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Pise: Software for building bioinformatics webs

D. Gilbert
2002 Briefings in Bioinformatics  
Pise is interface construction software for bioinformatics applications that run by commandline operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses.  ...  It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services  ...  Overall, if you want to build, or have someone build for you, a web interface to biology applications, look at Pise.  ... 
doi:10.1093/bib/3.4.405 pmid:12511068 fatcat:dw77hayqnzcobig656h7glgjbe

EMBOSS: The European Molecular Biology Open Software Suite

Peter Rice, Ian Longden, Alan Bleasby
2000 Trends in Genetics  
Most of the more friendly user interfaces in bioinformatics are simple forms which build the command line for the user, run the program, and present the results.  ...  Similar forms are available for other interfaces, including PISE ( seqanal/EMBOSS/). Table 2 lists the web and GUI interfaces we are currently collaborating with.  ... 
doi:10.1016/s0168-9525(00)02024-2 pmid:10827456 fatcat:kreanzyjtbbd5c2u264zg4cq3u

Bioinformatics process management: information flow via a computational journal

Lance Feagan, Justin Rohrer, Alexander Garrett, Heather Amthauer, Ed Komp, David Johnson, Adam Hock, Terry Clark, Gerald Lushington, Gary Minden, Victor Frost
2007 Source Code for Biology and Medicine  
This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology.  ...  The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm.  ...  The Eclipse project is an open source soft-ware framework that provides a development platform for building applications.  ... 
doi:10.1186/1751-0473-2-9 pmid:18053179 pmcid:PMC2228283 fatcat:vy6rrzbhlbdetcohxwmaiq5k7q

A Web interface generator for molecular biology programs in Unix

C. Letondal
2001 Bioinformatics  
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  ...  The generator uses XML as a highlevel description language of the legacy software parameters.  ...  ACKNOWLEDGEMENTS We are grateful to the persons who helped to make this software easier to install and to use by giving suggestions, and particularly to Stephane Bortzmeyer, Nicolas Joly and  ... 
doi:10.1093/bioinformatics/17.1.73 pmid:11222264 fatcat:orpou4k2kfbibcwdb7lnhkdm6u

GenoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

D. Samson
2003 Nucleic Acids Research  
), that are being integrated and made public at the public bioinformatics resource centre of Gé noplante: Gé noPlante-Info (GPI).  ...  is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for  ...  We are very grateful to our Génoplante colleagues for the submission of their data and/or tools to GPI, their participation in many bioinformatics meetings and task forces, and for their help in defining  ... 
doi:10.1093/nar/gkg060 pmid:12519976 pmcid:PMC165507 fatcat:2rggwjp6xbh3re6whcjibiblea

Network integration of data and analysis of oncology interest

P. Romano, G. Bertolini, F. De Paoli, M. Fattore, D. Marra, G. Mauri, E. Merelli, I. Porro, S. Scaglione, L. Milanesi
2006 Journal of Integrative Bioinformatics  
In this paper, we introduce the rationale for the creation of such a portal and present the architecture and some preliminary results for the development of a portal for the enactment of workflows of interest  ...  This huge amount of data and the heterogeneity of software tools that are used implies the adoption on a very large scale of new, flexible tools that can enable researchers to integrate data and analysis  ...  This work was partially supported by the Italian Ministry of Education, University and Research (MIUR), projects "Oncology over Internet (O 2 I)" and "Laboratory of Interdisciplinary Technologies in Bioinformatics  ... 
doi:10.1515/jib-2006-21 fatcat:nivkddesyzaydd3st5qdqiyu5u

Open source tools and toolkits for bioinformatics: significance, and where are we?

J. E. Stajich
2006 Briefings in Bioinformatics  
can serve as the foundation for building important applications, analysis workflows and resources.  ...  This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years.  ...  The PISE project [40] was one of the first to build a standardized web interface by generating an XML description of input, parameters, and output of over 150 bioinformatics and phylogenetic tools.  ... 
doi:10.1093/bib/bbl026 pmid:16899494 fatcat:x2dugkcc2vdv7j3b4ry6jkpiba

WebLab: a data-centric, knowledge-sharing bioinformatic platform

Xiaoqiao Liu, Jianmin Wu, Jun Wang, Xiaochuan Liu, Shuqi Zhao, Zhe Li, Lei Kong, Xiaocheng Gu, Jingchu Luo, Ge Gao
2009 Nucleic Acids Research  
To fulfill such requirements, we have developed a data-centric knowledge-sharing platform WebLab for biologists to fetch, analyze, manipulate and share data under an intuitive web interface.  ...  WebLab is publicly available at http://weblab.cbi., with all source code released as Free Software.  ...  While some of them are designed as wrappers for a few specified software packages, a number of systems provide further support to popular bioinformatic analysis tools.  ... 
doi:10.1093/nar/gkp428 pmid:19465388 pmcid:PMC2703900 fatcat:fjzepwjmvfbw5cpu7m2ylwe4pq

BIRCH: a user-oriented, locally-customizable, bioinformatics system

Brian Fristensky
2007 BMC Bioinformatics  
BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software.  ...  Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages.  ...  Christoph Sensen and the National Research Council Canadian Bioinformatics Resource for providing access to systems for testing downloading and installation of BIRCH.  ... 
doi:10.1186/1471-2105-8-54 pmid:17291351 pmcid:PMC1800872 fatcat:vnamwtkjdrcuhc644y5mbjbmae

Towards dynamic database infrastructures for mouse genetics

Morris A. Swertz, Damian Smedley, Katy Wolstencroft, Rudi Alberts, Michael Zouberakis, Vassilis Aidinis, Klaus Schughart, Paul N. Schofield, Ritsert C. Jansen
2008 2008 8th IEEE International Conference on BioInformatics and BioEngineering  
A growing array of biotechnologies is being used to study the genetics of complex biomolecular traits in laboratory mice as models for human disease.  ...  Combined analysis of these datasets provides much of the power of the approach of functional genomics but this depends on the ability of databases to exchange data with each other and with analytical software  ...  ) building on standard software tools.  ... 
doi:10.1109/bibe.2008.4696715 dblp:conf/bibe/SwertzSWAZASSJ08 fatcat:5poa5rcyqbbpxjcvzk2wmq3ixa

Codifying bioinformatics processes without programming

Thomas C. Hudson, Ann E. Stapleton, Jeffrey L. Brown
2004 Drug Discovery Today BIOSILICO  
Bioinformatics is bimodal,with results gathered either from rigid pipelines, their functions encoded in programs accessible only to specialists, or from ad hoc collections of scripts or web pages, used  ...  , then lost track of or thrown away.We discuss the possibility of developing tools to straddle this divide, in particular, tools using graphical dataflow programming, which have the potential to make bioinformatics  ...  but equally applicable to bioinformatics; (ii) PISE [11] , a toolkit for building web interfaces to traditional UNIX-script-style bioinformatics tools and linking them together; and (iii) JGraph (http  ... 
doi:10.1016/s1741-8364(04)02410-2 fatcat:2ccvw3lbbfg3hlwtga7m4naa44

Intelligent client for integrating bioinformatics services

I. Navas-Delgado, M. d. M. Rojano-Munoz, S. Ramirez, A. J. Perez, E. Andres Leon, J. F. Aldana-Montes, O. Trelles
2005 Bioinformatics  
Motivation: In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological  ...  The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the  ...  PISE (Letondal, 2001 ) is a Web interface generator for molecular biology command-line driven programs. The generator uses XML as a high-level description language of the legacy software parameters.  ... 
doi:10.1093/bioinformatics/bti740 pmid:16257987 fatcat:42okd4mai5hvzmxjhiyfjxlkp4

Applied Bioinformatics Tools [chapter]

Jingchu Luo
2013 Basics of Bioinformatics  
PISE -the main page to learn and download the PISE software designed by the Pasteur Institute, France. It can generate the web interface for the programs of the EMBOSS package.  ...  page for the EBI bioinformatics tools • NCBI tools -the entry page for the NCBI bioinformatics tools Web-Based Bioinformatics Platforms • WebLab -the comprehensive and user-friendly bioinformatics platform  ... 
doi:10.1007/978-3-642-38951-1_9 fatcat:ycrao5zo7baavjv3pxzzvljuye

Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench

Ross Lazarus, James Taylor, Weiliang Qiu, Anton Nekrutenko
2008 Summit on translational bioinformatics  
Although there is now plenty of genomic data and no shortage of analysis methods for translational genomic research, many biologists do not have efficient and transparent access to the computational resources  ...  The inevitable heterogeneity of data formats and of command syntax between data resources and software applications presents a major obstacle, particularly to those biologists lacking practical informatics  ...  For example, Galaxy builds on many design and architectural features, including the XML interface descriptor for executables, in Pise.  ... 
pmid:21347127 pmcid:PMC3041519 fatcat:2t56wogrrfc4hdcoicfvdm5lpu

Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

Alexandre G. de Brevern, Jean-Philippe Meyniel, Cécile Fairhead, Cécile Neuvéglise, Alain Malpertuy
2015 BioMed Research International  
To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence.  ...  This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools.  ...  Acknowledgments The authors would like to thank our colleagues of the ATRAGENE, ISOFT, University Paris Diderot, INTS, CNRS, University Paris Sud, and INSERM for their precious advice on this paper.  ... 
doi:10.1155/2015/904541 pmid:26125026 pmcid:PMC4466500 fatcat:slexkxvpmvcfxfuc5gfrsrp6n4
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