October 20, 2009

PathVisio 2.0 has been released! New in PathVisio 2.0 is the ability to import experimental datasets (microarray, proteomics or metabolomics) and create customized visualizations on pathways. This new version also includes over-representation analysis which lets you quickly find pathways that are most affected by experimental conditions. PathVisio is developed by the BiGCaT Bioinformatics group at the University of Maastricht. PathVisio is available as a standalone application and it also serves as the pathway editor for WikiPathways. For more information, see the Visual Tour, or visit the PathVisio website.

September 3, 2009

We are pleased to announce the release of three new GenMAPP Gene Databases for Arabidopsis thaliana, Plasmodium falciparum, Vibrio cholerae, and an update to the Escherichia coli K12 Gene Database. These databases were created automatically by the Bioinformatics Group at Loyola Marymount University using a suite of programs called XMLPipeDB, a reusable open source tool chain for building relational databases from XML sources (http://xmlpipedb.cs.lmu.edu).The databases are available for download through the Downloader tool in GenMAPP, as well as through SourceForge: http://sourceforge.net/projects/xmlpipedb/files/.

A new Contributed pathway archive for Arabidopsis is available for
download through the Downloader feature in GenMAPP. The pathways included in this archive were collected from WikiPathways (www.wikipathways.org).

March 18, 2009

We are pleased to announce that GenMAPP has been accepted as a mentoring organization for the 3rd consecutive year in Google Summer of Code (GSoC) 2009! Our participation is this program has funded summer positions for 12 students in the past. Our GSoC projects include Cytoscape, WikiPathways and GenMAPP-CS, under the organizational name of "GenMAPP".
Visit our official GSoC page to learn more about us and our projects.
STUDENTS: Apply now! Deadline is April 3rd.

March 5, 2009

A manuscript describing WikiPathways web services is in review at PLoS ONE. The paper describes a web service that is complimentary to WikiPathways.org and allows for programmatic access to WikiPathways content. Several detailed examples of how this web service can be used are included.

January 27, 2009

WikiPathways Milestone 10 was released. A new "Private Pathways" feature allows users to keep pathways hidden from the public for a period of time. This can be useful when working on content that is not yet published. Read more about Private Pathways here.
Support for two additional species, Arabidopsis thaliana and Oryza japonica was also added.

November 14, 2008

WikiPathways Milestone 8 was released. New for this release is that all pathways are now identified by stable identifiers, rather than by the pathway name. This makes linking to WikiPathways pathways more stable and reliable. Read more about stable identifiers here.

September 25, 2008

PathVisio was described in a publication in BMC Bioinformatics. The publication highlights PathVisio as a tool for visual compilation of biological knowledge, interpretation of high-throughput expression datasets, and computational augmentation of pathways with interaction information.

September 14, 2008

Version 1.19 of GO-Elite was released. This program works with lists of genes or probesets to identify over-represented GO terms and pathways, and reports a minimal set of non-redundant GO terms. GO-Elite also reports genes and gene overlaps between terms and allows for summarization of gene expression data at the pathway level. This latest version is compatible with Windows, Mac and Linux and can be used to automatically extract the most recent pathway content from WikiPathways. For more information, visit the GO-Elite website.

September 10, 2008

WikiPathways Milestone 7 was released. This release includes a WikiPathways web service, for programmatic acces to WikiPathways.
Several improvements have been made to the pathway pages:
- Curation tags can now be added to any pathway to inform the community about the state of the pathway. A complete list of curation tags is available at WikiPathways.
- Author names are now listed on top of each pathway page.
- Citation numbers are now visible on the pathway image.

July 22, 2008

An article introducing WikiPathways was published in PLoS Biology. The article generated an overwhelming response and interest by other media and the blogosphere. Here is a collection of "clippings":
- Interview by Mitch Waldrop to provide one of the main story lines for his Big data: Wikiomics Nature article
- Interview by Allison Doerr for her Nature Methods piece entitled, We the curators.
- Thetwo first authors received personal emails from Ward Cunningham (the father of the wiki) congratulating us on WikiPathways!
- News: Science, Nature, NBIC, Gladstone, El Mundo (spanish).
- Blogs: OpenHelix, Mining Drug Space, MindBlog, Science Surf, Sandwalk, Trailfire, Helixsoft, BioUnalm (spanish), Noticiasdot (spanish), Taringa! (spanish)
- Links: MetaBase, EcoliWiki, Wikipedia, Intute, Pathguide, GenMAPP
- Presentations: New Channels of Communication in Biology Workshop, tutorial videos.
- Citations: Emerging World of Wikis, CiteULike, Highwire Press.

July 20, 2008

Version 1.0 of the program AltAnalyze was released. AltAnalyze is a freely available, cross-platform program that allows you to analyze microarray data to identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. To learn more, visit the AltAlanyze website.

March 17, 2008

Google Summer of Code^TM is back again in 2008! Over the past three years, the program has brought together over 1500 students and 2000 mentors from 90 countries worldwide.

We are pleased to announce that GenMAPP is one of the mentoring organizations selected to participate.
Visit our Google Summer of Code^TM Ideas Page to learn more about us
and our projects.
If you are interested in participating you must act quickly as the deadline for student applications is March 31, 2008.

February 28, 2008

The latest databases for human, mouse and rat now include support for
Affymetrix whole-transcript expression arrays (Human Gene 1.0 ST,
Mouse Gene 1.0 ST and Rat Gene 1.0 ST). Databases are available for
download through the GenMAPP Data Acquisition Tool.

January 29, 2008

Updates are available for GenMAPP. Go to Tools>Updater in GenMAPP to
get the updates, or if you have GenMAPP set to automatically check for
updates, you will be notified of the updates on start-up.
The update relates to changes in the MAPP Information area, which now
supports hyperlinks as well as a new License field.

November 26, 2007

This past summer, GenMAPP participated for the first time in the Google Summer of Code^TM program. This year, the program included 900 students across 90 countries contributing to over 130 different open source software projects. The GenMAPP project was privileged to have 4 outstanding students who all made great contributions.
One of the students recently shared her experience on the Google Summer of Code blog, click here to read more.

November 2, 2007

We are pleased to announce Wikipathways.org, an open public space for content editing dedicated to biological pathways. WikiPathways.org is the first pathway database with wiki functionality and will now serve as the primary source of GenMAPP pathways. Currently in beta, WikiPathways includes just over 100 pathways reproduced in rat, mouse and human and uses an embedded PathVisio editor for wiki-style editing of pathway content.

PathVisio 1.0 has been released! PathVisio is a new cross-platform pathway visualization and editing tool developed by the BiGCaT Bioinformatics group at the University of Maastricht. PathVisio is available as a standalone application and it also serves as the pathway editor for WikiPathways.

The GenMAPP website has been re-designed. A new Google search feature on the front page makes it easier to search for GenMAPP pathways and Help documentation. A brand new Showcase section illustrates how GenMAPP is used in the literature and online.

GenMAPP has been awarded an NIH grant for continued development and maintenance of the GenMAPP software over the next 4 years. The R01 grant will specifically go towards the new GenMAPP-CS project, which will be platform-independent and will provide enhanced support for complex data types, integration with public resources and innovative pathway editing and layout features. For more information see our specific aims.

July 26, 2007

A new manuscript describing the latest version of GenMAPP (version 2) has been published at BMC Bioinformatics. This publication details new features and resources available with GenMAPP 2, intended to aid in pathway level analysis of complex genomic datasets. To view this manuscript, click on the following link (Salomonis et al. 2007, BMC Bioinformatics).

April 26, 2007

GenMAPP and WikiPathways were presented at RECOMB, the eleventh Annual International Conference on Research in Computational Molecular Biology. The posters are available for viewing here:

GenMAPP RECOMB2007 poster
WikiPathways RECOMB2007 poster

March 15, 2007

Last year Google spent $3,000,000 to fund 630 student projects across 90 countries with the help of over 100 mentoring organizations. Google Summer of Code^TM is back again in 2007!

We are pleased to announce that GenMAPP is one of the mentoring organizations selected to participate in Google Summer of Code^TM 2007! Click here to see the full announcement.

Visit our Google Summer of Code^TM Ideas Page to learn more about us and our projects.

January 29, 2007

New GenMAPP gene databases will be available soon. A new build procedure will allow for the creation of any Ensembl supported species (currently 26). Current gene database and pathway information is available by selecting these links.

January 4, 2007

A new release of GenMAPP 2.1 is now available!
The new release includes an improved user interface for displaying Multiple Color Sets (Documentation) as well as an updated Data Acquisition Tool that allows for the selection of a preferred download location (Documentation).
To receive this latest version, go to Tools>Updater in the GenMAPP program, or install GenMAPP using the latest installer here.
To see an example of how you can use the Multiple Color Sets feature in GenMAPP, click here to view a time course dataset of mouse uterine muscle during pregnancy.

Announcing PathVisio 1.0 beta
PathVisio is a new cross-platform pathway visualization and editing tool developed by the BiGCaT Bioinformatics group at the University of Maastricht. The current implementation of PathViso is available as a WebStart program that allows users to view and edit existing MAPP files or create new pathways on any operating system. The available GPML (GenMAPP Pathway Markup Language) pathways are converted directly from GenMAPP pathways and should appear exactly the same. Pathways generated in PathViso are also reverse compatible with GenMAPP by exporting the GPML to the MAPP format. For more information, visit the PathVisio website. 

September 1, 2006

We are pleased to announce the release of a GenMAPP Gene Database for
Escherichia coli K12. The database was created automatically by the Bioinformatics Group at Loyola Marymount University The database was created programmatically using XMLPipeDB based on the UniProt complete proteome set and GOA gene associations to Gene Ontology. The database contains several gene ID systems, including UniProt, Blattner, EchoBASE and EcoGene. It also contains annotation information from EMBL, Gene Ontology, InterPro, PDB and Pfam. The database is available for download through the Downloader tool in GenMAPP, as well as at http://www.cs.lmu.edu/~xmlpipedb/download.shtml. A detailed ReadMe document describing the database schema is packaged with the database.

GenMAPP is now also available for mosquito. A Gene Database Anopheles gambiae is available for download via GenMAPP, under Data>Download Data from GenMAPP.org.

July 26, 2006

Quantitative analysis of MAPPFinder results

GO-Quant is a program for quantitative analysis of MAPPFinder results, developed in the laboratory of Dr. Xiaozhong Yu at the Institute for Risk Analysis and Risk Communication at the University of Washington. GO-Quant is a standalone program that extracts quantitative gene expression values and calculates the average intensity or ratio based on functional gene category from MAPPFinder Results.
A publication describing the program is available at http://toxsci.oxfordjournals.org/cgi/content/full/92/2/560. To download the program, visit http://depts.washington.edu/irarc/Go-Quant/index.html.

GenMAPP is now available for fission yeast. A custom Gene Database and MAPP Archives for Schizosaccharomyces pombe have been created through a collaboration with NIPER, the National Institute of Pharmaceutical Education and Research, India. For more information and to download the database and MAPPs, see http://www.databases.niper.ac.in/Pombe/.

June 7, 2006

GenMAPP 2.1 is now available! GenMAPP now allows for simultaneous display of data from multiple Color Sets on MAPPs. Gene boxes are partitioned into colored stripes that each represents a Color Set selected. This feature was designed to allow for efficient display of complex data, such as time course experiments, but is applicable to any other GenMAPP dataset with multiple color sets. MAPP Sets export of multiple Color Sets now includes a summary view of all selected Color Sets. Additional new features in GenMAPP 2.1 include updates to the Downloader and the addition of a set of polygon objects in the Object Toolbox.

Updates to GenMAPP MAPP Archives - NetPath

A set of 10 cancer and 10 immune signaling pathways have been added to the GenMAPP Contributed MAPP archive, as part of an ongoing collaboration with NetPath. NetPath (http://www.netpath.org/) is a human pathway annotation project, initiated by the PandeyLab at Johns Hopkins University (http://pandeylab.igm.jhmi.edu) and the Institute of Bioinformatics (http://www.ibioinformatics.org). The 10 cancer signaling pathways were developed in collaboration with the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (http://cbio.mskcc.org) and with Gary Bader's lab at the University of Toronto (http://baderlab.org) for the Cancer Cell Map (http://cancer.cellmap.org). All 20 pathways are freely available in GenMAPP, PSI-MI and BioPAX formats at http://www.netpath.org.  The 10 cancer signaling pathways are also available for download and browsing from http://cancer.cellmap.org. All 20 pathways have been inferred from human to all other GenMAPP supported species.
These pathways are unpublished at this time; please cite these websites until the pathways are described in a publication.  Feedback about the NetPath site and its contents can be sent to: info@netpath.org

March 8, 2006

Updated gene databases for human (Hs-Std_20060127) and cattle (Bt-Std_20060127) are now available for download. The human database supports the full Affymetrix HG-U95 array set.

December 20, 2005

GenMAPP is now available for cattle. A Gene Database and MAPP Archives for Bos taurus are available for download via GenMAPP, under Data>Download Data from GenMAPP.org. These MAPPs were inferred from the human contributed MAPPs. Please note that the cattle MAPPs retain the human gene symbol as the gene label on the MAPP.

November 18, 2005

GenMAPP is now available for chicken. A Gene Database and MAPP Archives for Gallus gallus are available for download via GenMAPP, under Data>Download Data from GenMAPP.org.

GenMAPP Contributed MAPP archives have been updated for human, mouse and rat. The update includes a new format for the Backpage heading.

MAPPs for several species have been inferred from human MAPPs, using orthology information. These MAPPs are now available for download for chicken, dog, worm, yeast, zebrafish and fruit fly. The MAPP archives are designated as “Inferred”. Human was chosen as the template species for conversion and ortholog information between human and the applicable target species was obtained from Homologene and from Ensembl. The data utilized from these resources was restricted to the one-to-one gene relationships between template and target species. Conversion between species was accomplished using the Converter tool in GenMAPP. MAPPs were 50% or more of the genes converted between species were included in the archive.
A descriptive manual for how to convert MAPPs between species is available here. Detailed descriptions of each MAPP archive along with archive statistics can be accessed by clicking here.

A collection of yeast MAPPs based on the SGD Metabolic pathways (http://pathway.yeastgenome.org/biocyc/) is now available for download.

September 15, 2005

Source code for GenMAPP 2.0 applications are now available at SourceForge.net (http://sourceforge.net/projects/genmapp), under an Apache open source license agreement. In addition to GenMAPP 2.0, source code contributed by community GenMAPP developers will be posted here. To post new source code here, please contact us at: genmapp@gladstone.ucsf.edu.

July 31, 2005

A discussion group for GenMAPP users is now available at Google groups. The group is intended as an open forum for discussing GenMAPP, asking questions, reporting bugs and suggesting new features. Go to the GenMAPP Google group.

GenMAPP is now available for dog. A Gene Database and MAPP Archives for Canis familiaris is available for download via GenMAPP, under Data>Download Data from GenMAPP.org.

Updated Gene Databases for all supported species are now available for download. These new databases are based on Ensembl gene IDs (when applicable), and include several new gene ID and annotation systems, including Ensembl, EMBL, Pfam, OMIM, HUGO and PDB. The currently supported species are human, mouse, rat, dog, yeast, worm, fruit fly and zebrafish.

Several additional species databases are also available on request, including mosquito (A. gambiae), honey bee (A. mellifera), fugu (F. rubripes), chicken (G. gallus), chimpanzee (P. troglodytes) and pufferfish (T. nigroviridis). GenMAPP.org can readily build Gene Databases for additional species based on Ensembl genome assemblies (see current list at ensembl.org). For additional species, users can create their own custom databases.

July 28, 2005

A set of MAPPs depicting tissue-specific genes in mouse and human are now available for download. The MAPPs were developed in the Conklin Lab at Gladstone/UCSF in close collaboration with Jonathan Schug in the Stoeckert lab at the University of Pennsylvania Center for Bioinformatics. The primary purpose of these MAPPs is to allow researchers to identify tissue specific gene expression patterns in DNA-microarray data. For more information, click here.

February 4, 2005

A set of featured publications is now available. These articles highlight the functionality of GenMAPP 2.0 and MAPPFinder 2.0 for pathway expression analysis. Also available are related flash animation movies, further detailing and describing these analyses.

January 13, 2005

A new GenMAPP 2.0 software review, "GenMAPP: When you don't feel like going down the pathway interference road", was published in the Canadian Bioinformatics Help Desk Newsletter.

December 17, 2004

The official release of GenMAPP 2.0 is now available!! This version contains significant improvements over previous builds, including an updated database allowing multiple ID sources and support of new model organisms. Version 2.0 also integrates multiple programs into one package (MAPPFinder, MAPPBuilder, a MAPP/Dataset Converter and MAPP Set export). Each contains several enhanced features from previous builds. Version 2.0 beta has been tested by over 500 beta testers before this public release.

GenMAPP.org also has an updated and expanded set of Contributed pathway MAPPs. Over 15 unique annotated pathway MAPPs have been added to each the Contributed MAPP archives for human, mouse and rat that provide a robust base for pathway expression analysis. A separate archive of hundreds of Gene Ontology reference MAPPs have also been included, for quick reference to main Gene Ontology terms. Other improvements include an ontology based folder structure, standardization of gene names and IDs based on the LocusLink database, and removal of simple list MAPPs redundant with the provided Gene Ontology Reference set. HTML versions of all of the new MAPP archives are now available for web browsing.

November 23 , 2004

The MAPP Archives have been updated and reorganized. There are now several MAPP archives for each species. These new archives can be downloaded from within the GenMAPP installer or within GenMAPP version 2.0 using the Download option within Data file menu.

HTML versions of all of the new MAPP archives are now available for web browsing. Linked to from each of these archives are HTML browsable lists of genes found on each MAPP.

September 15, 2004

An XML schema has been developed for importing and exporting GenMAPP maps, Ferrante(2004). GenMAPP.org is currently working on implementation of import and export of maps in XML. This schema is posted for informational purposes and may be modified before implementation of this feature is completed. Questions should be directed to genmapp@gladstone.ucsf.edu

August 12, 2004

GenMAPP and Cytoscape. Future GenMAPP versions will support automatic layout features to aid in the creation of pathways. We are pursuing a coordinated effort with Cytoscape to integrate their network visualization tools with the MAPP building function of GenMAPP. Cytoscape is a Java-based open-community software project designed to generate network graphs from large databases of protein-protein and genetic interactions. Cytoscape's simple yet powerful interface will provide a key step in the process of transforming interaction data into meaningful displays of annotated pathways.

We have revised the GenMAPP acronym from "Gene MicroArray Pathway Profiler" to "Gene Map Annotator and Pathway Profiler". This change has been made in light of the fact that GenMAPP is now used for a wide variety of data types in addition to microarray data (e.g. gene trapping, SNPs, functional genomic experiments). The new GenMAPP definition reflects the use of GenMAPP to annotate pathways for use with any type of genomic data. If preparing a manuscript referencing the definition of GenMAPP, please use the new definition and additionally reference http://www.genmapp.org.

June 9, 2004

GenMAPP is pleased to announce that we are collaborating with BioPAX (Biological Pathways Exchange). Biopax is a community based initiative whose mission is to develop a flexible and extensible common exchange format for biological pathways data. GenMAPP’s efforts initial involvement will focus on implementing a Biopax to GenMAPP pathway converter.

April 20, 2004

GenMAPP 2.0 beta is now available!! Version 2.0 contains significant improvements, including an enhanced database allowing multiple ID sources and support of new model organisms. Version 2.0 also integrates multiple programs into one package (MAPPFinder, MAPPBuilder, a MAPP/Dataset Converter and MAPP Set export). Version 2.0 beta has been tested by over 100 pre-beta testers before this public release.

May 1, 2003

Source code for GenMAPP version 1.0 is now available.

April 4, 2003

New versions of MAPPFinder version 1.0 and several contributed MAPP archives are now available. MAPPFinder 1.0 features an updated database, featuring expanded Gene Ontology associations.

January 8, 2003

This month in Genome Biology, "MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data."

October 2, 2002

A new MAPP update is available. New Contributed MAPPs for Human, Mouse, and Rat are now available including the completed archive of Rat MAPPs. This update for Mouse and Human is a supplement to the existing archive of Contributed MAPPs.

August 5, 2002

MAPPFinder 1.0 Beta is now online. MAPPFinder works with GenMAPP and Gene Ontology to create a gene expression profile across all areas of biology. This tool will make it possible to rapidly identify those MAPPs and Gene Ontology biological processes, cellular component, and molecular function terms that are showing interesting gene expression changes.

May, 24 2002

This month in Nature Genetics, "GenMAPP, A New Tool for Viewing and Analyzing Microarray Data on Biological Pathways."

March, 11 2002

GenMAPP software reviewed in Science magazine.

The official release of GenMAPP 1.0 is available in the Download Area! Version 1.0 is a Windows compatible software package designed to visualize data from user's gene expression experiments in the context of biological groupings. This updated version contains several enhanced features, including a new and expanded Human-Mouse-Rat species database.

The official Yeast version of GenMAPP 1.0 is now also online. This program contains identical features to GenMAPP 1.0, but as a Yeast-specific program with a gene database based on SGD and SwissProt.

MAPPBuilder 1.0 Beta, an accessory application to GenMAPP 1.0 is now available. MAPPBuilder allows users to import large gene lists to aid in the creation of MAPPs.

The interactive online tutorial for GenMAPP v.1.0 has been updated for the latest version of GenMAPP.