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Another collaborative environment: Project Wonderland

This is a short post on the Sun’s Project Wonderland. Citing from its home page

Project Wonderland is a 100% Java and open source toolkit for creating collaborative 3D virtual worlds. Within those worlds, users can communicate with high-fidelity, immersive audio, share live desktop applications and documents and conduct real business. Wonderland is completely extensible; developers and graphic artists can extend its functionality to create entire new worlds and new features in existing worlds.

In my recent post I’ve mentioned Second Life and Croquet: two platforms that can evolve into decent 3D visualization environments. Obviously I didn’t research the topic enough, as I’ve just found Project Wonderland. It seems to have the best of both worlds – professional team of developers, pretty flexible architecture and possibility of running your own instance of “virtual world”.

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Have you spotted "Biogang" written on the whiteboard? 🙂

I didn’t play with it for a long time – current version is not very feature-rich (although it already contains video player with webcam support, PDF viewer, VNC viewer and a crude whiteboard), however the roadmap looks very interesting. I really liked extensive audio features – true stereo, sounds fade out with distance, special “cone of silence” (place where you can have a private conversation) – it proves that Sun is really trying to build an effective collaboration platform.

I haven’t seen yet much about data visualization in Wonderland – although below you can find interesting example of molecular simulation trajectory shown inside Wonderland.

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Posted by on December 29, 2008 in Education, Research, Visualization

 

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CLANS – java tool for cluster analysis of sequences

As frequent visitors of this blog have already noticed, I am a big fan of different tools for data visualization. Today I would like to point you to java software called CLANS (CLuster ANalysis of Sequences) developed by my former colleague Tancred Frickey. CLANS runs (PSI)BLAST on your sequences, all vs all, and clusters them in 2D or 3D according to their similarity. This method allows for rapid classification of huge datasets and has the advantage over, lets say, phylogenetic tree, that one can quickly assess results of the clustering in a visual way (I cannot imagine making any sense of looking at phylogenetic tree with 1500 branches, while the graphical output, as on the animation below, is pretty easy to read).

CLANS animation

Beauty of the idea behind CLANS is that you can apply this method almost to any dataset which can be translated into all-vs-all relations. CLANS page has examples from protein clustering, microarray analysis and (which I like the most) image showing how standard aminoacids cluster in space according to BLOSUM62.

 
 

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Linux screencasting software

Just a short note today. If you look for screencasting software for your linux box, I recommend two titles: recordMyDesktop and Wink.

The first one is a typical desktop activity recorder – you mark capture area and that’s all. No fancy options: just a pure video stream from your screen. Video has very good quality (theora and vorbis codecs).

Wink is a screencaster oriented towards preparing interactive tutorials and presentations. You can record screen activity, but also pause the video, add text boxes with explanations, buttons waiting for user interaction (for example “Next” buttons). Output formats are: SWF, standalone EXE (for Windows machines only), PDF, PostScript and HTML. No typical video files, which on the other hand is not really a problem, as the framerate of the recording is pretty small. Another issue is that it apparently cannot record properly windows rendered with OpenGL (like molecular viewers) – window’s interior comes black. Even with these limitations I think Wink is better for preparing tutorials (for example on usage of some online bioinformatics service) than typical screencasting software.

 
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Posted by on January 15, 2008 in Software, Visualization

 

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