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Cytoscape Plugin for MiMI

Cytoscape Plugin for MiMI. Is a widely used open source software tool for the analysis of bimolecular interaction networks. The power of Cytoscape is most apparent when it is coupled to databases of protein-protein, protein-DNA, and genetic interactions. Protein interaction data exists in many repositories, each with its own data format, molecule identifier and supplementary information. MiMI. For chosen networks graphic match against biological pathways. This plug-in provides users an interactive mo...

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Cytoscape Plugin for MiMI | mimiplugin.ncibi.org Reviews
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Cytoscape Plugin for MiMI. Is a widely used open source software tool for the analysis of bimolecular interaction networks. The power of Cytoscape is most apparent when it is coupled to databases of protein-protein, protein-DNA, and genetic interactions. Protein interaction data exists in many repositories, each with its own data format, molecule identifier and supplementary information. MiMI. For chosen networks graphic match against biological pathways. This plug-in provides users an interactive mo...
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Cytoscape Plugin for MiMI | mimiplugin.ncibi.org Reviews

https://mimiplugin.ncibi.org

Cytoscape Plugin for MiMI. Is a widely used open source software tool for the analysis of bimolecular interaction networks. The power of Cytoscape is most apparent when it is coupled to databases of protein-protein, protein-DNA, and genetic interactions. Protein interaction data exists in many repositories, each with its own data format, molecule identifier and supplementary information. MiMI. For chosen networks graphic match against biological pathways. This plug-in provides users an interactive mo...

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mimiplugin.ncibi.org mimiplugin.ncibi.org
1

Cytoscape Plugin for MiMI

http://mimiplugin.ncibi.org/tutorial.html

Install Cytoscape and MiMI Plugin. Getting literature information for selected edge and sort the result. Finding pathway matches for chosen network. Adding your own node/edge annotation. Finding paths among given genes. Install Cytoscape and MiMI Plugin. Click here to get instructions. Assuming that you already installed Cytoscape and MiMI Plugin. If you need to install Cytoscape, click here. Prepare a list of genes, see, for example mygene.txt. Load mygene.txt file. B) Load Gene File- your gene file name.

2

Cytoscape Plugin for MiMI

http://mimiplugin.ncibi.org/acknowledgement.html

Our Cytoscape MiMI Plugin. Queries interaction from MiMI and visualizes returned network with Cytoscape. Our plugin also integrates BioNLP database for literature information, MEAD for document summarization and SAGA for pathway matching. Here, we want to thank Cytoscape for providing this fabulous tool. We also thank CCMB. At University of Michigan. For providing MiMI, BioNLP, MEAD and SAGA. MiMI and the MiMI Cytoscape Plugin are supported by generous grants from:. National Institutes of Health: Grants ...

3

Cytoscape Plugin for MiMI

http://mimiplugin.ncibi.org/tryplugin.html

To launch the Cytoscape with the MiMI Plugin installed using Java WebStart (This may take a minute or two for the first time loading). JRE/JDK 1.5 or above are required in your system. For bug reporting please email: mimi-help@umich.edu.

4

Cytoscape Plugin for MiMI

http://mimiplugin.ncibi.org/bugs.html

Known bugs and issues. MiMI internal IDs are build dependent. This affects users node/edge annotations since we use this internal id as the identifier of node/edge annotation. It can also affect external storage and linking of data using MiMI IDs. For bug reporting please email: mimi-help@umich.edu.

5

Cytoscape Plugin for MiMI

http://mimiplugin.ncibi.org/download.html

Download Cytoscape and MiMI Plugin. Download Cytoscape from cytoscape.org. Download and Install MiMIPlugin. Install from within Cytoscape. A) Startup Cytoscape- Plugins- Manage Plugins- Available for Install- Network and Attribute I/O- MiMIPlugin. Download a sample input file. Users can upload a text file with gene list to start the interaction network query. Users can specify species, molecule type etc using GUI or put these parameters on the header lines of the input file. Here is a sample input file:.

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Cytoscape Plugin for MiMI. Is a widely used open source software tool for the analysis of bimolecular interaction networks. The power of Cytoscape is most apparent when it is coupled to databases of protein-protein, protein-DNA, and genetic interactions. Protein interaction data exists in many repositories, each with its own data format, molecule identifier and supplementary information. MiMI. For chosen networks graphic match against biological pathways. This plug-in provides users an interactive mo...

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