[BiO BB] Open Source Bioinformatics for Researchers (reminder)

J.W. Bizzaro jeff at bioinformatics.org
Thu Sep 14 14:54:20 EDT 2006

This course is being held on Tuesday and Wednesday of next week.  Some space is still available.


                         RADISSON HOTEL CAMBRIDGE
                               CAMBRIDGE, MA
                            SEPT. 19 & 20, 2006


(CS101 Introduction to Bioinformatics Programming: Perl I & R I for Biologists)

September 19th & 20th, 2006
Radisson Hotel Cambridge <http://www.radisson.com/cambridgema>, 777 Memorial Drive, Cambridge, Massachusetts

Poster <http://edu.bioinformatics.org/06a/poster.pdf> (172 KB PDF)


This is a course on the fundamentals of open-source programming, to help biologists understand how and when to use the right computer tools for solving computational biology problems, whether sequence analysis, gene expression, mass spectrometry, or systems biology.

This course is modularized so that researchers can understand two distinct tools: a programming and scripting language such as Perl and a data analysis and visualization language such as R. Armed with knowledge and some hands-on experience with these tools (including add-on modules like BioPerl and Bioconductor), scientists will be able to appreciate and use software better in their organization, and also be able to put research questions in the context of these tools. They will be able to do basic computational tasks themselves and better communicate with their IT group.


There are no prerequisites for this course other than having a need to
learn some of the fundamentals of programming, in case the scientist has
any bioinformatic tasks in their day-to-day work.


Day 1:

    Session 1:
    08:00 - 08:30 am: Registration
    08:30 - 10:00 am: Installation, Fundamentals of Perl
    10:00 - 10:30 am: Exercises - simple Perl programs
    10:30 - 10:45 am: BREAK
    10:45 - 11:30 am: Perl loops, file i/o, list operations, conditional statements
    11:30 - 12:00 pm: Exercises - more Perl programs

    Session 2:
    01:00 - 02:00 pm: Perl syntax - regular expressions, hash functions
    02:00 - 03:00 pm: Exercises - manipulate DNA sequence, annotation data
    03:00 - 03:15 pm: BREAK
    03:15 - 03:30 pm: Additional Perl syntax - subroutines
    03:30 - 05:00 pm: Exercises - automate BLAST queries

Day 2:

    09:00 - 12:00 pm: Basics of R
    12:00 - 01:00 pm: LUNCH
    01:00 - 04:30 pm: Bioconductor for microarray analysis 

Breakfast and afternoon tea are provided, but lunch is not.


When: September 19th & 20th, 2006
Where: Radisson Hotel Cambridge <http://www.radisson.com/cambridgema>, 777 Memorial Drive, Cambridge, Massachusetts

All attendees are encouraged to bring their own notebook computers, since this will be a hands-on workshop. CDs will be provided to install the necessary software, and lecture notes and exercises will be provided.


This course is certified by the Bioinformatics Organization, Inc. <http://bioinformatics.org/about/>, the largest international affiliation in the field, and it will count as *16* "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.


Commercial tuition: $600/person
Academic tuition: $300/person

Registration deadline: September 18th, 2006 or when filled

Available payment methods:

1. Online Registration Form <http://edu.bioinformatics.org/course/view.php?id=2> (account required)
Use this form only if paying by credit card (via secured PayPal).

2. Mail-in Registration Form <http://edu.bioinformatics.org/download/registration_form.pdf> (158 KB PDF)
Use this form for all other methods of payment.

You may also go to the course website <http://edu.bioinformatics.org/course/view.php?id=2> and click on "login as a guest" to view the online course materials.

Please send questions to <edu at bioinformatics.org>.

J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600

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