Getting started with GenMAPP

Prerequisites

To begin using GenMAPP, you will need a relatively powerful computer. For details, see our Technical Specifications.

Download and installation

1. Visit the GenMAPP website to register and download the program.
2. Install GenMAPP by double-clicking the installer. Follow instructions in the installer.
3. Start GenMAPP by double-clicking on the Desktop icon. You will be prompted to download accessory files, you can either proceed to do this immediately, or at a later time.

Download accessory files

GenMAPP works with 3 different file types:

Expression Dataset

Expression Dataset

 The Expression Dataset contains any experimental data you import to GenMAPP. This can be any large-scale data annotated with a GenMAPP-supported identifier. A number of example datasets are available for download through the Downloader. You will need to import your data to GenMAPP to create an Expression Dataset to view your data, or you can download one of the example datasets.

Note: The name Expression Dataset is historical. Any large-scale data can be used in GenMAPP, it is not limited to expression data.

Pathway MAPP

The MAPP file contains information about a particular pathway or process, including layout, gene and graphical annotation. GenMAPP.org distributes a set of MAPP archives for each supported species, which can be downloaded through the Downloader. Pathway MAPPs can also be created using MAPPBuilder and GenMAPP's drawing tools. To use GenMAPP, you will need to download at least one MAPP arhicve for your species of interest.

For descriptions of the contents of our MAPP archives, visit our website.

Gene Database

The Gene Database contains a species-specific collection of gene, protein and probe identifiers. GenMAPP uses the database to link identifiers form different systems (for example Ensembl and Entrez) when coloring MAPPs with data. The Gene Databases are distributed by GenMAPP.org and can be downloaded through the Downloader. To use GenMAPP, you will need to download the Gene Database for your species of interest.

Using the Downloader

1. To download accessory files, click Data>Download Data from GenMAPP.org in GenMAPP.
2. In the Data Acquisition Tool (Downloader) interface, expand the appropriate folder in the upper left browser. For example, to download a Gene Database, click the plus sign next to the Gene Databases folder.
3. Click on the subfolder for your species, for example Mus musculus for mouse.
4. Select a file to download in the upper right window. The file will be placed in the Download Queue.
5. Repeat steps 2-4 for MAPPs and Expression Datasets.
6. Check the Download Destination Locations and make necessary edits by clicking the Change buttons. It is recommended that you do not change the download destinations from the default.
7. Click the Start button to start the download. The selected files will be downloaded and extracted automatically. After each file is extracted, you may need to click OK to a  message informing you that the extraction is complete.
8. When all files are downloaded and extracted, click OK to close the Downloader.

Downloading accessory files with the Downloader

Do you have comments or questions about this tutorial? Contact GenMAPP Support.