Call for Paper - May 2019 Edition
IJCA solicits original research papers for the May 2019 Edition. Last date of manuscript submission is April 20, 2019. Read More

BioPCD - A Language for GUI Development Requiring a Minimal Skill Set

Print
PDF
International Journal of Computer Applications
© 2012 by IJCA Journal
Volume 57 - Number 6
Year of Publication: 2012
Authors:
Graham Gm Alvare
Abiel Roche-lima
Brian Fristensky
10.5120/9117-3273

Graham Gm Alvare, Abiel Roche-lima and Brian Fristensky. Article: BioPCD - A Language for GUI Development Requiring a Minimal Skill Set. International Journal of Computer Applications 57(6):9-16, November 2012. Full text available. BibTeX

@article{key:article,
	author = {Graham Gm Alvare and Abiel Roche-lima and Brian Fristensky},
	title = {Article: BioPCD - A Language for GUI Development Requiring a Minimal Skill Set},
	journal = {International Journal of Computer Applications},
	year = {2012},
	volume = {57},
	number = {6},
	pages = {9-16},
	month = {November},
	note = {Full text available}
}

Abstract

BioPCD is a new language whose purpose is to simplify the creation of Graphical User Interfaces (GUIs) by biologists with minimal programming skills. The first step in developing BioPCD was to create a minimal superset of the language referred to as PCD (Pythonesque Command Description). PCD defines the core of terminals and high-level non-terminals required to describe data of almost any type. BioPCD adds to PCD the constructs necessary to describe GUI components and the syntax for executing system commands. BioPCD is implemented using JavaCC to convert the grammar into code. BioPCD is designed to be terse and readable and simple enough to be learned by copying and modifying existing BioPCD files. We demonstrate that BioPCD can easily be used to generate GUIs for existing command line programs. Although BioPCD was designed to make it easier to run bioinformatics programs, it could be used in any domain in which many useful command line programs exist that do not have GUI interfaces.

References

  • Rice,P. Longden,I. and Bleasby,A. "EMBOSS The European molecular biology open software suite". Trends in Genetics. 2000. Vol 16. Issue 6. pp 276-277.
  • "The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics". 2003. Vol 19. Issue 14. pp 1837-1843.
  • C. Letondal (2001), A Web interface generator for molecular biology programs in Unix, Bioinformatics, Oxford University Press, 17(1), 2001, pp 73-82.
  • Hull, Duncan; Wolstencroft, Katy; Stevens, Robert; Goble, Carole A. ; Pocock, Matthew R. ; Li, Peter; Oinn, Tom (2006). "Taverna: A tool for building and running workflows of services". Nucleic Acids Research 34 (Web Server issue): W729–W732. DOI:10. 1093/nar/gkl320. PMC 1538887. PMID 1684510. 8
  • Smith SW, Overbeek R, Woese CR, Gilbert W, Gillevet PM (1994)The genetic data environment: an expandable GUI for multiple sequence analysis. Computer Appl. in the Biosciences 10 671-675
  • Linton E (2006) MacGDE: Genetic Data Environment for MacOSX. http://www. msu. edu/~lintone/macgde/
  • Fristensky B (2007) BIRCH: A user-oriented, locally-customizable, bioinformatics system. BMC Bioinformatics , 8:54
  • Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
  • Felsenstein, J. (1989) PHYLIP Phylogeny Inference Package. Cladistics 5:164-166.