Home.markdown

 ## About  ###
-The ModuleViewer project was originally started to browse [[LeMoNe]] and [[Enigma]] output efficiently on a desktop pc and independently of the rest of both applications that generate the data. We also wanted one common viewer to maintain, that could handle both data generated by Enigma and LeMoNe.
-Both applications were slightly altered to generate compatible output.
+ModuleViewer is a tool to directly generate annotated heat maps from gene clusters and diverse biological data. It visualizes gene expression profiles and co-regulated gene clusters and their predicted regulators in the context of regulatory networks.
 
-By separating the graphical libraries and the GUI application with parsers, and by keeping the code as generic as possible, ModuleViewer became a handy tool to generate figures for all kinds of expression matrices and their associated data.
-
-Click [here][presentation] to download a short presentation about ModuleViewer (BEG Lunch Meeting of 25 Oct. 2011.
-[presentation]: <wiki/docs/moduleviewer.odp>
-
-
-## File Type  ####
+## File Types  ####
 
 Creation of images relies on at least two types of data: the data matrix and the modules file. Optionally, this can be extended with regulator data, a condition tree, and annotation files.
 
@@ -16,9 +9,9 @@ Creation of images relies on at least two types of data: the data matrix and the
 * **gene file**: Either an XML file with modules and genes, possibly grouped together into a tree structure, or a simple list of modules with their genes.
 * **condition tree**: (optional) XML file with conditions to be displayed per module, possibly grouped together into a tree structure.
 * **regulator tree**: (optional) XML file with regulator genes or a simple list of regulators assigned to modules.
-* **annotations**: Most information that should be drawn around the central module matrices, can be described as: "Module number x lists genes or conditions y1, y2, y3, ... as having property z". Optionally each gene or condition can be linked to an extra data point (color, integer, ...). For this purpose, we created the [[MVFFormat]].
+* **annotations**: Most information that should be drawn around the central module matrices, can be described as: "Module number x lists genes or conditions y1, y2, y3, ... as having property z". Optionally each gene or condition can be linked to an extra data point (color, integer, ...). For this purpose, we created the [MVFFormat](MVFFormat).
 
-Demo data can be downloaded here: [[ModuleViewerDemoData]].
+Demo data can be downloaded here: [ModuleViewerDemoData](ModuleViewerDemoData).
 
 
 ## Running ModuleViewer ######