GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop tools and facilitates the transfer of data between tools via automatic format conversion. Analyses can use data from local or cloud-based stores. GenomeSpace consists of a web-based

user interface In the industrial design field of human–computer interaction, a user interface (UI) is the space where interactions between humans and machines occur. The goal of this interaction is to allow effective operation and control of the machine f ...

(UI) for users, and both a representational state transfer (RESTful)

application programming interface An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how t ...

(API) and a

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...

-based client development kit (CDK) for developers integrating their applications with GenomeSpace.

GenomeSpace tools

GenomeSpace is linked with several tools and data sources for genomics analysis:

Cytoscape Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available f ...

Galaxy A galaxy is a system of stars, stellar remnants, interstellar gas, dust, dark matter, bound together by gravity. The word is derived from the Greek ' (), literally 'milky', a reference to the Milky Way galaxy that contains the Solar System. ...

GenePattern GenePattern is a freely available computational biology open-source software package originally created and developed at the Broad Institute for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomi ...

, Genomica,

geWorkbench geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java (programming language), Java. geWorkbench uses a component architect ...

, InSilico DB, the Integrative Genomics Viewer (IGV), and the http://hgwdev-gs.cse.ucsc.edu/cgi-bin/hgTables

UCSC Genome Browser The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate spec ...

. These programs provide a wide variety of genomic analyses, including network analysis and visualization, sequence analysis, whole-genome analysis, general statistical methods, gene expression analysis,

proteomics Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

, flow cytometry, next-generation sequence analysis, and genomic datasets. Developers of other genomics software can use the GenomeSpace API to add their tools.

Collaborators

The GenomeSpace project is a collaboration of the Mesirov and Regev laboratories at the

Broad Institute The Eli and Edythe L. Broad Institute of MIT and Harvard (IPA: , pronunciation respelling: ), often referred to as the Broad Institute, is a biomedical and genomic research center located in Cambridge, Massachusetts, Cambridge, Massachusetts, U ...

; the Chang laboratory at

Stanford University Stanford University, officially Leland Stanford Junior University, is a private research university in Stanford, California. The campus occupies , among the largest in the United States, and enrolls over 17,000 students. Stanford is consider ...

; the Ideker laboratory at the

University of California, San Diego The University of California, San Diego (UC San Diego or colloquially, UCSD) is a public university, public Land-grant university, land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Insti ...

; the Nekrutenko laboratory at

Pennsylvania State University The Pennsylvania State University (Penn State or PSU) is a Public university, public Commonwealth System of Higher Education, state-related Land-grant university, land-grant research university with campuses and facilities throughout Pennsylvan ...

; the Segal laboratory at the

Weizmann Institute of Science The Weizmann Institute of Science ( he, מכון ויצמן למדע ''Machon Vaitzman LeMada'') is a public research university in Rehovot, Israel, established in 1934, 14 years before the State of Israel. It differs from other Israeli unive ...

; and the Haussler and Kent laboratories at the

University of California, Santa Cruz The University of California, Santa Cruz (UC Santa Cruz or UCSC) is a public university, public Land-grant university, land-grant research university in Santa Cruz, California. It is one of the ten campuses in the University of California syste ...

. GenomeSpace is funded by the

National Human Genome Research Institute The National Human Genome Research Institute (NHGRI) is an institute of the National Institutes of Health, located in Bethesda, Maryland. NHGRI began as the Office of Human Genome Research in The Office of the Director in 1988. This Office transi ...

of the

National Institutes of Health The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

References

External links

{{Official website, www.genomespace.org Free bioinformatics software