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:
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.

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.

Sunday, February 3, 2008

Avatar Entropy, Chaos, Information and Encryption in SL

Today I began some very simple experiments into the relationship between information, entropy, encryption and chaos in SL. Basically, I took three spheres (.5 m diameters) and made them so that they were kissing each other in 3D space. Then, I made a copy of these three spheres, placed them 5 meters apart from the first three spheres. I converted the 2x 3spheres into physical objects and dropped them from a distance of about 2meters from a floor plank. I repeated this experiment a few times. This is preliminary, but here is what I observed: The two sets of three spheres dropped side-by-side (simultaneously) followed similar (but perhaps not exactly identical?) paths. However, when the spheres were dropped at different times, the paths that the spheres followed upon collision with the floor plank appeared different. Caveat: this was a quick 5 minute experiment, and I simply eyeballed the results. But this is what I saw. This result brings up some interesting questions. I think the three touching spheres represents a chaotic system (someone please correct me if I am wrong). By putting 2 sets of three touching spheres side by side and dropping them simultanously, the Linden computer processors should be solving the same equations simultaneously, so the objects follow paths that are very similar to each other, upon collision with the floor plank. However, when the touching spheres are dropped at different times, the behavior of the processors may be different because the equations are not being solved simultaneously, so the paths that the spheres follow is different. Unlike a classical computer chaos experiment, it is not that the initial conditions as specified by the spatial positon of the spheres is different. Rather, the functioning of the Linden computers may be slightly different at different times. Related to this observation, one intersting question is whether 3spheres dropped SIMULTANEOUSLY at different sims from the same relative heights and relative positions would behave more similarly to each other upon collision with the floor plank, than if they werre dropped at different times. In such a case, it may be possible to encrypt information in the way in which that 3 (or more) touching spheres move upon collision with the ground, such that the information is both encoded and decoded at the point that the three three (or more) spheres are dropped from the same relative heights and positions. This encryption method would work if the physics of different sims are being processed by at the same time by the same computer. By analyzing the effect of time and distance upon differences in the paths followed by two sets of three touching spheres that are dropped from the same relative positions, it should be possible to analyze how the information content of the three touching spheres is lost as a function time and space. I will refer to this loss of information as Avatar Entropy. Nevertheless, these are preliminary observations that should be better controlled, measured and reproduced. I need to re-check that the position of the spheres are correct, that the floor planks are horizontal, etc...again these are preliminary observations. But, I want to get these results out there in case someone out there is interested in researching these questions in SL. Note: I am a pharmaceutical scientist, not an expert in information, entropy, chaos or encryption...I just think this question is sufficiently interesting that may be worth exploring. Here are a few more questions worth thinking about --- going back to a die that I was making the other day, I wonder: would two die dropped from the same position, height, and time in different sims behave the same way or differently? Would the same die dropped from the same height and position from the same sim --but at different times-- behave differently? How about the behavior of two touching spheres? How about the behavior of one sphere? How about the behavior of 1,2,3, n, n+1 kissing rods, hollow cyllinders, cubes, helices and other odd shaped objects (of the same or different geometric shapes)?

In the picture above, I am standing in front of my experimental set up, in the teaching space of Hiro Sheridan, my next door neighbor in SL. I will leave th2 2x3spheres prim behind for Hiro to take a look at. I IMed Hiro Sheridan about this. Hiro is a mathematical physicist, who works on encryption, SL, neural prosthetics, science fiction and other relevant subjects, for collaboration. Hiro will be scripting something to measure the position of the spheres where they land....measuring where the spheres land will certainly allow for a more objective assessment of my preliminary observations.

Saturday, February 2, 2008

Prim size limits, linking distance limits and the issue of scale

A while back I wrote a post about the issue of scale in SL As I have been researching in SL, I have come across two limitations of SL that bear on the issue of scale: the size limit of prims, and the distance limits of links. The size limit of prims essentially constrains any particular side of any prim to a range of 10 SL meters, to .0.01 SL meters. That means that a prim can be stretched or shrunk with the simple stretch command such that any one of its side is within 0.01 or 10 meters...not smaller, not greater. The distance link limits actually limits the distance across which different prims can be linked into a single object. How is linking and prim size limitations bear on the scale issue? Say, one wants to visualize a red blood cell, as in my previous post. I could make the red blood cell from a single prim, 10 meters maximum diameter. Or, I could make it out of cuboidal little prims -each 0.01 meters on each side-, linking them into a single object with the prim link command.

From a computer memory and speed standpoint, making the red blood cell out of a single prim is the way to go. That is the fastest and most efficient way of building the cell. But, this would mean the red blood cell is limited in size in SL, from 10 meteres to 0.01 meters. So, from ability to scale things, making them out of individual 0.01 cuboidal units would be the way to go. Except, there may be a limit to the number of prims that can be linked, and the distance over which they can be linked. Is the linking limit distance the same for small prims or for large prims? I need to find out.

Within a single prim, drug concentration can be encoded as a color or texture, but spatial variations in color or texture within the prim would not be possible. So, one would not be able to visualize concentration gradients inside the red blood cell. On the other hand, by making the red blood cell with many cuboidal 0.01 meter prims, a concentration gradient within the red blood cell could be visualized (say, for visualizing diffusion inside the cell, modeling drug transport with partial differential equations). Currently, 1cellPK models we are using do not capture intracellular concentration gradients, so visualizing cells as single (or a few) prims may be the way to go. But, if one makes the red blood cell 10 microns in diameter, than any larger cell that is scaled in relation to the red blood cell would have to be constructed from more than one prim.

In the future, if the intention is to visualize concentation gradients, it may be important to make the cells out of many single prims linked together. Actually, working with cells made out of linked prims may be unavoidable, as that is the way to visualize complex cell shapes (such as that of the red blood cell). But, there may be a limit to the number of prims that can be linked together. As things stand, this is a brief outline of the progress I have made on the scaling problem. I will proceed with more detailed visualization experiments, in terms of constraints on linking prims, and determine the interplay between number of prims, size of prims, and the distance over which prims can be linked.

Plasmodium feasting on hemoglobin (reversed time sequence)

What is the meaning of the word "visualization"? Rudolf Arnheim, Harvard University Professor, researched and wrote books about visualization and the role of visualization in guiding human thought. Short of reading these books, here is a nice, simple visuallization example: I am sitting atop a red blood cell, with a mock malaria parasite inside of it. Hemoglobin, the major protein inside the red blood cell, has a strong, red color. Through time, the malaria parasite feeds on the hemoglobin, so the hemoglobin disappears from the cell. In this visualization, the parasite is not growing, is not moving and is not reproducing. Only the hemoglobin is disappearing from the red blood cells. The top frame has less hemo than the bottom...hence I call it a reversed time sequence, because time is flowing from bottom to top frames). My avatar is about 2 microns tall, relative to the actual size of the red blood cell.
This is a very simple visualization, all done within SL. It took me less than five minutes to make this. Visualization is easier to some and harder to others, but SL is very easy, simple and fast when it comes to visuallzation work. There are no 1CellPk scripts controlling this visualization..just me manually changing the colors. So, it is just a simple illustration of visualization, meant for my graduate students to begin to understand how to use SL for 1CellPK visualizaiton purposes. In the future, I would be looking forward to my graduate students experimenting with visualizing changes occurring within the parasite inside the red blood cell. I would like to be able tosee us "treat" the red blood cell with drug (chloroquine, falcipain-2 inhibitors, etc) and visualize what happens to the drug as it distributes inside the red blood cell and then inside the parasite, and then see what it would happen inside the parasite as it is affected by the drug. Eventually, drug distributions should be controlled by mathematical models. We should be able to make simulations (5-D movies) of drugs with different chemical properties as they distribute inside the parasite. Then, we should be able to sort and analyze the dynamics observed in the movies based on drug's chemical structures. That is, Cheminformatic Assisted Image Arrays. The 5-D movies would be comprised of x,y,z spatial coordinates, signal and time. Linking the movies to chemical structures would make it 6D. Each chemical structure can be described as a multidimensional object, so in fact, a CAIA can have many, many dimensions.

Tuesday, January 29, 2008

My First Knit

Rear view of my first knit. The yellow thing is the holder. The green strand and pink strands are parallel to each other, with the red strand perpendicular. The red strand is woven between the loops of the green and pink strands.

Here I am stretching the knit with the white holder thingy attached to the pink strand...note how the green and pink strands come apart, with the red strand acting as a hinge

Here I let go of the white holder thingy. The pink strand bounces back and again is parallel to the green strand. How does one optimize the design of green, red and pink strands to get maximumum extension upon pull and maximum force upon release? That would be a nice question to ask Juan...also, I am not sure how gravity affects the behavior of this does strand length affect the elastic force? Does it obey Hooke's Law? That's just but a few questions to think about...unfortunately, knitting is really not my thing.

Last Friday, we had a very special guest visiting us in my lab: Prof. Juan P. Hinestroza. Prof. Hinestroza is faculty at Cornell University, in the Department of Fiber Science and Apparel Design. Not only did Juan deliver an awesome departmental seminar about nanofunctionalized
textiles and nanofiber fabrication, but he taught me how to knit in SL! Together, we made a really nice, simple knit in my Second Nature lab. The knit is made of 3 strands, each with two loops. The three strands are physical in nature. One strand is fixed to a knit holder. The middle strand serves as a link. The third strand has a little knob to which I stuck a white thingy that allows me to pull on it so as to test its elasticity. If one pulls on the third strand, the third strand swivels away from the first strand. If one releases the pull, the third strand swivels back to its original position, parallel to the first strand. The middle strand is perpendicular to the first and third strand. The strands are held together by their topology --no real linkages. And they are able to move and swivel relative to each other. In RL, knits are used to make elastic textiles from rigid fibers. How this works is clearly illustrated by the SL knit. According to Juan, The ancient Egyptians invented this knit, around 5,000 years ago. Juan was so impressed with the SL knit, that he got an avatar of his own. I have seen him in SL a few times now. I think he is making a needle....

Monday, January 21, 2008

A fractal solution to repetitive tasks

In SL, certain tasks can be quite repetitive such as loading a chromatography column with particles. The other day, I found a fractal solution to this loading problem: one makes one object, puts a copy in one's inventory. Then one takes the object from one's inventory, places is next to the first object, links it to the first object, and then makes a copy of the pair of linked objects in ones inventory. By iterating these steps, the mass of the object one is building increases exponentially. One can actually make very large, beautiful fractal structures in a few steps. To demonstrate this, I built a complex triangular pyramidal fractal composed of hexahedral subunits, which I then painted red and scaled to giant proportions and placed it on top of my lab for everyone to enjoy (and to direct the most curious ones to the behemoth SHRO institute inside the gigantic green block up, in the clouds...).

Sunday, January 20, 2008

Probability in SL

Another project I began working on is a project to test probability in SL. For this purpose, I began constructing a die. The die is perfectly balanced...a cube, 2meters on each side. Then the cube has nine dots. Each dot is equidistant from each other and from the edge of the cube. Each dot is actually .3 meters in diameter, and is .01 meters thick. The nine dots are arranged in 3 rows of 3. I colored the dots black, but tomorrow I will proceed to make some of them transparent so that the die will have six faces with 1,2,3,4,5,6 all dice. My goal will be to test whether the die really behaves as if it were perfectly balanced (as it should), or whether somehow the die (or SL) is 'loaded'.

Lastly, I did some chromatography experiments again..I made a larger gel which I put inside a column and then I ran some balls down the gel (to simulate atoms). I found that even the smallest balls would get stuck on the polymer of the gels. I am not sure why they are sticking this way. Larger balls would get stuck as well. So, I am going to simplify this set up. I am going to make an array of posts, and run the balls down the array of posts, to see how they behave. This is much like Bob Austin's DNA electrophoreses microdevice. Bob is a Princeton University physics professor, and about ten years ago published a paper about separating DNA fragments of different size using a microfabricated device consisting of vertical posts or pillars.

The avatar engine

For the past few days I have been working on several experiments. The one I am most proud of is the avatar engine. Actually, I have been thinking about how to make an engine in SL for quite some time. Finally, I realized that avatars can move things around, so they could be used to power a nice engine. To test this, I decided whether an avatar could be use to make a wheel turn. So I made a big hollow cyllinder and placed my avatar inside it. When my avatar walked, the cyllinder did not move. But as soon as I made my avatar run..lo and behold, the cyllinder began to turn with my avatar inside of it! What this means is that avatars can be used as a source of mechanical energy in SL, to power physical machines. Also, it leads to interesting questions about the amount of work an avatar can do, and if this amount of work is different for different avatars. I should be able to figure out the mass of an avatar.

Thursday, January 17, 2008

Loading columns and problems with chromatography

As a real life experiment, experiments in SL often run into problems. When loading the column, I am finding that the act of adding resin beads (beach balls) one by one is actually a pain. There should be some sort of script for performing such loading operations. Also, once the column gets loaded with 20 or more beads (first as physical objects then converted as non-physical), I am finding that to get additional beads to accomodate correctly leads to a considerable slow down of the computer. This is because the weight of one resin on another causes very slight shifts and these shifts in positoin are propagated to the entire group of objects. So, I will have to repeat the loading process. Next time, I will load the beads as physical, then convert to nonphysical, then link to the others so that they behave as a unit. At the end, it may even be possible to take away the column, and have the beads (or polymer resin) linked as a gel. This may turn out to make for a nice sculpture --maybe something I can make for the ACS site -- a large polymer gel... As in RL, I am finding that one experiment leads to another.
Next time I work in Second Nature, I also want to see if I can reduce the size of the linked objects I have been making. First, I will try to reduce the size of the Millipore filter. I am not sure if I can stretch the linked objects and all the parts will resize correctly, but I should find out.

Wednesday, January 16, 2008

The Lab Pet

My next door neighbors in Second Life are the people running an artificial ecology experiment. I once met one of their park rangers, but I still have not met the scientists. Interestingly, some of their life forms are able to cross over from the artificial ecology system...I am not sure how they do that, but the life froms are mobile. So, I proceeded to capture one of these organisms and keep it in my lab as a pet and to do experiments on. The artificial life forms promises to reproduce and evolve if one feeds it a dollar. I have fed it some Lindens, but no reproduction yet. I would like to learn more about how these organsms of these days I am looking forward to meet Lucifitias Neurocam who runs the artificial ecology experiment lab and chat with him about what he does and these creatures. Anyway, I am going to keep this artificial life form in my lab as a pet, unless my next door neighbors comes to claim it. I may do some experiments with it. Already, I know that it can be easily transported, so that is a good start...Anybody interested in buying these animals, I would also be happy to sell them.

Tuesday, January 15, 2008

Size Exclusion Chromatography Set Up

My avatar Caia Alter, hovering in front of the Rosania Research Group laboratory in Second Life. The blue chromatography column is in place, and the pink "Millipore filter" platform has been placed on top, to facilitate loading of the column.

A different view, from the teleporting entrance to Second Nature.

A nice view of my avatar, Caia Alter, hovering next to the blue column. Note that a single piece of polymer has been loaded in the column. I tested the column by dropping myself into it. Not only did I confirm the column is strong and firm, but it was also a really nice ride.

Today I worked on setting up the size exclusion chromatography experiment. I am finding out that filling the column can be quite difficult. Actually, I think I crashed the SL computer. I was loading physical polymer into the column, and then I accidentally moved the column (which I believe was NonPhysical). What ended up happening is that the polymer ends up crossing the column, part inside/part outside and this freezes the computers, at least for a while. Actually, as I was doing this, Edimayo from next door stopped by. He was complaining that Hiro was giving a presentation about SL to the ORU faculty, and that SL suddenly slowed down to a halt. Hiro, I am really, really sorry...I think it was me.

Fortunately, there must be some really good error correcting codes built into the software, because in a little while, the column had disappeared into thin air, and a pile of polymer was strewn around my lab. Nevertheless, there are several important lessons here: 1) there is a computer behind all this, so beware....SL software engineers are geniuses (hats off), but there is hardware behind all this, somewhere in RL. 2) Scientific applications/experiments may need to be done somewhere distant from where normal educational acitivities are happening... in case things explode, freeze, or go really, really wrong. I already spoke with Finola Graves about this. 3) One may need to coordinate activities so that experiments gone wrong do not ruin important presentations...this is really hard for people working on experiments around the clock. One last lesson: if one is giving a presentation or introducing SL to someone, make sure there are several back up sites available to retreat to, in case the original site crashes. I had a crash the other day while presenting SL to a friend. It was late Saturday night and several SL servers crashed, with everyone being sent to some distant island. What we saw at this island cannot be described....let's just say that Dante's Inferno paled in comparison. So, always have a nice back-up site to retreat to, in case a server crashes.

Anyway, back to chromatography. I am going to try a different way to pack the column (first, set the column to nonphysical object and locked so that it is not moved). Then, load physical polymer, one piece of polymer at a time. As soon as the polymer finds its way to the bottom of the column and is nicely settled, change it from physical to non-physical. Will it work? I don't know. Another thing that I did was that I moved the Millipore filter that I had made the other day directly on top of the column. One of the pores on the filter opens directly on top of the column. The Millipore filter is linked and locked, as is the column. This way, things are held in place. Hopefully the column can be loaded. Actually, I am thinking that before I load polymer, I am going to load physical balls because balls may be easier for the computers to handle.

Rigid Resin for Size Exclusion Chromatography

Caia Alter (me, Gus Rosania, left hidden) and CaiaLanz Alter (Nan Zheng, one of my grad students, right) discussing the pink polymer I built last night, to be used for size separations.

CaiaLanz Alter (Nan Zheng, one of my graduate student) and Caia Alter (me: Gus Rosania, RL) discuss polymers, separations, chromatography in front of a newly built, pink rigid resin. Note a single monomer lying on the floor, and the bottom left of the photo.

I had too little time yesterday to do the experiments I had set out to do. Instead, I decided to build a rigid resin for size exclusion chromatography, and save the actual chromatography experiments for later. As a monomer, a decided to use a torus. I used a thin torus, because I wanted to craft a porous structure out of thin rigid fibers. Then, I linked a dozen or so toruses together. As physical objects, the interlinked toruses behaved pretty well and natural (Today, Hiro Sheridan, my next door neighbor in SL, asked me if they behaved as a catenary? I did not know what that was...but based on what Hiro told me, if the physics are right then they should behave as a more thing to read about and test). In any case, after I interlaced the toruses (tori?), I linked them. This made them lose their physicality while becoming a rigid mesh. The mesh looks like a good physical model for rigid size exclusion chromatography resin, and perhaps also for polyacrilamide (or agarose) gels for molecular size-separation (although the polyacrilamide or agarose gel may be best modeled by the more flexibile physical object, than by the rigid linked object). Luckily, building the resin went fairly quick and easy.

Today in the morning, I asked Nan Zheng, one of my grad students, to stop by my SL lab and check out the resins I had bult. Nan has been rightfully skeptical of this whole enterprise of mine (as any good scientist should be!). I have told Nan that I only do this after hours, on weekends and during the Holidays (which to a great extent is actually true...). But then, after I told her that the resin was for simulation of chromatographic separations, she really liked my resin! So, I think Nan is getting it...I guess that a pharmaceutical scientist/chemist has no business playing around with balls and rings, but when the balls are molecules and the rings are monomers with which to make a polymer....then it is OK! I have enclosed some pictures of Nan and I discussing polymers and size-exclusion chromatography simulation in SL.

Monday, January 14, 2008

Cells on Pores, Millipore filters, size exclusion cromatography

Yesterday (Sunday) I switched the theme of my lab from building large massive objects to building more molecular-cellular type objects. Actually, I had told myself that I was going to take time off from building, to rest. I managed to do it for most of the day. But then at around 8pm, the itch started again and I worked from 8pm to about midnight. The first thing I decided to build was a millipore filter. This is the beginning of my "Cells on Pores" project in SL. I will have to explain the Cells on Pores project later on...there is a brief description of the RL Cells on Pores project in my website...Xinyuan Zhang is the grad student working on this. But, I also want to model cells on pores in SL. Actually, I started building a millipore filter in SL on Saturday, but I followed a wrong building strategy that ended exhausting me and the whole thing never looked good and actually fell apart at the end. I deleted this first try without even documenting it, but Jason stopped by lab and took a peek at it. If you ask him, he will tell you how horrible it looked :-.( The second time, I began building the millipore filter with a new building strategy. This one worked really well. The strategy is to embed a hollow cyllinder inside a hollow block. This, way each pore is embedded in a square, and the squares can be easily assebled and the spaces between squares filled in with blocks. So, I finished the filter and painted it pink.

Interestingly, I decided to build the filter really big. As big as I could. So, in SL, it floats far above my lab, in the sky. The filter is NonPhysical in nature. I decided to build it NonPHysical, because we would need space in the main floor of my lab to put a physical struture down --the only way I can build it up in space is to keep it Nonphysical. But, it could be easily translated into a physical object. Now, the existence of this "millipore filter" in SL makes me wonder: What size are the pores? I guess I could make them any size. As they are, they are bigger than an avatar, so as to let an avatar fly through the pore. But, if I am going to be building a virtual cell, should these pores be 1, 10, 100 nanometers or micrometers big? This issue of scale in SL is important. I am not sure I really know the right answer, but it will definitely affect the work we do in the future. As far as buildling goes, it is much easier to build big. But then, if the objects are phyiscal, one needs land to put them on. So, there are issues. Also, building a millipore filter is one things. But then, if one is going to build cells on top of those millipore filters, the bigger the filters the more work it will take to build the cells. And if one would want molecular detail in the cells (ie. atom resoultion) the pores would need to be bigger. It would be nice to know if one could rescale objects easily. That would obviate the problem. But as things stand, I don't know if rescaling things in SL is easy or not....I wished someone could answer these questions for me.

Nevertheless, Millipore filters are just one step away from doing a size exclusion cromatography experiment in SL. I want to be the first to do this...It will be fun and a nice experiment, and it will give me some time to think about the macromolecular crowding expeirments I was doing in graduate school with Joel Swanson. Will the size exclusion cromatography experiment work? My plan is to construct a size exclusion chromatography column phyiscally. I will build the column with a stack of hollow cyllinders. I will fill up the column with rigid balls. Then I will pour a mixture of small balls and big balls into the top of the column. To facilitate diffusion, I will add some "heat": physically shaking the column. If the column is vertical, the balls should fall down based on their gravity, thus simulating flow. I expect the small balls to separate from the big balls.But maybe there are other better ways to build columns. I can build it out of plates...millipore tube like plates. In fact, this is more in line with how I was taught how a chromatography column works: theoretical plates. So, maybe instead of balls, I will fill it up with theoretical plates... Easier to go back and forth between theory and simulation expeirment that way. But, filling it with balls may be more akin to a RL chromatography column. Anyway, it is an experiment...Maybe I am getting the theory wrong and it will take some time before I get some size spearatation. So, I will do both: a plate/filter based size exclusion column, and a bead-based size exclusion column.

Friday, January 11, 2008

Artificial Avatars, Chemreader and Plato

As I have been working in my SL lab, I have begun to realize the importance of employing an avatar so as to introduce visitors to the lab. This will become even more important when we begin to manage multiple labs in different locations. Since the task of introducing visitors to the lab seem to be quite repetitive, it seems natural that one could use an artificial, computer controlled avatar, instead of an avatar that is controlled by a RL human. One wonders if it may be possible to program an artificial, computer-controlled avatar that may be indistinguishable from a human-controlled avatar. Artificial avatars could be endowed with learning capabilities similar to Chemreader, a project that Kazu Saitou, his graduate student Jungkap Park and I have been working on for the past two years. Chemreader involves developing machine vision based on digital representations of the world, automatically improving the machine vision component based on feedback loops with the digital representation. It is a top-down approach to learning, paralleling Plato's philosophical concept of intelligence. We have been developing Chemreader in the contex to cheminformatics and the PubChem database. Pubchem is a database of all known molecules that have been synthesized. These molecules (over 20,000,000 of them, I believe) are stored in a digital form (a connectivity table, SMILES string, etc). From the digital form, one can generate a drawing of the molecule. Then the machine vision tool known as Chemreader (the equivalent of a human retina) can "see" the chemical drawing and draw what it sees in terms of a connectivity table or SMILES string. By comparing the connectivity table or SMILES string output of Chemreader with the original connectivity table or SMILES string digital representation used to draw the chemical structure, one can not only get a sense of how well Chemreader is seeing, but also develop an algorthim that will improve Chemreader's code. One can imagine applying a similar strategy to develop a machine vision algorithm that is able to provide vision to an avatar, in a manner that would allow the avatar to navigate the ever evolving 3D world, much like a human controlled avatar would. The Chemreader articles are in the process of being written and published. If anyone wants to learn more about Chemreader, please feel free to get in touch with us.

Thursday, January 10, 2008

Correction on Physical vs NonPhysical Interaction and follow up on Mobius strip

I experiments some more by inserting a linked Physical prim (made of 2 linked components) into a Non-physical peg attached to the non-physical structure of the buildilng. I found I was able to get the 2 objects to interact, with the Physical object obeying physical laws. So, there is no logical problem with interacting physical and non-physical prims (I just had not been able to insert the peg into the hole in the physical object before...I failed to position things correctly so the physical and non-physical were touching. But as long as the objects do not touch, one can be inserted into the other all right. Still, the question of whether one wants to keep Physical vs. Nonphysical prims separate is an important one, I think. it could be that construction is faster and everything is more stable if one combines both physical and non-physical. However, constructing a purely physical world may be more like the real world than constructing a world that is a combination of the two...or maybe not?...I am not sure... this really goes beyond my mathematical and philosophical abilities.

In terms of the Mobius strip, I was able to make one, but I am not sure if the circle is really closed or not. I took a copy of it, in my inventory.

The Physical and the NonPhysical in Second Life

The other day, I had a supermodel/photgrapher come by my lab and ask me what I was building. I told her I was experimenting with physical objects in SL, and that my interest was to build cells, tissues and organs and drug screening. She was very perplexed. The reason was because she was confusing the avatar and the avatar's world -which is nonphysical in nature- with the physical objects in SL, which exist both in a Physical and Nonphysical realm. How can testing a drug on an avatar help you develop a drug in RL? But, I was not talking about testing a drug on an avatar -rather, on a physical cell, tissue, organ or human, within the virtual world. Yes, it is confusing...Avatars can walk both on physical and non-physical platforms. But, physical platforms are subject to gravity, while non-physical platforms are not. In fact, I realize that most of what is constructed already in SL appears to be largely Nonphysical in nature. That is why visitors who come to my lab --even those that have been around in SL for two years-- are amazed when they get to see-saw with me on a plank. Interestingly, buildings -including my lab- are Nonphysical in nature. This may lead to problems in manufacturing later on. I am not sure. I have found that sometimes the Nonphysical and the Physical do not like to interact. I know that Non-physical objects can support a physical object, but in one case, when I tried to hang one of the physical pulley holders from a non-physical peg, the peg did not seem to support the pulley holder. I am not sure why that was. Maybe it had to do with the fact that the pulley holder was a linked object made of two physical objects? Maybe it is linking that is the is possible that even linking should be done physically, say with chain links or rivets, and not with the link command. At a larger scale it may be important to construct a physical-virtual world in SL, as opposed to the nonphysical world that the avatars now inhabit....I think this is maybe an issue that deserves attention right now that we are starting on this enterprise, as it may affect what we are able to do and how we do it later on. I am hoping mathematicians will consider this question and advice on it.

The Rosania Reseach Group Laboratory in Second Life

The Rosania Research Group is in the process of establishing a laboratory in Second Life. This virtual laboratory will explore mathematical modeling, simulations, and computer graphics of three dimensional structures including molecules, cells, higher order cellular organizations. In addition, we will explore visualizations such as cheminformatic assisted image arrays (CAIA).

The Rosania Research Group Laboratory is here:

Gus Rosania's avatar is Caia Alter, and other lab members will soon have avatars of their own.

If you have never heard of SL before, then you can read a recent article titled "Second Life: It is not a game" published by, as well as the Second Life entry in Wikipedia.

01.04.08. Gus Rosania: Today I built the Rosania Research Group Laboratory in SL. Joanna Wombat (Joanna Scott, RL) who is organizer of the Second Nature Island, owned by Nature Publishing Co. was kind enough to let me start building my lab over a piece of the ocean across from the artificial ecology experiment. The lab was built on a platform that floats on the ocean. It does not look half as pretty or neat as all the amazing stuff I've seen in SL, but labs were real scientists work are not supposed to look that nice in the first place. Also, I like the more realistic feel of work in progress. Horace Moody (JC Bradley, RL) stopped by to see how the construction was going, and he was impressed! He was kind enough to give me one of his bulletin board poster boards, and one of his powerpoint presentation boards. Joanna gave me one of those nice Bubblegum Molecule Rezzers. I found a chair in my inventory and a couple of other useless objects....I thnk I'd like to sit on crates better. So, we should be ready for our first SL lab meeting soon. Horace Moody and I introduced me to one of his good SL friends: Graham Mills (Peter RL). Graham showed us his protein rezzer --which converts a pdf file into a full 3D structure of a protein --pretty amazing...As I played with the objects in lab, I was able to learn how to select a group of objects, take a copy away to the object inventiory, and then paste them back to SL to duplicate the existing set. This is useful functionality for building complex repetitive (cellular) structures. I am envisioning a lab in the shape of a cyllinder, built from the ground up, with the bottom floors being information kiosks. The center of the cyllinder will be empty with no walls.

Click on the files below to see two pictures of me in front of the Rosania Research Lab in SL.
RosaniaLabSL010408_001.bmp (if you want these to show up in the wiki write image: instead of file: in the text editor - you can then resize with the visual editor to fit the page better - note that jpeg is easier on your visitors because the files are much smaller than bmp and quicker to load) Gus: I inserted two more file names and did as you said (in addition to the file names that you commented on).... ---Thanks JC!


01.06.08. Gus Rosania. I worked Friday night and almost all day Saturday, and the lab is really taking shape now. Jerry Yu stopped by on Saturday and started playing w prims (It was nice to see a rotation student stop by! )... As I had envisioned, no walls -just open spaces so one can easiy see who is working or visiting around, and to maximize interaction. I built a second shelf-like floor and began construction a third floor, all around a central open atrium., which should always be open so one can easily see the work or objects that is going on on top floors by flying up from the ground flloor. The entire edifice is between the shape of a square and a cyllinder, but the planks are not placed square with each other, so there are jagged edges that let one see how the whole thing is put together. This should make it easier for students and collaborators to understand how the lab was built, so they can continue buildinng their own floors, to their liking. I see this lab functioning as a virtual ant farm of gets added as it is needed. To join the second and third floors, I used 4 hollow cyllinders, that I made semi-transparent and then placed them as connectors at an angle, so thay serve as tunnels that let one access higher stories by walking from lower stories. Then, I put inforamtive bulletin boards around the first floor, which are linked to my blogs and websites so that the interested visitor can read more about my RL efforts and get a sense of how SL and RL fit each other pretty lab, in terms of my own work. I experimented with cyllindrical obejcts (prims they are called in SL)--I found that the prims are able to be deformed, twised, carved, and that they are subject to physical force (tension/compression). I am wondering how two prims interact: can one deform a rubbery prim by placing a solid prim on top? The force of gravity acting on each prim can be adjusted, so in a sense one can make a prim as light or heavy as one pleases. But, I have not experimented with falling prims, or with one prim sitting on top of another, so I really do not know how if there is any air resistance to gravity, or if one prim can exert force against another. Also, I would like to know if two prims that are linked behave as one prim Ultimately, I would like to be able to see if one can build tensegrity type structures with this objects...I have been dreaming about builiding a home in RL in a tensegrity structure like the one that sits in my office. SL may be a way to begin testing if and how one could construct such an object in RL! The current research lab structure is made with free-floating weightless prims. I imaging that one may be able to build RL structures like this one day, with carbon nanotubes ---very, very light, and very, very strong!. I painted the flloors white, and bulletin boards colorful. Aesthetically, I really like my new lab. I think it is a really innovative design -SL-wise. A lot of the people who have been building places in a SL have the mindset of a person living in RL --make a building and then have other people use it/inhabit it. The Rosania Research Group lab in SL is a different concept, more akin to the building of a city: start a buildilng and then let other people use it and expand it as they see fit. And, Open Notebook Science = transparency....NO WALLS! It really helped having spent a couple of weeks visiting different sites in SL, to get an idea of how the lab should look, feel, and function. I am really, really happy with it!

Click on the files below to see the Rosania Research Lab in SL on 01.06.08
Lab photo 010608a_001.bmp

Lab photo 010608a_002.bmp


01.09.08. Gus Rosania. I have been too busy working in Second Life to write my notes, but today the servers at SL are down for an upgrade, so I have some time. In the past few days, I have been experimenting with Newtonian experiments - qualitative data gathering --or shall we say, play? I made some big ball prims, little ball prims, and then hollow sphere prims. I toggled them physical, which allows them to behave as physical objects (subject to gravity and F=ma?)...I am not sure how similar Linden physics are to Newtonian physics but I either read about it and believe it, or I find out about it myself through experiment. So, yes, l found large big balls are easier to move than small hollow balls. I found some beach balls too in my object inventory. These are very light indeed. I painted the hollow small balls red and tossed them arround the lab so that avatars who walk in can experience the physics as they walk into the balls and move them around while visiting the lab. I painted a large solid ball green. I also made a lever that is so large that it can support one or more avatars. It allows one to fly onto it and then walk on it back and forth. One can see-saw with two avatars (my next door neighbor Hiro stopped by late last night and I see-sawed with SL one gets used to such very strange but fun experiences with other avatars one does not necessarily know...). Then as HIro was standing on the platform, I flew up to the sky and then clicked the stop flying button, but Hiro got off the plaform before I hit it, and wam!...landed right on my face with Hiro laughing at my side! VERY FUNNY! I also began building a pulley, but found out that there is no rope prim -at least one that behaves as a rope in physical sense. I spoke w Hiro about this and he said we could script it out of short cillindrical prims. As I think about this, maybe one could do some sort of chain instead of rope by linking toroidal structures together....maybe it will work! (I will try this as soon as the linder servers are up and running.). Also, I asked Hiro about a spring, and he said it would be a similar problem that a rope. I will work on the chain first, and then figure out what to do about springs. I was able to make a large rotary cam. Could support a windmill or a Ferris Wheel. I am thinking a Ferris Wheel may be neat....something that avatars can ride on. Which makes me think I might as well see if I can build a pendulum (swing?). Actuallyl, maybe I can build a giant roller coaster. I think my lab is starting to sound a lot like an amusement part or a circus....but I guess that's what happens to a scientist who would like to experiment-play with the Newtonian laws of physics in SL (I would say this is a lot more fun and educational than most of the other things people are doing in SL....).

Another thing I have been doing these past few days is playing around in the underwater part of the lab (my lab has an underwater station). I found that there are artifical life forms there that swim across the ocean, from the artificial ecology experiment. These life forms that cross ask you for $1L and in exchange they promise they will evolve and reproduce. These are movable llife forms (one can push them) so I decided to put a cyllinder prims around them (tank) and study them. I have been feeding a couple of them 1$L and then some more money (probably spent ($L80) on this) and they have not reproduced. I was hoping they would make good pets, and could see some future in them as laboratory animals --organisms that we could get to grow reproduce, modify, and maybe get to look and behave like cells and sefl assemblee...but Maybe they are a ripoff? Well the other night I got to talk with one of the park rangers from the artificial ecology experiment -a squirrel (I forgot the avatar's name). The squirrel ranger told me that these organisms would reproduce sometimes...I am not sure what that means. The squirrel said that I should only feed it $1Ls, not $5 or 10 or 20....just $1Ls. So maybe I will feed them again some other day. I invited the ranger to visit my lab but as soon as the squirrel saw it, it gave out a loud "aaaaaa!" yell and teleported off to who knows were....I guess he/she did not like the lab. I did not get how funny it was then, but the next morning I got it...VERY FUNNY!!! During the past few days I have had several visitors: Marijo Roiko, Jason Baik, Jerry Yu (from my lab) as well as avatars who pop by the Second Nature site --amongst them a postdoc from Stanford U, another postdoc from UChicago, and also non-scientists including a "model". Models in Second Life probably make no money, because everyone here either looks like a model (or looks like a cat, or a squirrel, or some other name -ess beast) With Jason, I went checking some places out...interesting places in Second Nature. I also discovered the SHRO (Sbarro Human Research Organization) far above the clouds in the SEcond Nature site, and found the way to get in. In RL I showed SL to Kathleen Springer and Steve Erickson. They were impressed. Also, today I made a draft department flyer for Pharm Sci faculty meeting. I put one of the photos of my lab (above) in the flyer....I just thought it would be a nice opportunity to let other faculty know about where technology is heading. It is reallly amazing, to see how the separation between Virtual and Real is beginning to blur.Ah, and something else I thought of at the time I was writing this before, but did not write down: if one cannot link toroids/rings to form a chain, then I am wondering if one could make interlinked links of a chain with a mobius strip and cutting it lengthwise....could one make a mobius strip in the first place? Worth a try....4pm 01.09.2008--I DID IT! ONE CAN MAKE CHAIN LINKS BY INTERLACING RINGS!!!

01.10.2008. GusRosania. I met Finola Graves finally...she told me about the ACS site and invited me to become a resident scientist. I would be happy to get involved, at least throw in some suggestions and set up a larger, more adequate lab for manufacturing/assembly purposes (like the work I have been doing in my lab) and for my utlimate goal of constructing virtual cells, tissues, and organs for drug screening. For starters, I am finding that to build large "physical" prims, we really need flat land...perfectly flat land. I know flat land = boring land, but for scientific purposes, flat land would be very important. Oh, and I actually figured out how to make rope: you can make physical interlacing donuts (nice topological feature). I made one 3 link chain in my lab. I think I shoiuld be able to make elastic fibers with these chains.I will be speaking with a textile expert on how to make physiscal elastic fibers. With elastic fibers we can make physical springs. With [hysical springs we can get phyiscal tension, and with tension we can build tensegrity structures. My mechanical experiments are bringing forth a lot of issues --assembly issues. Fortunately, I am good friends/collaborator with Kazu Saitou, who is an expert ME/CS person --a world recognized expert in assembly. He may be good for helping me set up a factory. Actually, making chains would be good for a factory, as would be making textiles. I am speaking with Juan P. Hinestroza, who is an expert in textiles and woven fibrous materials. The interlkined rings lead to a lot of topological qustions worth exploring. I am not much of a topologist. Then with fibers there are knots. Actually, I found that for some reason, the short three-ringed chain that I made cannot be taken as a copy to the inventory. Also, it seems that one cannot hold IP rights to it. Maybe this is a problem with what I was doing, but maybe there is some logical inconsistency that voids making such objects part of the inventory. In this case, this objects would be the type of thing that cannot be really copied, but would have to be manufactured and then shipped to distant sites. But, I am really not sure. Nevertheless, I already know that large complex physical objects cannot be really transported. They cannnot be linked, because as soon as one unlinks them, then all the links fall apart and the whole thing falls to the ground. I am not sure that SL has a different layers of linking prims, like powerpoint has....Once one unlinks a complex object, all the links fall off. Hmmm...I wonder if this was designed like this on purpose or if this is a design flaw. Maybe there needs to be a 'manufacturing" application built on top of the basic GUI, for more advanced manufacturing processes. I think this is the perfect problem for Kazu. I hope Kazu can test SL soon. I am really looking forward to what he thinks about it. I think he can make some imporatant contributions in designing automated manufacturing processes. And Juan Hinestroza should be able to help with fibrous materials, knots, textiles, filters and the like, and with elastics and springs. I am attaching two pictures of the present lab. As one can see, no longer a nice, clean lab...
Rosania Research Lab January 10, 2008..note the lever, three interlaced links, and rotary shaft
Rosania Research Lab January 10, 2008..note the lever, three interlaced links, and rotary shaft

The Rosania Research lab on Jan 10, 2008 view from above...
The Rosania Research lab on Jan 10, 2008 view from above...
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About Me

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