| Open Source Web Service Development with perl |
| The MidSouth Bioinformatics Center will be offering a workshop series this Spring/Summer, giving attendees the opportunity to learn the programming skills required to create bioinformatics software and deliver it via the WWW. Researchers and students from all organizations are invited to attend. |
| This workshop focuses on using perl, CGI scripting, BioPerl, and BioMOBY. Perl is a popular open source language available for nearly every platform. It was credited with 'saving the Human Genome Project' when project programmers used perl's short development cycle and built-in "string manipulation" capabilities to reorganize seemingly endless fragments, eventually prevailing before commercial interests locked in invaluable intellectual property. BioPerl is an open source software package designed and built by scientists and programmers from all over the world, including researchers from the NCBI, EMBL, and several major universities. It is used daily in production at those facilities. |
| The cost is $65 for the entire workshop series of four sessions, or $20 per session. Each session will be six hours, including a break for an included meal, and will meet in the ETAS building at UALR. Anyone just interested in specific sessions is welcome to register for just those of interest. Notes, slides, and code examples for each session are freely available online. |
The four sessions are:
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| Beginning perl scripting |
This session is for the new-to-programming and the new-to-perl alike.
- Programming basics
- Software tradeoffs
- Perl facts and perl faqs
- How to create and run a perl program
- Introduction to data types, control structures, and I/O
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| Advanced perl scripting |
This session will rapidly review the first session and focus on developing solutions using some of the hundreds of available perl modules.
- Review of data types, control structures, and I/O
- Perl subroutines and parameters
- References and composite data structures
- Modules and CPAN
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| CGI development with perl and mySQL |
The CGI session will focus on rapid application development using the IOSea library.
- Generating HTML
- Configuring the library
- Using perl DBI and mySQL
- Website and data security
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| BioPerl and BioMoby development |
BioPerl delivers both ad hoc and more permanant features for sequence analysis. BioMOBY is a growing effort to develop a more dynamic system for delivering web services for bio sciences.
- Sequence data manipulation
- Sequence similarity searches
- Sequence database access
- Sequence alignment
- Sequence annotation
- Genome database management
- Biological literature (PubMed)
- Analysis workflow
- Phylogentic trees
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The MidSouth Bioinformatics Center is supported by the Arkansas BRIN and UALR's CyberCollege.
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