Resource: Second Life Interactive Dendrogram Rezzer (SLIDR)

About half a year ago, I began experimenting with Second Life as a tool for virtual conferences (I should add that my experiences have since improved). However, I believe that imitating real life in a virtual world is not necessarily the best way to use the technology – it may be better to use virtual reality for doing the things that are difficult to do in the real world. A good example of this is Hiro’s Molecule Rezzer, which is one of the best known scientific tools in Second Life. It, and its much improved successor Orac, allows people to easily construct molecular models of small molecules in Second Life.

After speaking with several other researchers in Second Life, who like I are interested in evolution, I set out to build a similar tool for visualization of phylogenetic trees. The result is SLIDR (Second Life Interactive Dendrogram Rezzer), which based on a tree in Newick format constructs a dendrogram object. The first version of SLIDR can handle trees both with and without branch lengths; however, I have not yet implemented support for labels on internal nodes or for bootstrap values.

The picture below shows an example of a dendrogram that was automatically generated by SLIDR based on a Newick tree:

SLIDR closeup

There is a bit more to SLIDR than this, though. After the dendrogram has been built, it can be loaded with a photo and/or a sound for each of the leaf nodes. When click on a node, the corresponding sound will be played and the photo will be shown on the associated screen (the white box in front of which I stand):

SLIDR posing

I plan to work with collaborators in Second Life to construct dendrograms for evolution of bats (including their echolocation sounds and photos of the animals) and for the fully sequenced Drosophila genomes. Please do hesitate to contact me if you would like to use SLIDR on another project. I intend to make SLIDR available as open source software once I have implemented support for the full Newick format.

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One thought on “Resource: Second Life Interactive Dendrogram Rezzer (SLIDR)

  1. Lars Juhl Jensen Post author

    Imported from FriendFeed:

    Jean-Claude Bradley, Ruchira S. Datta, Pedro Beltrao, Andrew Lang and Peter Miller liked this.

    cool :) – Pedro Beltrao

    thanks – I’m also thinking about making something similar for protein interaction networks, but first I would need to find a good algorithm for doing network layout in 3D – Lars Juhl Jensen

    A few thoughts: I have a *very* limited setup on the giant TB genome with just one level of interactors and then you tp across the genome if you want to delve further. If you want something largescale, you are presumably looking at particles (to save prims) which are unfortunately limited by the fact that a node can only act as the source of one stream (so you need to duplicate/overlap nodes). Once you get your algorithm sorted, it might be worth talking to Erich Bremer about strategies for rezzing large numbers of nodes so as to avoid the grey goo fence. – Peter Miller

    Reply

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