Tag Archives: Second Life

Resource: Real-time text mining in Second Life using the Reflect API

Sometimes things just come together at the right time. The past few weeks Heiko Horn, Sune Frankild, and I have made much progress on the new version of Reflect, which we hope to put into production very soon. One of the major new features is that Reflect can now be accessed as REST and SOAP web services. When Linden Lab made available the beta version of Second Life viewer 2, which enables you to place a web browser on a face of a 3D object, I simply had to try to put the two together to provide real-time text mining inside Second Life.

The system works as follows. The Reflect Second Life object contains an LSL script that listens to everything that is said in local chat. It sends any text that it picks up to the Reflect REST web service, which returns a simple XML document listing the entities (proteins and small molecules) that were mentioned in the text. The LSL script parses this XML, constructs a URL pointing to the Reflect popup that corresponds to the set of entities in question, and sets this as the shared media to be shown on the Reflect object in Second Life.

The result is an information board that automatically pulls up possibly relevant information related to what people close to it are talking about. The picture below shows the result of me typing a sentence that mentioned human and mouse IL-5 (click for a larger version).

I am well aware that this may not be particularly useful to very many people in Second Life. However, I think it is a nice technology demo of how much can be accomplished with the new Reflect API and just a few lines code.

Editorial: What is the difference between Twitter and Second Life?

I admit that this may seem a strange question. One is a microblogging platform that allows you read and write messages of at most 140 characters. The other is a 3D virtual world. They are, however, both communication tools, and I think there is a completely different reason why Twitter is so much more useful to me than Second Life is.

If I go to the Twitter web site and log in, I see this:

It is Twitter. It immediately shows me the main content: tweets. It also allows me to create content, that is to tweet.

By contrast, if I go to the Second Life web site and log in, I see this:

It is not Second Life. It is a complex web interface that gives me access to account administration tools and shows me lists of blog posts by Linden lab, comments from Second Life users, items for sale on Xstreet SL, and video tutorials. In the lower left corner it shows me the only really useful information, namely which of my friends are online. That is, the friends that I would have been able to chat with, had I been in Second Life and not on the web site, which does not allow you to read or write messages.

Imagine if the web interface of Second Life would instead show me this:

It would be Second Life. It would immediately show me the main content: the virtual world. It would also allow me to interact with the content, that is to move around, to chat with people, and even to create content. Do you think Second Life would have more users if it would run inside your web browser? I think so. Linden Lab is and has been focusing on improving the initial user experience in Second Life to improve the retention rate (i.e. the fraction of new users that continue to come back). I am not saying that this is not important, but I think that most of the potential users are lost long before they even get into the virtual world.

This is by no means a problem that is specific to Second Life. Today, asking users to install a piece of software on their computer will cause the majority of people to shy away before they have tried your product. Even just asking users to create an account will cause many to turn around and walk away. When it comes to social networks, the decisive factor is users. If your friends are not there, why should you? Imagine a virtual world that would run in your web browser and which you could sign into using OpenID, Twitter Connect, or Facebook Connect. Would your friends be there? Would you?

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.

WebCiteCite this post

Editorial: Virtual conferences in Second Life

This blog has been very quiet for a long time. There are several reasons for this, most of which are positive: I have not had many boring or negative results to write blog posts about, I have been busy writing manuscripts about the positive results instead, and I have moved to Copenhagen where I am busy starting my own research group at the Novo Nordisk Foundation Center for Protein Research. There is also one more reason for the absence of blog posts from me: I have spent a lot of time experimenting with Second Life, and that is the topic of this blog post.

I first got interested in Second Life when I heard that Nature Publishing Group was setting up a virtual conference center called Elucian Islands. In the beginning I felt very alone on Elucian Islands. There was a good reason for that – I was alone most of the time. My view on Second Life was thus that it was pretty (see images below) but rather useless.

I obviously took a look at the SciFoo presentations (seen in the background of the image above) and the other scientific displays at Elucian Islands and elsewhere in Second Life. However, these mostly reinforced my negative view of Second Life being fairly useless, since almost everything I saw was already being served better by dedicated resources. For example, slide shows are much more conveniently viewed and shared in SlideShare than in Second Life, and 3D protein structures can be examined and analyzed better in programs such as PyMOL.

Over at FriendFeed, Jean-Claude Bradley fought a brave fight trying to convince me that Second Life is in fact useful for science. His key point was that Second Life is all about interacting with people, so I should try to go to some scientific events in Second Life. Sadly, there are still not many such events, and although they have changed my view on Second Life, they have also shown that there are many problems that remain to be solved.

The first virtual seminar I went to was “Cancer, Cell Cycle, and Check Points” organized by Digi S Lab. This was a perfect match since I work on cell-cycle regulation myself. The seminar consisted of two excellent presentations given by Letizia Cito from Sbarro Health Research Organization and Fayamdria Foley from the American Cancer Society.

Meeting on Cancer and Cell Cycle 1

Meeting on Cancer and Cell Cycle 2

Whereas the presentations were great, the seminar also illustrated several of the problems that need to be overcome before virtual conferences in Second Life are ready for prime time. When the first talk started, I could not see any of the slides. Restarting my Second Life client did not solve the problem, nor did a reboot of my computer. After giving up solving the problem, the entire region in which the seminar took place suddenly crashed causing speakers and participants to all be logged out. When it came back online after some minutes and everyone had found their way back, I could suddenly see the slides. Even then, however, they took so long to appear on my screen that the presenter had typically explained half of what was on a slide by the time I could see the slide. I see this as a major problem that must be solved before Second Life conferences can work properly – it must be possible to change slides without a noticeable delay.

The second event I went to was the “ESRC Complexity Research Seminar in Second Life” that took place at Elucian Islands. This seminar was very different from the one described above in that it was not a purely virtual seminar; instead it was a video feed from a real-world seminar that was being transmitted into Second Life. Think of it as a virtual overflow room – the image below shows the people who had gathered shortly before the event started.

ESRC Complexity Research Seminar

Sadly, this event was marred by technical problems. The sound stream was of such poor quality that the Second Life participants could barely understand a word of what the speakers were saying, and the video stream was of too low quality to be able to read their slides. I do not want to dwell on this but just note that good quality microphones and cameras are a prerequisite for streaming events into Second Life.

The third event I went to was the “Virtual Conference on Climate Change and CO2 Storage“, which again took place at Elucian Islands. This was again a mixed event taking place both in the real world and in Second Life. The presentations were excellent and important lessons had been learned from the previous events. The microphones worked perfectly this time, and the video feed had been abandoned in favor of showing a copy of the actual slides in Second Life, which greatly improved the readability.

In addition to these events, Elucian Islands now also runs regular events such as the weekly Nature Podcast event where a fairly large group of people gather to listen to the latest podcast shortly after it has been released (image from Joanna Scott’s blog).

Nature Podcast at Elucian Islands

Regular events are crucial in SL because they bring people together in the same place at the same time. The need for people to be online at the same time is in my view one of the major drawbacks of Second Life compared to other tools that researchers can use for social networking. In my view Second Life should thus not be seen as competing with tools like FriendFeed or Twitter, which you can read when you feel like it, but rather as virtual reality alternative to video conferences. I think that Nature Publishing Group is on the right track with this, and I hope that the few remaining technical hurdles will be overcome in the near future.

Full disclosure: I have been working with the staff from Nature Publishing Group trying to solve technical challenges on Elucian Islands.