CS102A Perl for Biologists, Level 2
From Bioinformatics.Org Wiki
Taught in the context of biological research, this course shows biologists how to use the scripting language Perl to automate certain tasks. It is a continuation of CS101A Perl for Biologists, Level 1 and covers advanced topics and projects.
- Day 1: Perl basics (a quick review):
- How to use Perl commands in scripts and functions
- Good programming practices
- Specials notes, shortcuts, basic commands you may have forgotten
- Case study: Automating BLAST
- Downloading sequences and formating them for querying using the “formatdb.exe” program
- Creating FASTA file with sequences on which to use BLAST
- Writing a program to call “blastall.exe”, finding the best hits
- Case study: Gene expression analysis
- Reading ~20000 gene scores in a text file corresponding to 8 samples, and a gene information file
- Performing thresholding and normalization for this data
- Calculating fold change, difference, t-statistics, p-value, confidence intervals, etc.
- Outputing the filtered results, sorted by lower confidence interval, and removing Affymetrix control genes
- Day 2: Creating and using modules, namespaces, packages. References and object-oriented programming
- Day 3: The Perl DBI and DBD for the MySQL DBMS. Using BioPerl for sequence analysis
- Day 4: Project: Microarray database with sequence information
- Use SantaLucia rules to calculate the delta-G value of all 25-mer Perfect Match (PM) probe sequences.
- Create tables in a database using Perl to accommodate the data.
- Day 5: Project discussions
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, register using instructions below.
- Course ATC (online), January 28-February 2, 2008
- Course ACG (online), December 3-7, 2007
- Course TG (online), September 24-28, 2007
- Course GA (online), July 9-13, 2007
- Course AR (online), April 9-13, 2007
- Course AG (online), February 19-23, 2007
- Course AD (online), January 15-19, 2007
Registration comprises of two steps. First, 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.
For an additional USD $49, students who attend this course may order data discs containing full-resolution lecture videos and extra copies of the slides, scripts and data files.
Registration deadline: When full
- Returning student discount: A 20% (rounded up) discount applies for students who have paid the base tuition (without a similar discount) for a course at Bioinformatics.Org that does not fall in the CS101 range (e.g., CS102A/B) (please use the mail-in registration form rather than PayPal if taking this discount).
- Cluster course discount: A 50% (rounded up) discount (cannot be combined with the 20% discount) applies for students who have paid the base tuition for a course that does fall in the CS101 range (please use the mail-in registration form rather than PayPal if taking this discount).
Tuition (all prices USD):
|Base tuition||If taken with a non-CS101
course at base tuition
|If taken with another CS101
course at base tuition
For full-time students and the unemployed, please inquire about an additional discount (verification required).
Online courses are offered on the ASAP online meeting system. Access information will be provided prior to the start of the course. Each lecture will last 45 to 90 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. Please check the specific system requirements for your computer. A microphone and webcam is not required for this course. The necessary software, lecture notes and exercises will be provided.
If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 508 890 8600.