CS101 Introduction to Bioinformatics Programming
From Bioinformatics.Org Wiki
This course teaches biologists how to use programming as a way to automate biological data analysis and develop algorithms or workflows, and how to manage vast amounts of data using database technologies. Data could be DNA or amino acid sequences, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. Perl programming and database management will be covered. (This course is a combination of CS101A Perl for Biologists, Level 1 and CS101C MySQL for Biologists, Level 1.)
The course is divided into 8 sessions, roughly 1-1.5 hours each, and 2 sessions are held every day. The course is completed in 4 days, with the 5th day being reserved for project discussion and any other issues the students may want to discuss.
- Session 1: Fundamentals of databases and deciding what to store. How to install a database management system (MySQL).
- Session 2: Database concepts, such as creating and designing a database, and populating the database with sample data.
- Session 3: Data retrieval and manipulation concepts using SQL queries (Select, Update, Delete, Insert).
- Session 4: Additional topics, such as interfacing the database with the Microsoft Access front end and mining the data using a Perl database interface.
- Session 5: Installation issues and a simple exercise that illustrate how to create and execute simple Perl programs. The Perl environment will be introduced.
- Session 6: Fundamentals of programming 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.
- Session 7: Functions/subroutines, hash arrays and regular expressions.
- Session 8: Installation of Perl packages, and some examples of using the famous package BioPerl, for manipulating sequences, automating BLAST queries, etc. A project will be assigned.
No database experience is required, just a need to learn how to work with databases. No programming experience is required, just a need to learn how to program.
This course has been offered several times. Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues. If you are interested in an upcoming course, please register using instructions below.
- Course GTG (online), December 8-12, 2008, 15:30-17:30 GMT daily
- Course GGA (online), September 15-19, 2008, 15:30-17:30 GMT daily
Registration is done in two steps. First, if you haven't already done so, create an online account to access the educational section of our website. Second, register for this course by making a payment using either the online registration form (click on the scheduled course above; use this form only for credit card payments via secured PayPal), or by sending in the Mail-in registration form (~150 kB PDF, use this form if paying by US checks, credit card or corporate purchase order). Please check the tuition rates and discounts below.
Registration deadline: When full
Tuition & discounts
The fee for this course is $995 USD (commercial, government)
Discounted rates are available, as follows:
- Academic and non-profit research organizations, $664
- Students paying for themselves (not getting reimbursement) and unemployed individuals (verification required), please inquire.
- Professional members get an additional 20% discount.
- Limited scholarships may also be available for those in low-income economies.
Online courses are offered via an online meeting system. Access information will be provided prior to the start of the course. Each lecture will last 90 to 120 minutes, depending on the topics covered. For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as Flash videos (resolution reduced by 30%) each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.
Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and the Adobe Flash plugin. A microphone and webcam are not required for this course. The necessary software, lecture notes and exercises will be provided.
This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 10 "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 978 562 4800.