Biopipe statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

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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


Add your version

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 in publications

 (7)
PMCID: 3747863
PMID: 23786315
DOI: 10.1186/1471-2105-14-201

[…] 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, […]

PMCID: 3444262
PMID: 22859681
DOI: 10.1093/jxb/ers193

[…] 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 (). […]

PMCID: 3180464
PMID: 21899774
DOI: 10.1186/1756-0500-4-331

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]


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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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