Monday, March 17, 2008

DataViz Presentation at Life2.0 Conference

The DataViz panelists, up close.

Visiting the Dataviz site at Scilands, after the panel discussion.

The Life2.0 auditorium filled to capacity, with the best crowd in the world.

Today was quite a remarkable day. I attended a talk by Mitch Kapor (the originator of Lotus 123 and one of the pioneers of the PC revolution). I met with 3 student debate groups from my pharmaceutics class. I had lab meeting with my graduate students. I hundreds of emails. But the most important part of the day came at 5pm, when I participated in my first Second Life conference as a speaker in a panel discussion, invited by Melanie Swan (Xantha Oe, SL). This was at the Life2.0 conference. The conference program was outstanding. Mitch Kapor (KMitch Linden, SL) who is now Chairman of Research at Linden Labs gave the opening talk a few hours earlier, which got me really excited to begin with. But, the most important thing was that the panel discussion was a great success. For one, the auditorium was pretty much filled to capacity. The slides projected really well on the screen and there was little lag. Most importantly, the talks were excellent. Each presentation was only ten minutes long, but each one of us panelists had packed it full of information. And, the information covered a huge variety of Data Viz applications. Melanie did a really great job with the organization. She has posted the presentations for everyone to see. Here they are:

By far, this is one of the best conferences I have ever participated in. Not only was the quality of the presentations excellent. It was a tremendous learning experience for me. And, as soon as the conference was over, we visited the data vizualization sites at Scilands, and then Melanie took everyone to see the CAIA-ACS lab for themselves. I stepped out early, because I had other RL things to do. But at the end of the day, I was able to go home and relax....looking back, all I can say is "Wow!". Melanie, thank you for this incredible experience. I am looking forward for my next conference in SL.

Here is a Flickr slide show of the presentions.

Sunday, March 2, 2008

Creation of the Data Visualization Interest Group in Second Life

An important applications that is much needed in SL is the ability to plot data from a spreadsheet. While SL has excellent graphics and visualization capabilities, it is presently not possible to plot even the simplest of all graphs, because there simply are no user friendly plotting tools in SL..... Not even a simple application to plot a histogram, bar graph, 2D or 3D scatter plot from data in a spreadsheet is available.

Speaking about this with several other people in SL, we decided to form a Data Visualization group, so as to begin consolidating all the existing plotting and data visualization tools into one site, and then allow for application developers to make these graphing tools user friendly. I like to refer to a user friendly plotting tool as "Excel-SL" -- in analogy to Microsoft Excel in terms of its simplicity and basic graphing capablities. Beyond that, we really need a more sophisticated graphing tool like Miner3D (from Dimension5) or Spotfire. In fact, the graphics in SL are much better than the graphics in either one of these two software packages, so this would be a great opportunity for someone to develop a highly competitive, marketable product.

Leading this data visualization effort, I have teamed up with Melanie Swan (Xantha Oe, SL). Melanie and I have had several brainstorming sessions about DataViz lately. One of the interesting things to emerge out of our conversations is that a wiki has been created by Melanie, so that now we are able to begin building an SL community interested in data visualization tools, both from a user standpoint as well as a developer standpoint. This wiki can be accessed at the following site:
Anyone who is interested in the development of data visualization tools in SL should IM me (Caia Alter) or Xantha Oe, so as to become part of the wiki. Xantha is working on acquiring some land in SciLands, so that at least we can start creating a common, centralized repository for all graphing and data visualization tools, where people can borrow any of the tools for their own use, as well as contributing tools of their own to the community.

Saturday, March 1, 2008

Installation of Quadscreen Virtual Reality Workstation at the Burnham Institute

This sign welcomes Burnham02 Alter to SL. It is strategically placed at the home base of the virtual workstation, in my lab in Second Nature.

Ramses took this one...after 3 days of work, the workstation was no longer stalling.

Jeff Price and Ramses, discussing Second Life, with Burnham02 Alter hovering in front of my ACS-SL CAIA lab. The virtual reality workstation itself is strategically placed right next to the fridge.

This past week I went to the Burnham Institute in La Jolla, CA, to install a quadscreen Virtual Reality workstation powered by SL, in the lab of Dr. Jeff Price. This was an interesting visit, as the Burnham Institute is the site for one of the Molecular Libraries Screening Network Centers, part of the National Institutes of Health initiative in Molecular Libraries. Jeff Price is a prominent figure in high content screening instrument development. He was the founder and CEO of Q3DM, one of the original high content screening companies, which was acquired by Becton Dickinson several years back before Jeff moved on to academia and then to the Burnham. At the Burnham, Jeff is in charge of the high content screens of the MLSCN center. When I was at Cellomics, Jeff and the other scientists at Q3DM were one of our this was an interesting visit, for sure.

The installation of the Virtual Reality workstation came about as part of the collaboration between MACE -The Michigan Alliance for Cheminformatic Exploration- and the MLSCN center at the Burnham. Marc Mercola, Jeff Price and the other scientists at the Burnham have always been very supportive of the interaction between the Chemiformatic Centers and the Screening Centers so they welcomed me to their Center and they were more than happy to see what it was that I was going to show them. Well, as soon as I showed them the ACS CAIA, Jeff and the other members of his high content screening group were immediately impressed by the powerful graphics of SL, as well as the ability to interface with the wikis so that images can be annotated by human users as well as by machines. Jeff, and everyone else in Jeff's lab quickly grasped the importance of this technology in terms of image data visualization and communication. Fortunately, itt really does not take too much effort to convince the experts of how good and powerful SL graphics capabilities are... so the visit can be declared a success!

As expected, the installation of the workstation was not a simple matter, involving a lot of blood, sweat and tears. Immediately after I installed it and began testing it, I found out the workstation was freezing when the avatar went into the ACS CAIA. I was able to figure out the problem after two days of troubleshooting, and then came up with a work around: I found out that the memory usage of SL was maxing out at about 400MBytes, wereas in my laptop SL memory usage would not max out until reching about 700MBytes, within the same sim. The maxing out would cause the quadscreen to stall, whereas my laptop would cruise through the sim without any glitches because its memory was not maxing out. I found out there was plenty of RAM memory left on the quadscreen, so the maxing out of the memory was not due to the lack of RAM (I put 4G Bytes RAM on the quadscreen same as my laptop, and I was only using about a fourth of it, with 1.2 GBytes left).

Looking further into the hardware components, I found out that the NVIDIA graphics cards that went into the workstation had 256 MBytes memory each, while the graphics card powering my laptop had 512 MBytes memory. I believe this is the root cause of the problem. As a workaround, I limited the memory cache in the SL setting to 64MBytes. This, plus other adjustments on the SL graphics settings (such as setting the maximum sight distance to less than 120 meters) improved the quadscreen performance so that one can navigate around the ACS CAIA without stalling or freezing. Nevertheless, there is some lag everytime the avatar moves to a new view on the CAIA, since the images have to be loaded through the network as opposed to being stored in the graphics card memory. But, this lag is only apparent if one has been cruising around the ACS CAIA from a better my laptop. So, I figured I wouuld leave the virtual reality workstation as is. If anyone at the Burnham is actually going to put it to good use, I will work to upgrade the workstation's graphics cards, so that they get best experience possible. For the time being, I will work on getting the Burnham scientists set up with some avatars, help them through "disorientation island", and then set my SL lab as home so I can tour them around and guide them through the world when they decide to enter again on their own.

About Me

I am Assistant Professor at the University of Michigan College of Pharmacy, Department of Pharmaceutical Sciences