Tag Archives: programming

On-site summer course by our friends at Bioinformatics.org

Just got this notice in my mail–from Bioinformatics.org:


CS101 Introduction to Bioinformatics Programming

July 28-29, 2011

*ON-SITE* in Cambridge, Massachusetts, USA


***This is a special offering of our introductory programming course, given in-person in Kendall Square, Cambridge, Massachusetts.***


This course teaches IT specialists, entry level bioinformaticians and biologists to leverage Linux and various open-source bioinformatics tools, together with scripting and data management tools, to perform computations in biological research and create information from data. Examples in this course will use data from DNA and amino acid sequences, microarray profiles, images, mass spectrometry, LIMS, and biological annotations.


The course is divided into 4 sessions, with roughly 1-1.5 hours of lecture, and additional time for lab exercises. A 5th session is reserved for project discussion and any other course relevant issues the students may want to discuss.

Session 1 will cover an overview of the computing landscape for bioinformatics. Common data management and mining issues will be highlighted, alongwith an overview of challenging problems and their solutions. Linux OS overview will be done, alongwith lab exercises to get participants familiar with Linux.

Session 2 will cover fundamentals of scripting with Perl, such as scalars, arrays, variable interpolation, operators (mathematics, conditional, logical), file input/output, printing, loops (if-then-else, for, while), list operations, etc. Lab exercises will be conducted

Session 3 will cover functions/ subroutines, hash arrays and regular expressions. Participants will be introduced to MySQL databases.

Session 4 will cover the installation of Perl packages, and some examples of using the famous package BioPerl for manipulating sequences, automating BLAST queries, etc. Project will be assigned that uses BioPerl and the Perl Database interface

PREREQUISITES:  No programming experience is required, just a need to learn how to program.

FOR MORE INFORMATION:  For tuition costs and other inquiries, please contact edu@bioinformatics.org.

Note: This is not associated with OpenHelix, we just know and like the Bioinformatics.org team and wanted to spread the word.


Bioinformatics Courses

We at OpenHelix train researchers how to find and use genomics and bioinformatics resources. There are a lot of databases and analysis tools out there and lot of researchers, biomedical and bench scientists who need help past that hurdle of figuring out which ones to use, what data or analysis they might have and the basics of how to use them

That said, there are some of you out there who want and need to learn how to do some basic querying and programming, things like mySQL, perl and R. The resources available to you just aren’t quite enough. Well, there are a lot of resources out there to help you, as a biologist, get started. Among them are the courses at Bioinformatics.org . I taught one once last year. These are live web conferences and a good way to learn some of the basics of programming you might want to know as a biologist. They’ve just announced a new set of courses for April.

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