Biopipe statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Biopipe
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Tool usage distribution map

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Associated diseases

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Protocols

Biopipe specifications

Information


Unique identifier OMICS_22375
Name Biopipe
Interface Web user interface
Restrictions to use None
Input data A Biopipe workflow file or a Galaxy workflow file.
Input format GA,XML
Computer skills Basic
Version 0.0.1
Stability Stable
Maintained Yes

Maintainers


  • person_outline Saima Tithi
  • person_outline Na Meng

Additional information


The web application is available at http://bench.cs.vt.edu:8282/Biopipe-Workflow-Editor-0.0.1/index.xhtml

Information


Unique identifier OMICS_22375
Name Biopipe
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Requirements
JAVA (JDK), Docker
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Saima Tithi
  • person_outline Na Meng

Additional information


The web application is available at http://bench.cs.vt.edu:8282/Biopipe-Workflow-Editor-0.0.1/index.xhtml

Publication for Biopipe

Biopipe citations

 (13)
library_books

Bioinformatic pipelines in Python with Leaf

2013
BMC Bioinformatics
PMCID: 3747863
PMID: 23786315
DOI: 10.1186/1471-2105-14-201

[…] these tools are also suitable for researchers without programming skills.A thinner abstraction layer is provided by a number of pipeline design tools based on formal languages, such as Anduril [] and Biopipe []. The purpose of these tools is to provide robust general frameworks for data analysis that can recognize and integrate heterogeneous data structures. Unlike the higher-level tools, these ap […]

call_split

Transcriptional analysis of apple fruit proanthocyanidin biosynthesis

2012
J Exp Bot
PMCID: 3444262
PMID: 22859681
DOI: 10.1093/jxb/ers193
call_split See protocol

[…] criptor First Strand cDNA synthesis kit.Genes encoding apple flavonoid biosynthesis pathway enzymes and branch points were identified by best BLAST homology in the Plant & Food Research EST database (BioPipe and BioView – automated cDNA sequence annotation pipeline and viewer system © Dr Ross Crowhurst and The New Zealand Institute for Plant & Food Research Ltd) and in the apple genome (). Where a […]

library_books

Agile parallel bioinformatics workflow management using Pwrake

2011
BMC Res Notes
PMCID: 3180464
PMID: 21899774
DOI: 10.1186/1756-0500-4-331

[…] iles can be used to describe scientific workflows, the necessity of workflow systems arises to satisfy the four aspects mentioned above. Therefore, full-featured scientific workflow systems including Biopipe [], Pegasus [], Ptolemy II [], Taverna [], Pegasys [], Kepler [], Triana [], Biowep [], Swift [], BioWMS [], Cyrille2 [], KNIME [], Ergatis [], and Galaxy [] have been applied in the bioinform […]

library_books

A lightweight, flow based toolkit for parallel and distributed bioinformatics pipelines

2011
BMC Bioinformatics
PMCID: 3051902
PMID: 21352538
DOI: 10.1186/1471-2105-12-61

[…] actment in grid environments (e.g., PEGASUS[]), high-level "enactment portals" that require less programming effort by users (e.g., BIOWEP[]), or flower-level software libraries (e.g., the Perl-based BIOPIPE[]). Indeed, the recent proliferation of WMS technologies and implementations led Deelman et al. [] to systematically study a taxonomy of features", particularly as regards the four stages of a […]

library_books

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

2009
BMC Bioinformatics
PMCID: 2755485
PMID: 19732427
DOI: 10.1186/1471-2105-10-279

[…] yze bioinformatic data [-]. In recent years various tools have been introduced to aggregate services, among them workflow environments like Taverna [] and Cyrille2 [], and scripting environments like BioPipe []. This aggregation of services shows great potential, as exemplified in the successful experiment in [] where microarray data, genomic sequence information, and pathway databases were integr […]

call_split

Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment

2008
BMC Bioinformatics
PMCID: 2259424
PMID: 18315855
DOI: 10.1186/1471-2105-9-S1-S23
call_split See protocol

[…] productive. Most of these tools require an understanding of programming or scripting languages, such as Perl, Python, Java, and UNIX-scripts. Recent examples of such systems in bioinformatics include Biopipe [], BioWBI [], Taverna [], Wildfire[], KDE Biosciences [], gRNA [], Biowep [], and BioWMS []. Each deployment is therefore subject to its own code development and testing. Although programming […]


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Biopipe institution(s)
Department of Computer Science, Virginia Tech, Blacksburg, VA, USA; Department of Crop and Soil Environmental Science, Virginia Tech, Blacksburg, VA, USA; Graduate Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, USA
Biopipe funding source(s)
Supported by the Virginia Agricultural Experiment Station (Blacksburg) and the USDA National Institute of Food and Agriculture.

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