Thursday, January 10, 2008

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