Personal Info

My name is Márcio Rosa da Silva and you can contact me at: mmrsva (a) gmail com

I am a PhD student at the Systems Biology group of the German Research Center for Biotechnology in Braunschweig, Germany.

I work at UNISINOS (Universidade do Vale do Rio dos Sinos), a university in south of Brazil as an assistant professor.

Cytoscape work

Plugins

I developed some plugins for Cytoscape. They can be downloaded from here:

http://csresources.sourceforge.net/

Other tools

Are you a former user of Pajek that use Cytoscape now? Need to convert Pajek files to Cytoscape (including conversion of Pajek cluster files to Cytoscape node attributes)? See: pyNetConv

Documents

I have worked with many languages before, but Java is something new to me. I decided to learn it because I wanted to write plugins for Cytoscape. So I have run into some problems in the beginning, like: "how to start?" So I decided to write some documents about this experience. I'll put this documents here at the wiki and in the csresources page. Up to now, I wrote only one. It can be found here:

SettingUpEclipseForPluginDevelopment

Drafts

Cytoscape programming tips: CodeTips
Changing default behavior of MetaNodes plugin to show only one edge between metanodes: MetaNodesOneEdgeHack
Discussion about changing node views: ChangingNodeView
Is it possible to LoadAttributesFilesInsideJar?
How to make PluginsWithJython?
How_to_use_external_libs_in_a_Cytoscape_plugin

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