GenMAPP (Gene Map Annotator and Pathway Profiler) is a free,

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

software tool designed to visualize and analyze

genomic Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...

data in the context of pathways (

metabolic Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...

signaling In signal processing, a signal is a function that conveys information about a phenomenon. Any quantity that can vary over space or time can be used as a signal to share messages between observers. The ''IEEE Transactions on Signal Processing'' ...

), 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 San Francisco (; Spanish language, Spanish for "Francis of Assisi, Saint Francis"), officially the City and County of San Francisco, is the commercial, financial, and cultural center of Northern California. The city proper is the List of Ca ...

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, supporting analysis of

DNA microarray A DNA microarray (also commonly known as DNA chip or biochip) 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 ...

data from

human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

mouse A mouse ( : mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus' ...

rat Rats are various medium-sized, long-tailed rodents. Species of rats are found throughout the order Rodentia, but stereotypical rats are found in the genus ''Rattus''. Other rat genera include ''Neotoma'' ( pack rats), ''Bandicota'' (bandicoot ...

and

yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constitut ...

. In 2004, GenMAPP 2.0 was released, combining the previously accessory programs MAPPFinder 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 biology Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...

tools, GenMAPP is not designed for cell/systems modeling; it focuses on the immediate needs of bench biologists by enabling them to rapidly interpret

data with an intuitive, easy-to-use interface. GenMAPP is implemented in

Visual Basic Visual Basic is a name for a family of programming languages from Microsoft. It may refer to: * Visual Basic .NET (now simply referred to as "Visual Basic"), the current version of Visual Basic launched in 2002 which runs on .NET * Visual Basic (cl ...

6.0 and is available as a stand-alone application for

Microsoft Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

operating systems, including Boot Camp or

Parallels Workstation Parallels Workstation is the first commercial software product released by Parallels, Inc., a developer of desktop and server virtualization software. The Workstation software consists of a virtual machine suite for Intel x86-compatible computer ...

on a Mac.

Content and Features

GenMAPP builds and maintains gene databases for a variety of key

model organism A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...

s: * human - ''

Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

'' * mouse - '' Mus musculus'' * rat - '' Rattus norvegicus'' * yeast - ''

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...

'' * zebrafish - '' Danio rerio'' * worm - ''

Caenorhabditis elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' (ro ...

'' * fruit fly - ''

Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly" or "pomace fly". Starting with Ch ...

'' * dog - '' Canis familiaris'' * cow - ''

Bos taurus Cattle (''Bos taurus'') are large, domesticated, cloven-hooved, herbivores. They are a prominent modern member of the subfamily Bovinae and the most widespread species of the genus ''Bos''. Adult females are referred to as cows and adult ma ...

'' * mosquito - ''

Anopheles gambiae The ''Anopheles gambiae'' complex consists of at least seven morphologically indistinguishable species of mosquitoes in the genus ''Anopheles''. The complex was recognised in the 1960s and includes the most important vectors of malaria in sub- ...

'' * ''E.coli'' - ''

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

''
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.

References

External links

*
GenMAPP – Data Links

Cytoscape

PathVisio

WikiPathways
* {{sourceforge, genmapp Bioinformatics software Free science software Systems biology Windows-only free software

History

Usage

Content and Features

See also

References

External links