Programming for Biology
October 16 - 31, 2017
Application Deadline: July 15 2017


Simon Prochnik, Intrexon, Inc
Sofia Robb, Stowers Institute for Medical Research

See the roll of honor - who's taken the course in the past

More often than not, today’s biologist is studying data that is too complex or numerous to be analyzed without a computer and only boilerplate analysis can be performed with existing tools. Questions specific to the data set require novel analysis pipelines to be designed and written in computer code. Designed for lab biologists with little or no programming experience, this course will give students the bioinformatics and scripting skills necessary to exploit this abundance of biological data. The only prerequisite for the course is a strong commitment to learning basic UNIX and a scripting language. Lectures and problem sets from previous years are available online, and students are welcome to study this background material before starting the course.

This year, we are offering the course in Python, an easy-to-learn scripting language with a growing code base and community of users. The course begins with one week of introductory coding, continues with practical topics in bioinformatics, with plenty of coding examples, and ends with a group coding project. Formal instruction is provided on every topic by the instructors, teaching assistants, and invited experts. Students will solve problem sets covering common scenarios in the acquisition, validation, analysis, and visualization of biological data. They will learn how to design, construct, and run powerful and extensible analysis pipelines in a straightforward manner. Final group projects will be chosen from ideas proposed by students and will be guided by faculty. Students will be provided with a library of Python reference print and e-books that they can bring home with them.

Note that the primary focus of this course is to provide students with practical programming experience, rather than to present a detailed description of the algorithms used in computational biology. For the latter, we recommend the Foundation of Computational Genomics course.

Support & Financial Aid

Major support is generously provided by the National Human Genome Research Institute

Access to cloud computational resources may be supported by an education grant from Amazon Web Services

Financial aid is available to help offset tuition costs as follows:


1) Financial aid for US applicants is provided by the NIH National Human Genome Research Institute
2) Financial aid for international applicants is provided by the Howard Hughes Medical Institute
3) Interdisciplinary Fellowships (transitioning from outside biology) & Scholarships (transitioning from other biological disciplines) are provided by the Helmsley Charitable Trust

Please indicate your eligibility for any of these funding sources in a financial aid request submitted as part of your application materials. Financial aid requests do not affect selection decisions made by the instructors.

Cost (including board and lodging): $4,165 

The following button links to a short form which confirms your interest in the course, but is not an official application form. To apply to the course, click the Application tab above. No fees are due until you have completed the full application process and are accepted into the course.

Students accepted into the course should plan to arrive by early evening on October 15 and plan to depart after lunch on October 31.