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Programming Languages and the Biological Sciences by SZ4v6I

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									   Programming Languages
  and the Biological Sciences

       by   James McGuffee, Ph.D.




CCSC: South Central Regional Conference
            April 27, 2007
PRESENTATION OUTLINE

• Motivation

• Scripting Languages

• XML and Data Storage

• Functional and Logic Languages

• Future Research
          MOTIVATION


  What unique
 contributions can
   be made by a
computer scientist?
                 MOTIVATION
                      “… biologists need
                        software that is
                        reliable and can
                        deal with huge
                        amounts of data,
                        as well as
                        interfaces that
                        facilitate the
                        human-machine
                        interactions.”
                          Jacques Cohen,
                         Brandeis University
(Photo: R.R. Jones)
 Algorithms frequently used in Bioinformatics


1)   compare sequences

2)   construct evolutionary (phylogenetic) trees

3)   detect patterns in sequences

4)   determine 3D structures from sequences

5)   infer cell regulation

6)   determine protein function and metabolic pathways

7)   assemble DNA fragments
         SCRIPTING LANGUAGES




• BioPerl is a toolkit of Perl modules

• Three Design Principles of the BioPerl project
   1. separate the interface from the implementation
   2. provide a base framework for the respective operation by
      generalizing common routines into a single module
   3. use the “Factory and Strategy” patterns (Erich Gamma)
     SCRIPTING LANGUAGES




• Biopython is a toolkit of Python modules

• Key work with BioPython project
   1. creating parsers for biological data
   2. designing a useful interface to represent sequences
          SCRIPTING LANGUAGES



• Formerly known as GenePHP, the BioPHP project seeks
  to encourage the use of PHP as a “glue” language to
  bind web-based bioinformatics applications and
  databases

• Tasks coded with BioPHP
   1. read biological data in the GenBank, Swissprot, Fasta, and
      Clustal ALN formats

   2. perform simple sequence analysis tasks
       SCRIPTING LANGUAGES




• Ruby is an object-oriented scripting language

• BioRuby project is supported by
   – Human Genome Center at the University of Tokyo
   – Bioinformatics Center at Kyoto University
    XML and DATA STORAGE

• XML is an extensible, universal
  format for structured data exchange
  and documents

• Two Notable Attempts
  1. Bioinformatics Sequence Markup
     Language (BSML)
  2. BIOpolymer Markup Language (BioML)
FUNCTIONAL and LOGIC LANGUAGES




• Robert Giegerich’s research group
  – implemented dynamic programming algorithms,
    including those in RNA folding grammars
 FUNCTIONAL and LOGIC LANGUAGES




• Biomedical Logic Programming (Blip)
  – a collection of modules intended for
    bioinformatics and biomedical applications
  – integrated query system
  – written in SWI-Prolog
 FUNCTIONAL and LOGIC LANGUAGES




• BioBike is an interactive, web-based programming
  environment that enables biologists to analyze
  biological systems by combining knowledge and data
  through direct end-user programming

• developed with BioLisp
  (common Lisp with added biological functionality)
        FUTURE RESEARCH

1. What is the best scripting language
   to use in Bioinformatics?

2. What is the best way to store and
   access biological data?

3. Can languages be designed so that
   biologists themselves become
   programmers?
    For More Information…



 Bio-Languages Research Laboratory
http://faculty.stedwards.edu/jameswm/blrl/

								
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