GMS 6232

 

Advanced Application of Bioinformatics in Genetic Research.

This is a special topic course designed for students who took GMS6014 and want to have more hands-on experience in applying bioinformatics and computational approaches to solve real research problems. Unlike GMS6014, knowledge of programming (i.e. a college level course in basic programming concepts or previous experience in writing scripts) is required. In lieu of this requirement, a strong commitment to learn the programming language Python in parallel to this course must be demonstrated by communicating with the course director.

In addition to learn basic scripting skills using Python and the Biopython library, students will take a bioinformatics project pertinent to their research work (or assigned by the instructor) and develop it through the 5 weeks period. Examples of suitable projects include, but not limited to, analyzing high throughput sequence data sets, comparative analysis of sequences, automated data extraction and integration, modeling a biological process, etc. Class will meet at 11:00-12:30 every Tuesday for module1-2 of the Fall semester (August 23 -October 29). In person meeting will be in CGRC-351, Zoom is optional for the second half.

There will be two types of class meetings. The lectures will be given by the instructors on topics related to the interest of this group. The discussion classes will be mediated by the faculty to discuss the resource, strategy, planning, and development of the projects in a learn-from-peer environment.

The class is limited to a maximum of 6 students. A laptop computer with wireless connection is required for participating in discussion and sharing information.

 

·  Recommended references:

Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools.” by Vince Buffalo (2015, O’Reilly; Amazon Link) – this book is more useful for those who already had some exposure with the Linux (Unix) system but want to be more efficient.

 

·  Course Directors:

Dr. Lei Zhou (leizhou@ufl.edu),

Dr. Raad Gharaibeh (Raad.Gharaibeh@medicine.ufl.edu)

 

Tentative schedule – based on the last time this course was offered. The actual schedule will be modified based on the projects involved.

 

Date

TOPIC

 

 

Concept

Practice

Instructors

Location

Aug. 24

Intro.  How plan for a bioinformatics project.

Initiation of projects

LZ, RG

CGRC-291

Aug. 31

Intro to Python

Initiation of projects

LZ, RG

CGRC-291

Sep.7

Microbiome analysis

Microbiome analysis

RG, LZ

CGRC-291

Sept. 14

Intro to RNA-Seq

Machine learning

RG, LZ

CGRC-291

Sept. 21

Project discussion

RG, LZ

CGRC-291

Sept. 28

Intro to R Studio

Machine learning with R

RG, LZ

CGRC-291

Oct. 5

Project discussion

LZ, RG

CGRC-291

Oct. 12

ScRNA-Seq

ScRNA-Seq

LZ, RG

CGRC-291

Oct. 19

Final progress report

RG, LZ

CGRC-291

Oct. 26

Final progress report

LZ, RG

CGRC-291