z-library Z-Library project

Programming for Science Informatics (B573)

Credit Hours: 3
Day/Time: Tuesdays, 6–8:40 pm
Location: IT 270, 535 West Michigan Street, Indianapolis, IN 46202 [map]
May have some guest lectures, not necessarily in the same room and time
First Class:
Website:
Instructor: Sarath Chandra Janga, Ph.D., Assistant Professor, Bioinformatics
Office Hours: Tuesdays and Thursdays, 11 am–12 pm or by Appointment
Office: WK 309, Walker Plaza Building, 719 Indiana Avenue, Indianapolis, IN 46202 [map]
Phone: (317) 278-4147 (Office)
Email: jangalab@iupui.edu
Website: http://www.iupui.edu/~jangalab/
Prerequisites:

Description

In this course, we will cover the basics of programming as they are relevant to understanding and analyzing biological datasets. This will be achieved by giving a biology background to motivate a computational need/task. At the end of the course, you should be able to describe solutions (preferably elegant) to address a wide range of basic biological and biomedical problems.

The course is aimed at giving a good foundation in UNIX based administration, PERL programming, MySQL database management, R statistical analysis and application development in omics settings using these programming languages/tools.

The instructor will give introductions to each of these programming languages and commonly used applications in bioinformatics/systems biology in the first 10 weeks. Then the students will be asked to present recent articles published in the last 4 years (each student has to present a paper), present a project work (as a group of 2 to 3 students on a particular theme/problem) and submission of the project report.

Translational Bioinformatics Applications (B656)

Credit Hours: 3
Day/Time:
Location: WK 321, Walker Plaza Building, 719 Indiana Avenue, Indianapolis, IN 46202 [map]
May have some guest lectures, not necessarily in the same room and time
First Class:
Website:
Instructor: Sarath Chandra Janga, Ph.D., Assistant Professor, Bioinformatics
Office Hours: Tuesdays and Thursdays, 11 am–12 pm or by Appointment
Office: WK 309, Walker Plaza Building, 719 Indiana Avenue, Indianapolis, IN 46202 [map]
Phone: (317) 278-4147 (Office)
Email: jangalab@iupui.edu
Website: http://www.iupui.edu/~jangalab/
Prerequisites:

Description

Translational medicine (TM) attempts to bring clinical and biomedical research practices and outcomes to patient care (“bench to bedside”). Informaticians have assisted clinicians and biomedical scientists in dealing with the large volumes of data derived from various high-throughput methodologies, developing disease models and drug design. This course will focus on the complexities of low, medium and high-throughput applications in translational medicine and train the students in solving translational medicine data management problems employing various informatics frameworks.

Computational Approaches for Analysing High-throughput Data in Biology (I590)

Credit Hours: 3
Day/Time: Mondays, 6–8:30 pm
Location: IT 271, 535 West Michigan Street, Indianapolis, IN 46202 [map]
May have some guest lectures, not necessarily in the same room and time
First Class:
Website:
Instructor: Sarath Chandra Janga, Ph.D., Assistant Professor, Bioinformatics
Office Hours: Tuesdays and Thursdays, 11 am–12 pm or by Appointment
Office: WK 309, Walker Plaza Building, 719 Indiana Avenue, Indianapolis, IN 46202 [map]
Phone: (317) 278-4147 (Office)
Email: jangalab@iupui.edu
Website: http://www.iupui.edu/~jangalab/
Prerequisites:

Description

In this course, we will cover the advanced concepts of genomics, molecular and systems biology and explore different (computational) approaches for analyzing high-throughput datasets resulting from these respective fields. This will be achieved by giving a biology background to motivate a computational need/task with most assignments involving a computational exercise to handle such datasets or to implement relevant algorithms. At the end of the course, you should be able to describe solutions (preferably elegant) to address a wide range of basic biological and biomedical problems.

The course is aimed at students who have some experience in programming (or are willing to learn it at a quick pace) and are willing to apply these skills in omics settings using a variety of programming languages/tools.

The instructor will give a detailed introduction to each of the areas below and introduce commonly used applications in bioinformatics/systems biology in the first 9-10 weeks. Then the students will be asked to present recent articles published in the last 2 years (each student has to present a paper or two) along with details of their project work (each student chooses a particular theme/problem related to the paper/s presented) and submit a project report on the research problem (project work) they addressed, towards the end of the semester.

Next Generation Genomic Data Analytics (B636)

Credit Hours: 3
Day/Time: Thursdays, 6–8:40 pm
Location: WK 321, Walker Plaza Building, 719 Indiana Avenue, Indianapolis, IN 46202 [map]
May have some guest lectures, not necessarily in the same room and time
First Class: August 27th, 2015
Website:
Instructor: Sarath Chandra Janga, Ph.D., Assistant Professor, Bioinformatics
Office Hours: Tuesdays and Thursdays, 11 am–12 pm or by Appointment
Office: WK 309, Walker Plaza Building, 719 Indiana Avenue, Indianapolis, IN 46202 [map]
Phone: (317) 278-4147 (Office)
Email: jangalab@iupui.edu
Website: http://www.iupui.edu/~jangalab/
Prerequisites: I573 or basic knowledge of programming, R, and Unix system management

Description

This course covers advanced concepts of genomic sequencing datasets from a number of sequencing platforms, including how the data motivates computational needs and tasks for analysis. The student learns how to devise approaches for analyzing massive clinical and biomedical sequencing datasets and for developing sound hypotheses and predictions from them.