Where can I find Perl resources to get me started programming in Perl?
What is it?
The Perl programming language is a widely used programming language that is predominant in bioinformatics. Perl runs on every platform and should probably be the language that laboratory biologists resort to first to address their data analysis issues.How to learn it
A great way to learn Perl is to look at the examples in Tom Christiansen's and Nathan Torkington's Perl Cookbook (eBook) while reading Schwartz et al's Learning Perl, also available as an eBook.The Perl Cookbook is also very useful when trying to resolve a coding problem you just know has been addressed many times already by others...
Installing Perl
You can download and install Perl itself here.A good way to create, debug and run Perl programs is to use the free and excellent Open Perl Integrated Development Environment (IDE).
Extending Perl for biologists: BioPerl
Available as elective components to the Perl interpreter, BioPerl provides a tremendously extensive collection of Perl packages to perform biological data analysis and manipulation, right out of the box. For this reason, BioPerl is widely used as a way of quickly coding powerful analytical program (see publication list).What's in it?
BioPerl is made up of a vast collection of so-called Perl modules to handle most biologically-related data analysis tasks.What is it for?
Example applications of BioPerl:- Accessing sequence data from remote databases
- Converting between formats
- Identifying amino acid cleavage sites
- Running BLAST automatically
- Analyzing phylogenetic trees
- Manipulating 3D structure objects (e.g., proteins)
Key references
- Learn by example: Christiansen and Torkington's excellent Perl Cookbook, (2003) (eBook & hardcopy).
- Excellent reference on Perl: Brown, Martin C. Perl: the complete reference, (2001).
- Schwartz, Randal L., Phoenix, Tom, Foy, Brian D.: Learning Perl, (2005) (eBook version).
- A very practical book (eBook/physical): Genomic Perl: From Bioinformatics Basics to Working Code, (2002).
- BioPerl's excellent tutorials.
- eBook: Perl programming for biologists, D. Curtis Jamison (2005).
- More advanced applications of Perl to bioinformatics, including good coverage of BioPerl: Mastering Perl for Bioinformatics, (2003).
- Lane Library's BioFAQs involving Perl - not to be missed!
- All Lane Library resources on Perl.
Source
Lane LibrarianRecord created 8/22/2006.
- Anesthesia
- Biomedical Ethics
- Bioresearch
- Cardiology
- Clinical
- Consumer Health
- Emergency Medicine
- Global Health
- Hematology
- Internal Medicine
- LPCH Heart Center Nursing
- Medical Education
- Multicultural Health
- Neurology
- Nursing
- Obstetrics & Gynecology
- Oncology
- Ophthalmology
- Otolaryngology
- Pathology
- Pediatrics
- Pharmacy
- Physical Medicine & Rehabilitation
- PICU
- Psychiatry
- Pulmonary
- Reference Desk
- Special Programs
- Spiritual Care
- Student (IL)