GSoC ’09: Mesquite

Mesquite NeXML Viewer walk-through August 17, 2009

Filed under: Uncategorized — kasiahayden @ 6:29 pm

My project was to build a Mesquite package to view Phenex-generated NeXML files.

Here are some pictures that demonstrate my additions to Mesquite.

The first half of the summer I worked on getting the Phenex-generated annotations to show up for each cell in the annotations box directly underneath the matrix. See the Phenex tool and the annotations box outlined in green in the picture below:

NeXMLAnnotations_MesquiteNexmlViewer

After that, the second half of the summer was dedicated to getting a visual representation of a given cell’s annotations to appear when the cell was clicked. For this I used Graphviz and the Grappa Java package to generate Graphviz dot graphs. See the Grapviz dot tool and the Graphviz dot graph pop-up outlined in green in the picture below:

dotGraph_MesquiteNexmlViewer

It is possible to zoom in on the graph by right-clicking on the pop-up (or Ctrl-clicking for Mac users). There is also a lot more that can be done with Graphviz than generate this simple graph, which leaves plenty of room for advancements in the future.

Of course, to see this matrix in the first place you must import a NeXML file using the nexml package that Rutger Vos wrote. When nexml is installed, you simply open a NeXML file and choose the nexml option among the interpreter options, like in the picture below:

NeXMLImportFile_MesquiteNexmlViewer

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One Response to “Mesquite NeXML Viewer walk-through”

  1. […] check out Kasia’s walk through of the project.  Her blog also traces the progress and frustrations of learning about ontologies, Mesquite, NeXML […]


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