bioKepler statistics

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Citations per year

Number of citations per year for the bioinformatics software tool bioKepler

Tool usage distribution map

This map represents all the scientific publications referring to bioKepler per scientific context
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Associated diseases


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bioKepler specifications


Unique identifier OMICS_01139
Name bioKepler
Software type Framework/Library
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Weizhong Li
  • person_outline Ilkay Altintas

bioKepler citations


Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] ife Technologies’ LifeScope cloud computing service, which provides one core of a 2.4-GHz Xeon processor with a 4 GB memory for $0.17 per core hour. There are also open source cloud solutions such as BioKepler, GenomeSpace, and Cloud BioLinux, which are accessible through Amazon EC2 cloud, as well as downloadable versions [,,].Infrastructure as a service (IaaS): In this model, the service provider […]


Mapping cell populations in flow cytometry data for cross‐sample comparison using the Friedman–Rafsky test statistic as a distance measure

PMCID: 5014134
PMID: 26274018
DOI: 10.1002/cyto.a.22735

[…] oconductor package ( We are also in the process of implementing and incorporating FlowMap‐FR into the GenePattern FCM suite and the bioKepler workflow platform , so that it can be used along with other FCM data processing and analytical methods that have been deployed in these platforms. A common FCM computational workflow consist […]


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

Biomed Res Int
PMCID: 4466500
PMID: 26125026
DOI: 10.1155/2015/904541

[…] ful distributed computing options to distribute workflow execution on cluster, grid, or cloud.Recently, Kepler has been used for bioinformatics purposes. For intensive computing and NGS analysis, the bioKepler project [] has been initiated. The bioKepler module is an extension for Kepler that integrates bioinformatics components in order to execute bioinformatics tools (e.g., BLAST [] and HMMER [] […]


A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

Evol Bioinform Online
PMCID: 4362911
PMID: 25861210
DOI: 10.4137/EBO.S21501

[…] CRA services will also be made available through the web application offered by the National Center for Genome Analysis Support (NCGAS). Plans are also under way to incorporate CRA services into the bioKepler workflow tool, so that CRA tree inference services can be incorporated into more complex workflows in a visual programming environment.The CIPRES group is developing worked examples/code sam […]


Cytoscape: the network visualization tool for GenomeSpace workflows

PMCID: 4133763
PMID: 25165537
DOI: 10.5256/f1000research.4805.r5291

[…] brief app demonstration highlighting the resulting user interface and data transfer functionality.While there exists a number of workflow engines that can perform biological analyses (e.g., Taverna , BioKepler , and Galaxy ), GenomeSpace distinguishes itself by combining a collaboration-oriented file system (incorporating sharing and stored metadata), a robust and user-extensible spectrum of genom […]


Workflows for microarray data processing in the Kepler environment

BMC Bioinformatics
PMCID: 3431220
PMID: 22594911
DOI: 10.1186/1471-2105-13-102

[…] ble to develop a straightforward solution to this issue (creating a script then executing). Finally, there are far fewer prepackaged bioinformatics resources in Kepler as compared to Taverna, but the bioKepler project [] should change this situation.Making Kepler workflows more widely accessible, e.g., through popular workflow repositories [], will allow pipeline developers to share workflows more […]

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bioKepler institution(s)
San Diego Supercomputer Center University of California, San Diego, CA, USA; Center for Research in Biological Systems University of California, San Diego, CA, USA
bioKepler funding source(s)
Supported by NSF SDCI Award OCI-0722079 for Kepler/CORE, NSF ABI Award DBI-1062565 for bioKepler, the Gordon and Betty Moore Foundation award to Calit2 at UCSD for CAMERA, and an SDSC Triton Research Opportunities grant.

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