Friday, July 4, 2008

Official Release of PrimPlotter at SL5B Conference

The Plotter Prim Vendor at the DataViz site.

The Image Array at DataViz site. Each one of the four orthoganal panels is rezzed by a single Plotter Prim, which can be seen at the uppermost vertex.

The DataViz Panel Presentation at SL5B.

The past few months I have been experimenting with Second Life in various different areas. During this time, I designed and engineered my first SL application: PrimPlotter. The actual scripting was done by Annie Obscure, a software engineer. PrimPlotter is a RL-to-SL script that generates 2D or 3D scatter plots from data in a spreadsheet. It consists of two parts: 1) an excel spreadsheet template that serves to input the data to be plotted and controls the dimension of the graph and the size and shape of the datapoint prims; and 2) an SL "Plotter Prim" which actually rezzes the scatter plot within SL.

PrimPlotter was officially released at Linden Lab 5th Birthday conference, on July 2nd, 2008 in SL. For more information about PrimPlotter, including downloading the application and obtainin a copy of the Plotter Prim, please visit the data visualization wiki. The user manual of the application, as well as download instructions can be found here. In SL, the Plotter Prim component of the application can be found at the Data Viz Site in SciLands. At the site, one can actually find 96x4 image panel array similar to the one in ACS island, except this one can be generated autmoatically by the PrimPLotter application.

In addition to the PrimPlotter application, I have also been experimenting with the ability to incorporate SEcond Life into the classroom. As part of the Pharmacy students' Pharmacogenomics and personalized medicine class, Iintroduced them to Second Life. I had the students visit the emerging health-related sites, and introduced them to the concept of virtual patient groups and other web2.0 developments such as wikis and blogs, which are becoming increasingly relevant in the context of personalized. medicine, personal genomics, and the general trend of patients increasingly taking healthcare into their own hands. One of the drawbacks I found was that SL took too much of the student's attention away from the material(although the average time spent by the students in SL for the entire class was between 2 and 3 hours total). On the positive side, I was able to interact with all the students in SL far more than I have actually ever been able to interact with them in RL.

To explore the potential use of SL in promoting educational collaboration and exchange, I invited Dr. Jesus Olivero, a professor from Universidad de Cartagena, who specializes in studying environemental health problems in Colombia. While he visited my lab, I introduced Prof. Olivero to SL. Later on in June, I visited his lab at Universidad de Cartagenta, and gave two talks there: one about our pharmaceutical sciences research work , the other about exploring Second Life as an educational tool and to promote communication. I was pleasantly surprised to find two of the students attending my talk were able to visit me in world a couple of days later, after I had returned to the US.

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: http://sldataviz.pbwiki.com/
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 competitors....so 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 computer...like 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.

Thursday, February 14, 2008

New Pharmaceutical Sciences Flyer Artwork from Second Life

My fourth attempt at a PharmSci department flyer photo from SL.
(unanimouosly REJECTED because the colors were inappropriate).

The official photo for the 2008 PharmSci department flyer.

I am pleased to report that the faculty of the Department of Pharmaceutical Sciences approved a photo from Second Life for its official flyer! This was not easy, by any means. It actually took me five different tries over a period of a month. For the first three tries, the Second Life photo and composition was rejected after much back-and-forth discussion and argument between me and the rest of the faculty: "Colors are too bright", "The composition is too complex", "It takes too much time to figure out what is going on in this photo", "The objects do not look clear to me", "This represents you , not the department", etc. etc. But I was determined. On the third try, the biggest criticism was that the colors were still too bright. So, I emailed the faculty and told them I was going to make the colors really, really, dull. I proceeded to make the objects green and white --the colors of Michigan State, our biggest football rivals. Immediately after I emailed them the Michigan State version. I hear back from them...." the students will not like these colors" So, I immediately reworked the colors to Maize and Blue, and emailed them the photo with a text message saying "GO BLUE!"....sure enough, the photo was finally approved!

Friday, February 8, 2008

CAIA Test Successful -SL handles smoothly

I am happy to report that we have successfully uploaded 4x96 images from our styryl library dataset onto the CAIA visualization facility at ACS island in Second Life. The visualization went really well. Each image is an 8 bit black and white, 512 x 512 jpg. One is able to navigate through the images very smoothly, from my lap top computer. I am running a Dell Precision M90. Intel(r) CoreTM 2 Duo Processor T7600 (2.33GHz/667MHz/4MB) with 4GB memory. The images were displayed at full resolution and there were absolutely no glitches. Avatar navigation and camera functions were very smooth and seamless. I was later joined by my grad students CellPK Alter, CaiaLanz Alter, Kaisla Harbour, and Graziella Shostakovich, (Xinyuan, Nan, Marijo, Lilly). Diomedez Delpiaz (Prof. Juan Hinestroza) stopped by as well. It was really a lot of fun to see this running as I have been thinking about doing this for five or so years now. I must say that this really topped the Miner3D visualization software. We celebrated with virtual Bloody Mary's (which Nan and Xinyuan refused...even though the Bloody Mary's were non-alcoholic... ) with Diomedez skating around in the lab for a bit.

Sadly, from my lab's Dell quadscreen workstation, the results was not as good: when I got into the CAIA, the quadscreen practically froze. My quadscreen workstation runs the same processors and memory as my lap top, with the four 24inch LCDs powered by 2 NVidia graphics card. Marijo, one of my grad students was able to enter ACS island and navigate through the CAIA with her iBook computer no problem, so the problem was with the quadscreen and not with SL. My quadscreen is operating with Windows XP, so perhaps the problem is that I am not able to make use of the full memory and processor capabilities? My goal is to try SL on Windows Vista by the end of February, and see whether I can get any improvement in performance from the quadscreens.

Tuesday, February 5, 2008

CAIA Lab at American Chemical Society (ACS) island

Over the past week, I have been constructing a Cheminformatic Assisted Image Array (CAIA) visualization laboratory at the American Chemical Society Island in Second Life. The photo above shows the lab layout. Each side is an 8x12 array of square 2x2 meter panels, corresponding to a 96 well plate used for drug screening. Each square in the array can hold one image. In addition, each square is hyperlinked to an URL address, that can be openned by right clicking on each square.
For CAIA visualization, one can hover in the middle of the structure. Then one can get into mouselook view. From the mouselook view, it is easy to spin around with the move, and scan each side with the left and right arrows. To zoom in and out, one can use the top and bottom arrows. I gave it a try, and it is REALLY fast! Much faster than any other visualilzation software I have tried. But there is a caveat: I do not have any actual images uploaded..just the scaffold, at this point. Over the next week, I will be working with Kerby Shedden to upload some images. We are looking forward to test how the software handles with 4x96 images projected onto the scaffold.

About Me

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