Perl for Biologists  
March 6 - June 12 2013

The aim of this workshop is to teach practical Perl programming skills in the context of biology and bioinformatics. The workshop will span 15 hour-and-half long sessions. It will start from the very basics, no previous programming experience necessary. After completing the workshop each participant should be able to create Perl scripts for common bioinformatics tasks.   The workshop is open to all Cornell researchers. The registration fee is $250. 

 The workshop will include practical exercises, that can be conducted on your own machine, or on CBSU BioHPC Lab workstations especially reserved for the workshop. Our workstations run Linux operating system, so if you are going to use our machines and are new to Linux computing environment you may want to addend our free "Linux for Biologists" workshops (part 1 March 4, part 2 March 11). You can also use "Linux for Biologists" materials posted online to refresh your Linux skills

Please note that you will need to bring your own laptop to connect to CBSU workstations.

Access to BioHPC Lab workstations requires a Lab account. If you do not yet have an account on BioHPC Lab system, we will create one for you. Also, we will assign a machine for you to work on during  the workshop (during and after the sessions). Machine reservations will be active from Wed March 6th until end of the day Sat June 29th.

machine allocations

The materials for each session will be posted on session pages (below). Each session will be a combination of a lecture and practical exercises. There will be also practical problems for solving on your own, reviewed during the following session. Please feel free to contact us with any questions or concerns, workshop coordinator can be contacted by e-mail at or phone 254-6333 anytime. For the duration of the workshop we will be available for you for face-to-face conversation during workshop office hours held every Tuesday 1:00pm-4:00pm in 623 Rhodes (alternative workshop office hours locations are 618, 620 and 621 Rhodes when 623 is busy or not available).

Workshop Outline
Session 1 3/6/2013 3:30:00 PM 655 Rhodes Hall
Session 2 3/13/2013 3:30:00 PM 655 Rhodes Hall
Constants, variables and functions - basic
Session 3 3/20/2013 3:30:00 PM 655 Rhodes Hall
Control flow statements
Session 4 3/27/2013 3:30:00 PM 655 Rhodes Hall
Arrays and lists
Session 5 4/3/2013 3:30:00 PM 655 Rhodes Hall
Session 6 4/10/2013 3:30:00 PM 655 Rhodes Hall
Files, directories and I/O operations
Session 7 4/17/2013 3:30:00 PM 655 Rhodes
Regular expressions
Session 8 4/24/2013 3:30:00 PM 655 Rhodes Hall
Practical examples
Session 9 5/1/2013 3:30:00 PM 655 Rhodes Hall
Subroutines and functions
Session 10 5/8/2013 3:30:00 PM 655 Rhodes Hall
Objects and modules 1: Introduction to Object Oriented Programming.
Session 11 5/15/2013 3:30:00 PM 655 Rhodes Hall
Objects and modules 2: BioPerl.
Session 12 5/22/2013 12:00:00 AM 655 Rhodes Hall
Interacting with websites and ftp sites
Session 13 5/29/2013 3:30:00 PM 655 Rhodes Hall
Practical examples
Session 14 6/5/2013 3:30:00 PM 655 Rhodes Hall
Practical examples
Session 15 6/12/2013 3:30:00 PM 655 Rhodes Hall
Practical examples

The workshop is taught by CBSU staff.

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