Programming for Biology
October 16 - 31, 2023

Key Dates
Application Deadline:  July 15, 2023
Arrival: October 15th by 6pm EST
Departure: October 31st around 12pm

CSHL Courses are intensive, running all day and often including evenings and weekends; students are expected to attend all sessions and reside on campus for the duration of the course.

Instructors:
Simon Prochnik, Circularis Biotech Inc. 
Sofia Robb, Stowers Institute for Medical Research
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COVID-19: All participants planning to attend in-person will be required to attest to recent COVID vaccination (within one year of the course’s start date) with an FDA or WHO approved vaccine. Additional safety measures will be in line with current NY and Federal Guidelines applicable in Fall 2023.

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

More often than not, today’s biologist is studying data sets that are too complex or large to be analyzed without a computer and even so existing software tools provide only boilerplate analyses. Questions specific to the data set require novel analysis pipelines to be devised and written in computer code. Designed for lab biologists with little or no programming experience, this course will give students the bioinformatic sand scripting skills they need to derive biological insights from this abundance of 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.

We use Python, an easy-to-learn scripting language with an established 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, processing and analysis 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

       

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): $4,660

No fees are due until you have completed the full application process and are accepted into the course. 

Before applying, ensure you have
1) Personal statement/essay;
2) Letter(s) of recommendation;
3) Curriculum vitae/resume (optional);
4) Financial aid request (optional). More details


If you are not ready to fully apply but wish to express interest in applying, receive a reminder two weeks prior to the deadline, and tell us about your financial aid requirements, click below: