GenMAPP
Encyclopedia
GenMAPP is a free, open-source bioinformatics
software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease. First created in 2000, GenMAPP is developed by an open-source team based in an academic research laboratory. GenMAPP maintains databases of gene identifiers and collections of pathway maps in addition to visualization and analysis tools. Together with other public resources, GenMAPP aims to provide the research community with tools to gain insight into biology through the integration of data types ranging from genes to proteins to pathways to disease.
data from human, mouse, rat and yeast
. In 2004, GenMAPP 2.0 was released, combining the previously accessory programs MAPPFinder [2] and MAPPBuilder, and expanding support to additional species. GenMAPP 2.1 was released in 2006 with new visualization features and support for a total of eleven species.
tools, GenMAPP is not designed for cell/systems modeling; it focuses on the immediate needs of bench biologists by enabling them to rapidly interpret genomic data with an intuitive, easy-to-use interface.
GenMAPP is implemented in Visual Basic
6.0 and is available as a stand-alone application for Microsoft Windows
operating systems, including Boot Camp or Parallels Workstation
on a Mac. The program is freely available for download and includes an automatic update feature that allows rapid and reliable distribution of updates to the program and documentation.
s:
GenMAPP provides tools to create, edit and annotate biological pathway maps.
GenMAPP allows users to visualize and analyze their data in the context of pathway collections and the Gene Ontology
.
Pathways and associated data can be exported for the web as HTML. See examples:
Kristina Hanspers,
Nathan Salomonis,
Kam Dahlquist,
Scott Doniger,
Jeff Lawlor,
Alex Zambon,
Lynn Ferrante,
Karen Vranizan,
Steven C. Lawlor,
Bruce Conklin
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease. First created in 2000, GenMAPP is developed by an open-source team based in an academic research laboratory. GenMAPP maintains databases of gene identifiers and collections of pathway maps in addition to visualization and analysis tools. Together with other public resources, GenMAPP aims to provide the research community with tools to gain insight into biology through the integration of data types ranging from genes to proteins to pathways to disease.
History
GenMAPP was first created in 2000 as a prototype software tool in the laboratory of Bruce Conklin at the J. David Gladstone Institutes in San Francisco and continues to be developed in the same non-profit, academic research environment. The first release version of GenMAPP 1.0 was available in 2002 [1], supporting analysis of DNA microarrayDNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
data from human, mouse, rat and yeast
Saccharomyces cerevisiae
Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
. In 2004, GenMAPP 2.0 was released, combining the previously accessory programs MAPPFinder [2] and MAPPBuilder, and expanding support to additional species. GenMAPP 2.1 was released in 2006 with new visualization features and support for a total of eleven species.
Usage
GenMAPP was developed by biologists and is focused on pathway visualization for bench biologists. Unlike many other computational systems biologySystems biology
Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
tools, GenMAPP is not designed for cell/systems modeling; it focuses on the immediate needs of bench biologists by enabling them to rapidly interpret genomic data with an intuitive, easy-to-use interface.
GenMAPP is implemented in Visual Basic
Visual Basic
Visual Basic is the third-generation event-driven programming language and integrated development environment from Microsoft for its COM programming model...
6.0 and is available as a stand-alone application for Microsoft Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
operating systems, including Boot Camp or Parallels Workstation
Parallels Workstation
Parallels Workstation is the first commercial software product released by Parallels, Inc., a developer of desktop and server virtualization software...
on a Mac. The program is freely available for download and includes an automatic update feature that allows rapid and reliable distribution of updates to the program and documentation.
Content and Features
GenMAPP builds and maintains gene databases for a variety of key model organismModel organism
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
s:
- human - Homo sapiens
- mouse - Mus musculus
- rat - Rattus norvegicus
- yeast - Saccharomyces cerevisiaeSaccharomyces cerevisiaeSaccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
- zebrafish - Danio rerioDanio rerioThe zebrafish, Danio rerio, is a tropical freshwater fish belonging to the minnow family of order Cypriniformes. It is a popular aquarium fish, frequently sold under the trade name zebra danio, and is an important vertebrate model organism in scientific research.-Taxonomy:The zebrafish are...
- worm - Caenorhabditis elegansCaenorhabditis elegansCaenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
- fruit fly - Drosophila melanogasterDrosophila melanogasterDrosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
- dog - Canis familiaris
- cow - Bos taurus
- mosquito - Anopheles gambiaeAnopheles gambiaeAnopheles gambiae is a complex of at least seven morphologically distinguishable species of mosquitoes in the genus Anopheles. This complex was recognised in the 1960s and includes the most important vectors of malaria in sub-Saharan Africa and the most efficient malaria vectors known.This species...
- E.coli - Escherichia coliEscherichia coliEscherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
GenMAPP provides tools to create, edit and annotate biological pathway maps.
GenMAPP allows users to visualize and analyze their data in the context of pathway collections and the Gene Ontology
Gene Ontology
The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
.
Pathways and associated data can be exported for the web as HTML. See examples:
- IGTC
- GenMAPP archives
- Embryonic Stem Cell Differentiation (dataset from GEO: Andrade Lab, Ottawa Hailesellasse et al. 2005-submitted)
- Mouse Uterine Pregnancy Timecourse (dataset from Salomonis et al. 2005 Genome Biology 6:R12.16)
See also
- WikiPathwaysWikiPathwaysWikiPathways is a community resource for biological pathways.-What is WikiPathways:WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways represents a new model for pathway databases that enhances complementary...
- CytoscapeCytoscapeCytoscape 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...
- EnsemblEnsemblEnsembl is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project...
- KEGG
- NetpathNetpathNetPath is a manually curated resource of human signal transduction pathways. It is a joint effort between Pandey Lab at the Johns Hopkins University and the Institute of Bioinformatics , Bangalore, India, and is also worked on by other parties....
- ReactomeReactomeReactome is a database of biological pathways. There are several Reactomes that concentrate on a specific organism, the largest of these is focused on human biology, but includes pathway steps inferred to exist in humans based on experimental data from model organisms and pathways computationally...
- Gene OntologyGene OntologyThe Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
External links
- GenMAPP Website
- GenMAPP – Data Links
- Cytoscape
- PathVisio
- WikiPathways
- GenMAPP on SourceForge.net
Developers
Alexander Pico,Kristina Hanspers,
Nathan Salomonis,
Kam Dahlquist,
Scott Doniger,
Jeff Lawlor,
Alex Zambon,
Lynn Ferrante,
Karen Vranizan,
Steven C. Lawlor,
Bruce Conklin