FastSemSimGui

This section explains how to start and use FastSemSimGui, the graphical front-end included in FastSemSim.

Using fastSemSimGui

FastSemSimGui has been designed to be easy to use.

gui requires wxWidgets package. It is not usually included in basic Python distributions, but is easy to install and is available under all the most common platforms (Microsoft Windows, OS X, Linux).

It currently allows to load an arbitrary Gene Ontology and annotation corpus.
When running fastSemSimGui, you will find a "status panel" in the top-right corner of the main window. Some icons will display the status of the respective section in the main window. To be able to start the calculation of the semantic similarity scores you need to correctly set up all the sections. A green "V" sign in the status panel means you have correctly configured the corresponding section.

There are currently five sections:
Gene Ontology: you need to provide an ontology. See [Gene Ontology] page for more details.
Annotation Corpus: you need to provide an annotation corpus See [Annotation Corpora] page for more details.
Semantic Similarity Measure
Query
Output Parameters

Starting fastSemSimGui

Also FastSemSimGui is written in Python, and requires the wxWidgets library to work. You have to install the generic wxWidgets library and the Python bindings.

WxWidgets can be downloaded from http://www.wxwidgets.org/.
The Python bindings are available at http://wxpython.org/download.php

Local running

For Linux (and OS X ?) users: just execute fastSemSimGui.sh from the main folder

In general: you should run the file startGui.py from the main folder. To do that, you should execute (export PYTHONPATH=. && python startGui.py)

Running the installed version

For Linux (and OS X ?) users: If you have installed fastSemSim, you should be able to run the FastSemSimGui tool from anywhere simply by typing

fastSemSimGui

For Windows users: A compiled version of FastSemSimGui is available.
In the Download section, look for files containing the string "build").
Once unzipped, you should run startGui.exe

Warning

I used py2exe to create the executable version of fastSemSimGui.

The executable version of fastSemSimGui is still under testing. It works perfectly on Windows 7 (both at 32 and 64 bits). It should NOT be necessary to install the WxWidgets library (http://www.wxwidgets.org/) and the Microsoft Visual C++ library (http://www.microsoft.com/download/en/details.aspx?id=5555). If Windows complains about missing library you may want to install these two libraries too.