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Bionimbus specifications


Unique identifier OMICS_02160
Name Bionimbus
Alternative name Bionimbus Protected Data Cloud (PDC)
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Version 3.0
Stability Stable
High performance computing Yes
Registration required Yes
Maintained Yes


No version available


  • person_outline Robert L Grossman
  • person_outline Team Bionimbus

Publication for Bionimbus

Bionimbus citations


Public–Private Partnerships in Cloud Computing Services in the Context of Genomic Research

PMCID: 5247451
PMID: 28164085
DOI: 10.3389/fmed.2017.00003

[…] r Institute, and the Ontario Institute for Cancer Research; (2) the Cancer Genome Collaboratory (CGC), whose partners are the Open Cloud Consortium, the Ontario Institute for Cancer Research, and the Bionimbus Protected Data Cloud; (3) MSSNG that partners Autism Speaks and Google; (4) 100,000 GP which joins Genomics England (GE) with AbbVie, Alexion Pharmaceuticals, AstraZeneca, Berg Health, Bioge […]


Shared Genetic Signals of Hypoxia Adaptation in Drosophila and in High Altitude Human Populations

Mol Biol Evol
PMCID: 4866538
PMID: 26576852
DOI: 10.1093/molbev/msv248

[…] library was first sequenced in a single lane of Illumina HiSeq2000 producing 50-bp single end reads. A 100-bp paired-end sequencing was performed in multiple lanes.Data analysis was performed on the Bionimbus cloud (, an Open Science Data Cloud project focused on biological data, especially Next Generation Sequencing data. FastX toolkit ( […]


Parallel computing in genomic research: advances and applications

PMCID: 4655901
PMID: 26604801
DOI: 10.2147/AABC.S64482

[…] ure prediction is considered as a very computing intensive task. The ProteinSPA tool is mainly based on mpiBLAST, which allows for parallel execution. It can be deployed both on clusters and on grids.Bionimbus is an open source and cloud-based system used by a variety of genomic experiments. Bionimbus is based on OpenStack, and it aims at creating virtual machines in the cloud on demand, depending […]


Whole Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg Size Variation in Drosophila melanogaster

Mol Biol Evol
PMCID: 4576704
PMID: 26044351
DOI: 10.1093/molbev/msv136

[…] ute of Genomic and Systems Biology at The University of Chicago. The 100-bp single and paired-end reads for each library were generated using an Illumina HiSeq2000. Data analysis was performed on the Bionimbus cloud of the Open Science Data Cloud (, last accessed June 15, 2015). FastX toolkit was implemented to check the quality of each read. Reads were map […]


Genomic cloud computing: legal and ethical points to consider

Eur J Hum Genet
PMCID: 4592072
PMID: 25248396
DOI: 10.1038/ejhg.2014.196

[…] lows researchers to use technologies, such as application programming interfaces (APIs) to launch servers (). Various cloud computing platforms have emerged for genomic researchers, including Galaxy, Bionimbus and DNAnexus, which allow researchers to perform genomic analyses using only a web browser. These platforms in turn may run on specific clouds provided by cloud service providers (CSPs).Four […]


Cloud based uniform ChIP Seq processing tools for modENCODE and ENCODE

BMC Genomics
PMCID: 3734164
PMID: 23875683
DOI: 10.1186/1471-2164-14-494

[…] ools and workflows are designed to work with human, mouse, worm, and fly genomes and thus cross species comparisons are possible. For advanced users, we also provide machine images on both Amazon and Bionimbus Clouds so the same consistent and reproducible analysis can be done from the command line. […]


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Bionimbus institution(s)
Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA; Computation Institute, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago IL, USA
Bionimbus funding source(s)
Supported by part by the US National Institutes of Health (NIH/SAIC contract 13XS021/HHSN261200800001E and NIMH/NIH P50MH094267).

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