Today all started when...

My meat avatar decided to get a web cam to use with his desktop. Well the USB cable was too short so he decided to rearrange the office and computer. That meant a lot of cleaning and throwing away of stuff. Then testing the computer and the new monitor arrangement and the web cam. And then booting up SL and spending a delightful afternoon listening to jazz and doing some simple building. I had forgotten how therapeutic building in SL can be. So here is the first pass at the Tree of Life...


Pretty rough but lots of fun...more to come at http://maps.secondlife.com/secondlife/Carmine/133/181/144

An SL Biology Event-call for volunteers

I just received a note from a Biology professor who is asking for volunteers to help access from student projects in Second Life.

Stephen Gasior(SL=Stephen Xootfly) writes:

Dear Biologists-

Hi. I am teaching a nonscience majors biology class in Second Life this summer. I am having my students make a presentation board about an animal. Basically 3 static textures. I am going to grade the content, but I would like to have biology faculty come talk to them about it. You can also note that they seem to know what they are talking about and confirm that they did the work. In other words, if you can tell me whether they should pass/fail the assignment.

Preferably, I would like to have other university or college faculty with a background in biology. If you would like to volunteer, please send me a link to your faculty profile page.

The event will take place in SL on Tuesday July 20th from 12:40 to 1:40 CST (10:40 to 11:40 SLT). If you are interested in helping me out, please let me know. By July 15th. Location will be on the Louisiana Board of Regents Island (look in my profile).

Thank you.

Stephen Gasior
sgasior@uno.edu

Stephen Xootfly in SL

Sounds like fun and its on a Tuesday when I am not teaching.

SLPro Conference Day 3 Invasion!

Just down the road from my project is this collection of marvelous insects made with scupted prims...and they are flyable according to the menu options. But I guess you have to be the owner to fly them.








The Dragonfly is spectacular!
















The builder by the way is Strat Inshan.

JCCC Chromosome module

Chromosome Build at JCCC site. This is part of the evolution unit being installed at the JCCC site. It currently includes the human chimp ideograms courtesy of ENSI. You can see two of my real simple viewers, the one on the left with some narrative and the one on the right with the human chimp chromosome ideograms.







On the side directly behind me are some red and blue chromosome, that illustrate reciprical and non reciprical translocations. The four cylinders with the colored horizontal stripes illustrate basic chromosomal rearrangements. Because of their importance, I want to have a separate activity for duplications and the evolution of gene families if I can keep it simple.

On the right hand side of the picture a some of my human chromosomes that link into the Ensemble web site.

The chromosome build is at http://slurl.com/secondlife/JohnsonCountyCommCollege/38/94/65

This is open access but the rest of the JCCC sim is currently not.

Mitosis in the Morning...

As part of my evolution build I wanted to have an activity related to chromosomal rearrangements. We know these are important in evolution, some of the clearest examples are in our own evolutionary history. So I developed a series of human chromosomes similar to those over at Genome Island.

These consist of representations of human chromosomes, textured with the standard banding patterns (ideograms) that geneticists use. When the user clicks on the chromosome, menu dialogue allows the user to look at the similarities between the human chromosome and the chromosomes of selected mammals: mouse, chimp, and the macaque. This is done using a data base portal called Ensembl. This displays regions of synteny, which in the bioinformatics context refers to regions of chromosome that have the same arrangement of genes in both species. Here is a quick example for human chromosome 1 showing the regions of synteny in chimp chromosomes to human chromosome 1.

It's probably hard to see what's going on here. But the big white structure in the center represents huna chromsome 1, and the chimp chromsomes with regions of synteny for human chromosome 1 are shown to the left and right. Human chromosome one has synteny with most of chimp chromosome 1 with just a little region of synteny with chimp chromosome 2A and chimp chromosome 10.

Speaking of chromosomes, Max Chatnoir was wishing for a build related to mitosis and meiosis so to help me think about this, I spent the last couple of days building mitosis at my carmine site. None of this is scripted and it still isn't clear what the best strategy for this is.







Here is a quick look at my mitosis builds. These are quite large and I will probably scale them down a bit. They are relatively simple but do take up a fair amount of real estate-not prims but literally really real estate.

This shows prophase, prometaphase, metaphase, anaphase and telophase. You can see me in the bottom of the picture. Each of the "cells" is 10m in diameter.

I don't normally build this big, but it seemed easier to do this big. The mitosis build is currently at:
http://slurl.com/secondlife/Carmine/120/190/138








Here is a close up of metaphase when the chromosomes (shown in red and blue) are lined up in the middle of the cell.
















My thinking is rather than animate mitosis, having this build (maybe on a smaller scale) and then an activity center where students can play with chromsome models like they do in lab. I think it is possible to script the chromosomes to sense a proper arrangement. That would provide a nice collaborative activity.

Speaking of collaborative activities, I also tweaked my predator natural selection module and installed it on my college land site. The module is packaged appropriately with a velociraptor texture so hopefully student predators will get in to the spirit of things.












Here's the module installed at http://slurl.com/secondlife/JohnsonCountyCommCollege/41/95/64. I am also building an activity center just above Predator which students will do first to study natural selection under less challenging conditions.

Caminalcules Spotted at Genome Island!

No need to panic. I sent Max Chatnoir a pair of them for her to break as a beta tester, which she very nicely did in about 1 minute. So made some changes based on her feedback. The Caminalcules can now do various modes of inheritance and can either mate with each other of self fertilize as any proper organism for genetic studies ought to be able to do. Did I mention they also do linked genes? The picture show Max with her first brood. There had been a problem with permissions which caused a bit of grief until I tracked the problem down.






This coming week will see lots of frantic designing and building for the Caminalcule project including plans for a build on Genome Island once the prototype build is finished at Carmine. But a good part of today and Saturday I will be at the Virtual World best Practices Conference. Oops! Starting in about 10 minutes.

A Building Frenzy...

Well not really. But one real nice thing about doing Second Life projects is that there are so many different things to do. So, if you OD on scripting there is always something to build. I like doing both and I decided that maybe when I dream about scripting that it is time to do something else. So last night I played a bit more with Blender and sculpted a pair of very simple guard cells for my photosynthesis project.



This picture shows the result. Probably the sort of thing a master builder would snort at but they are pretty dramatic. Guard cells have a much more complex form than what I show here so for advanced students I might want to show that. Right now these are phantom and the visitor has to walk through them to enter the photosynthesis module. And since Mat Chatnoir has already asked about this...yes eventually they will be scripted to open and close: eventually ;-).

I have also redone the sky box* that my photosynthesis module is in. Originally it was built like the lab where I do my scripting and prototyping as a 20m x 20m x 10m box made from 10 x 10 x .1M prims, plus extra prims for window framing and entrances. My lab module bare bones has 16 prims. But since I currently do my work on my own private region on the mainland I need to watch prim count. You can visit the photosynthesis module in world at http://slurl.com/secondlife/Carmine/118/142/296

In my inventory I have the infamous mega prim package from Alberto Linden, so decided to play with them. Generally I avoid mega prims because the big ones are really intrusive. In fact one of my neighbors has rezzed a big one for some weird reason and it goes right up to my property line...but that is another issue. My neighbor seems to only speak Japanese and while I typically wear a Kimono, I do not. Fortunately my neighbor did blend it so it is textured the same as the region's ground. A few eucalyptus trees and that mega prim is hidden.



At any rate I put together a barebones box, the same size as my SL lab/office but uses only 4 prims rather than 16. Astute biologists will recognise that it is textured with a scanning electron micrograph of the upper epidermis for a leaf. In fact both the inside and the outside were originally textured the same way which is really cool and immersive but maybe over kill. So I retextured the inside with the same sorts of window textures I use in my lab/office and the result is basically what you see in the first picture showing the guard cells at the entrance to the photosynthesis module.

Also this weekend, worked a bit more on the Caminalcule menuing system so that it is a bit more sensible; I was making things way to complex to follow and so I am having to reorganize the scripting a bit.

You're also welcome to stop by my lab/office at http://slurl.com/secondlife/Carmine/174/217/137 You can also TP there from the photosynthesis landing spot.

* Generally I loathe skyboxes..but creatively textured they do have their uses.