TableOfContents

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 [http://www.gbf.de/SystemsBiology Systems Biology group] of the [http://www.gbf.de German Research Center for Biotechnology] in [http://www.braunschweig.de Braunschweig], Germany.

I work at [http://www.unisinos.br 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: [http://pynetconv.sourceforge.net 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"]

Wiki Tips

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