Bioinformatics Vol. 17 no. 1 2001
Pages 73-82
© 2001 Oxford University Press
Original Paper |
A Web interface generator for molecular biology programs in Unix
1 Institut Pasteur, Service
d’Informatique Scientifique, 28 rue du Docteur Roux, 75724
Paris Cedex 15, France
2 Laboratoire de Recherche en Informatique,
URA 410 du CNRS, LRI - Bâtiment 490
- Universitéde Paris-Sud, 91405
Orsay Cedex, France
Received on May 16, 2000
; revised on June 27, 2000
; accepted on July 7, 2000
Motivation: Almost all users encounter problems using sequence analysis programs. Not only are they difficult to learn because of the parameters, syntax and semantic, but many are different. That is why we have developed a Web interface generator for more than 150 molecular biology command-line driven programs, including: phylogeny, gene prediction, alignment, RNA, DNA and protein analysis, motif discovery, structure analysis and database searching programs. The generator uses XML as a high-level description language of the legacy software parameters. Its aim is to provide users with the equivalent of a basic Unix environment, with program combination, customization and basic scripting through macro registration.
Results: The program has been used for three years by about 15000 users throughout the world; it has recently been installed on other sites and evaluated as a standard user interface for EMBOSS programs.
Availability: The program is freely available over the Internet at the following URL: http://www.pasteur.fr/~letondal/Pise/.
Contact: pise{at}pasteur.fr
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  B. Neron, H. Menager, C. Maufrais, N. Joly, J. Maupetit, S. Letort, S. Carrere, P. Tuffery, and C. Letondal Mobyle: a new full web bioinformatics framework Bioinformatics, November 15, 2009; 25(22): 3005 - 3011. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Duan, R. Li, D. Cheng, W. Fan, X. Zha, T. Cheng, Y. Wu, J. Wang, K. Mita, Z. Xiang, et al. SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology Nucleic Acids Res., September 30, 2009; (2009) gkp801v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. S. Ooi, C. Y. Kwo, M. Wildpaner, F. L. Sirota, B. Eisenhaber, S. Maurer-Stroh, W. C. Wong, A. Schleiffer, F. Eisenhaber, and G. Schneider ANNIE: integrated de novo protein sequence annotation Nucleic Acids Res., July 1, 2009; 37(suppl_2): W435 - W440. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Kumar and J. Dudley Bioinformatics software for biologists in the genomics era Bioinformatics, July 15, 2007; 23(14): 1713 - 1717. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Stajich and H. Lapp Open source tools and toolkits for bioinformatics: significance, and where are we? Brief Bioinform, September 1, 2006; 7(3): 287 - 296. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Navas-Delgado, M. d. M. Rojano-Munoz, S. Ramirez, A. J. Perez, E. Andres Leon, J. F. Aldana-Montes, and O. Trelles Intelligent client for integrating bioinformatics services Bioinformatics, January 1, 2006; 22(1): 106 - 111. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gracy and L. Chiche PAT: a protein analysis toolkit for integrated biocomputing on the web Nucleic Acids Res., July 1, 2005; 33(suppl_2): W65 - W71. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Falquet, L. Bordoli, V. Ioannidis, M. Pagni, and C. V. Jongeneel Swiss EMBnet node web server Nucleic Acids Res., July 1, 2003; 31(13): 3782 - 3783. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Samson, F. Legeai, E. Karsenty, S. Reboux, J.-B. Veyrieras, J. Just, and E. Barillot GenoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics Nucleic Acids Res., January 1, 2003; 31(1): 179 - 182. [Abstract] [Full Text] [PDF]
|
|