samples

Learn about GEO and their data format. Download Ebola-infected sample data and manipulate it using Linux commands

 

2. R and gene expressions in Ebola-infected samples 

Overview: This workshop provides statistical methods in the context of disease research. Though it is the second session of a two-day workshop, each day’s session can be taken on its own. R is a statistical tool and programming language, useful in various application areas such as medicine, public policy, and economics. After introducing R basics, we will use R to analyze RNA expression data of Ebola-infected samples. No prior knowledge is needed but some understanding of RNA expression will be beneficial. Bring your laptops.

Date: February 1, 2015 (Sunday)             Time: 1 – 5 pm

Location: Room 2244 Undergraduate Science Building, University of Michigan

Fee: $45 (Light lunch will be provided)

Sponsor: WISE

Registration Form  Please use your umich account to access the link.

Agenda

12:45 – 1:00 pm

Check-in

1:00 – 1:30 pmEbola

Overview, Current status

1:30 – 2:30 pmBasics of R

Calculation, Variable, Vector, Matrix, Function


Goal: Understand basic programming concepts

2:30 - 3:00 pmPractice R

Simple calculations using R


Goal: Be able to calculate gene expression data using R

3:00 – 3:30 pm

R function competition

Play games to memorize R functions

Goal: Become familiar with statistics and R

3:30 – 4:00 pmR Graphs

Visualize data using R


Goal: Make graphs using R

4:00 – 5:00 pmHeat map generation using R

Statistical calculation of gene expression data in Ebola-infected samples


Goal: Understand statistics in graphs 

 

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