Tag Archives: bioinformatics.org

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.


OpenHelix Presents UCSC Genome Browser Workshop at African Virtual Conference

OpenHelix Workshop on how to use the UCSC Genome Browser workshop will be presented on February 20th at the first annual African Virtual Conference on Bioinformatics (AfBix’09).

Seattle WA (PRWEB) February 10, 2009 — OpenHelix will present a 90 minute online workshop on the UCSC Genome Browser at the first annual African Virtual Conference on Bioinformatics 2009 (AfBix’09), February 20th at 16:00 GMT.

The UCSC Genome Browser introductory workshop will cover the topics needed to effectively use this powerful, free, publicly-accessible genomics tool, including: basic functionality of Genome Browser searching and BLAT use. The workshop will be open to all registered participants in the conference and can be accessed online from either the participants’ location or one of several ‘hubs’ in Africa

The Afbix’09 virtual conference, which is the first of its kind in Africa, is supported by the Bioinformatics Organization, Regional Student Group Africa (RSG Africa), Regional Student Group Morocco (RSG Morocco), and African Society of Bioinformatics and Computational Biology (ASBCB). The dates for the conference are 19th to 20th February 2009.

Participants can register for the conference at bioinformatics.org.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

About Bioinformatics.Org
The Bioinformatics Organization, Inc. was established in 1998 to create a collaborative environment for bioinformatics practitioners and neophytes throughout the world. The Organization provides these individuals, as well as the public at large, free and open access to the materials and methods used in bioinformatics research, development (i.e., computer programming), and education. The Organization helps to lower the barrier to entering and participating in bioinformatics, as access to commercial resources can be prohibitively expensive for those working individually, in small groups, at poorly-funded institutions or in developing nations. Currently, there are more than 25,000 members and 400 hosted projects.

Learn about protein-protein interactions.

Bioinformatics.org is a great organization and web site (disclosure: I’ve taught an online course with them :D) and they regularly have online course in the field of bioinformatics that are more in the theory and analysis area of bioinformatics (where ours is more in the use and access of resources). If you need bringing up to speed on protein-protein interactions, there is room in next week’s course on said subject.

We have training in several protein-protein interaction resources such as STRING, soon MINT, so this bioinformatics course seems a nice complement. To learn more about the course, follow me under the fold…

Continue reading

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.

Continue reading