bioKepler statistics

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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


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  • person_outline Weizhong Li <>
  • person_outline Ilkay Altintas <>

bioKepler in publications

PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] 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 […]

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

[…] 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 […]

PMCID: 4466500
PMID: 26125026
DOI: 10.1155/2015/904541

[…] 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 […]

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 […]

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

[…] 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 […]

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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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