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CS102A Perl for Biologists, Level 2

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.

Session 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
Session 2
Creating and using modules, namespaces, packages. References and object-oriented programming
Session 3
The Perl DBI and DBD for the MySQL DBMS. Using BioPerl for sequence analysis
Session 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.

This course is taught by Shailender Nagpal, M.S.

Registration

Registration for courses at Bioinformatics.org takes two steps:

Step 1
If you haven't already done so, create an on-line 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 this course by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

On-demand course held on-line

This course might be taught on-demand, on-line. Please check the list of on-demand courses to see if this course can be taken as such.

An on-demand version provides pre-recorded video lectures. Once registered, you may begin by viewing the first lecture video, and if you have any questions, you may then email the instructor.

Slides are available with both on-demand and live of courses, and many also have examples (such as data and scripts). Assignments are also provided for your edification but are not graded. And, when finished, you may request a certificate of attendance.

On-demand course tuition:

  • For-profit & government: $300 USD
  • Non-profit & self-pay: $200 USD
  • See below for additional discounts.

Students who've taken the on-demand version of this course can access the course page here.

Live course held online

This course might also be taught live, on-line. Please check the calendar to see if it will be held in the near future.

Live, online course tuition:
  • For-profit & government: $500 USD
  • Non-profit & self-pay: $300 USD
  • See below for additional discounts.

Registration deadline: When full

Students who've taken the live course can continue to access their course pages here. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

Live course held on-site

We can come to your facility to teach this course. Please contact us for additional information.

Discounts

Additional discounts are available as follows:

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

Certification

This course is certified by Bioinformatics.org, one of the oldest and largest international affiliations in the field, and it will count as 3 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within Bioinformatics.org. Students completing the course will receive a certificate attesting to that.

Refund policy

For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.

Additional information

Please contact us for questions or additional information.

See also

 

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