CS102A Perl for Biologists, Level 2

From Bioinformatics.Org Wiki

Jump to: navigation, search

Contents

[edit] Objectives

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.

[edit] Instructor

[edit] Syllabus

  • 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

[edit] Scheduled courses

If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

[edit] Registration

Registration for courses at Bioinformatics.Org takes two steps:

Step 1
If you haven't already done so, create an online account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.
Step 2
Register for the course by making a payment using either the online registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

Please also check the course tuition rates and discounts.

Registration deadline: When full

[edit] Tuition & discounts

Payee and costs:

  • Employer (for-profit & government): $600 USD
  • Employer (non-profit & academic): $400 USD
  • Yourself (not being reimbursed): $200 USD

Additional discounts are available as follows:

  • Professional members: 20% discount
  • Limited scholarships may also be available for those in low-income economies (please inquire).

[edit] Logistics

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 about an hour, 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 is not required for this course. The necessary software, lecture notes and exercises will be provided.

[edit] Certification

This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 5 "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.

[edit] Additional information

Please contact us for questions or additional information.

[edit] See also

Retrieved from "http://www.bioinformatics.org/wiki/CS102A_Perl_for_Biologists,_Level_2"
Personal tools