Onion skinning

Another molecular simulation experiment:


On a related note, I've just upgraded to Vimeo Plus, so all my videos can now be viewed in HD while embedded, which means you don't have to click through to vimeo.com to get a nice quality version.

Later,
Stuart

More molecular simulations

Some more experiments on molecular dynamics.



Later,
Stuart

70S Ribosome

Here is my finished image of the 70S Ribosome:

I created this piece with Maya, molecular Maya, After Effects and Illustrator. This was an exercise in learning more about molecular Maya and nParticles, and to create an informative molecular visualization using real data. The 70S ribosome exists in prokaryotes (i.e. bacteria and archaebacteria) and also in mitochondria. The two subunits clamp around a piece of mRNA and proceed to translate the genetic information into a growing polypeptide chain, reading from 5′ to 3′. Interestingly, the ribosomal RNA, or rRNA provides the catalytic function of the ribosome, rather than the protein components. The exploded view in the image includes a slightly longer polypeptide chain, since this “second” ribosome has translated more of the mRNA. This polypetide is beginning to fold, although this is artist’s representation, and I believe that folding (such as formation of alpha helices) actually begins in the exit tunnel within the 50S subunit.

I've copied the text for this post from our research group's site:
https://bmc.med.utoronto.ca/sciencevis/?p=139

Later,
Stuart

Some particle experiments

I've been doing some experiments in Maya at work to get a better understanding of nParticles and molecular Maya. The first series involves creating chaotic molecular motion with random collisions. The particles here are not to scale (the water is huge and not plentiful enough) but it serves the desired technical purpose.

I've also been creating an explanatory still image of a bacterial ribosome. A screenshot of the piece in progress is below. You can see that these are large complex structures, and it's been really fun examining the structural data to determine where and how the molecules fit together. Most of that information is embedded in the pdb data, but I had to look elsewhere to see how the growing nascent polypeptide navigates through the exit tunnel. The final piece will show this better I hope. I also didn't have mRNA data, so I generated a RNA-like structure with nParticles converted to geometry.

If you enlarge the image, you can probably see that I'm working with almost 6 million polygons (not by counting; the number is in the upper left). But the viewport (thanks to the Quadro K4000) is still butter smooth, tumbling and zooming.

Later,

Stuart

New Job

Okay, some updates on life. After finishing my Master's at UofT, I had some vacation time, went back home to see family, and had some R&R at home in September. That was a really good break from everything; I read some books, played some video games, and just took a break from Maya and all that. I think it was the right decision, although it does feel pretty slow getting back into being creative and doing personal projects. Partly that is the adjustment to working full-time, which brings me, in this blog post, to the job I'm doing now.

I'm employed as a Research Associate (which feels like a bigger more important title than I deserve, but I'm eager to grow into it) at the Science Visualization Group at the University of Toronto Mississauga. There's just a few people in the "group" and we are starting out on a three year project that will involve creating, testing, and disseminating new visualization strategies for addressing common misconceptions in molecular biology undergraduate students.

It's a really great opportunity, because I get to be involved at every level of the research process. We're in the process of creating a simple wordpress site that will serve to share updates on our ongoing research, so I'll share that in the near future and also will probably link to pieces from time to time that I'm involved in.

Sorry, this will be lots of text again and no pictures... maybe I can find a TL;DR photo. Oh no, wait; I do have an image of me at work.

Am I doing Movember at this point? Hard to tell... but you can donate something if you feel so inclined here: mobro.co/stwert

So, one of the awesome parts of starting on this project was I got to put together an amazing computer for doing intensive Maya simulations and things. Not to brag, but I basically got to choose every component I wanted (within a budget of course). So some of the specs are:

• i7 3790k (six core 3.4GHz CPU designed for overclocking, which I need to try out at some point)
• 32 GB DDR3 RAM
• 256 GB SSD
• 3 TB HDD plus 3 TB external backup
• One of the biggest cases on the market so it's super cool and quiet. It doesn't look that big in this photo, but everybody that sees it in person is slightly amazed; you can look up Corsair 900D
• Logitech G710+ mechanical keyboard which is a noisy joy to type on (sorry Andrea)
• Logitech Performance MX mouse which is almost, but not quite as good as my MX Revolution at home (why discontinue it Logitech‽ <- interrobang="" li="">
• ATH-M50 headphones which sound amazing but hurt the top of my head. Might need to mod them: http://www.head-fi.org/t/553303/ath-m50-cush-x2-mod-for-incredible-comfort-and-sound-5megapixel-photos (they're attached to the AUNE DAC I brought from home)
• Two monitors 1920x1080 and 1920x1200... only problem is one is 27" and one 24" so the pixels are quite different sizes and it creates a weird visual thing when I drag windows from one to the other (one monitor is turned around and attached to another computer in the above photo because we're doing eyetracking testing on some existing animation)
• And a huge steel-series mousepad which makes the mouse butter smooth :)
• Oh yeah, how could I forget my first ever Quadro video card, the K4000, which is supposed to be excellent for Maya and other intensive computer work

So you can tell I'm pretty excited about all that hardware.

And, what else is there to say? Not too much, but I'm reading another book on Typography and I'm hoping to start some fun creative projects now. I've got a huge long list of ideas and it's time to stop doing so much planning and start doing so much doing.

Hope you're having a great weekend!

Later,

Stuart

PS TL;DR photo

Interview with SimplyMaya

I had the privilege of doing an interview for SimplyMaya, a forum I have been a member of for quite a few years. I've also done a few tutorial reviews for them in the past. This time they had a number of questions for me regarding the BMC program and what it is like studying for scientific visualization. Check out the article here:

More updates on my work and my fancy computer and convocation coming soon!
Later,
Stuart

Breaking the silence

Phew! Made a post. Feels good. See you soon.
Later,
Stuart

PS Since I started my blog, I haven't gone more than a few weeks without posting, and now a few months goes by! I haven't forgotten, but somehow the gaping lapse creates anxiety for posting, so this post is just to get that over with.

Updated Demo Reel

I've just uploaded an updated and revised demo reel including some of the better shots from my master's project. Hope you enjoy it. Thanks again to PowersWithin for the fun music.

Later,
Stuart

Recording the Illuminated Neuron - Final Project

My Master's Research Project and indeed the BMC program has come to a conclusion. Without further ado, you can check out the full project here: http://bmc1.erin.utoronto.ca/~stuart/RIN/

Please watch the animation, (direct link: https://vimeo.com/70039214) and if you can spare a little more time, feel free to play with the simulator too. I don't expect non-biologists or neuroscientists to understand most or all of it, but hopefully the visuals and interactivity are interesting.

Here's a couple of stills from the animation at very large resolutions. Feel free to download and use as wallpapers etc. (Edit: Okay, blogger apparently has a max res of 1600 on the long edge. Send me an email if you want a larger version... up to 4K).

Now I get to acknowledge everyone like an Oscar speech!
Thanks to Nick, Yves, and Michael (my committee), to all the BMC faculty, my 13 BMC colleagues (very good friends all), members of Yves' lab, my non-BMC friends, all you people that read this blog, and of course my family and Rebecca and God.

Woohoo! Done! What's next? Looking forward to a conference next week that I'm presenting a poster at. I do have some job leads and there is industry day at the end of the month. I'll keep you posted. This blog isn't going anywhere; it's been a terrific outlet for me these past ~4 years and it will continue to be that.

Thanks again everyone, and I hope you continue to check in here and see what the next stage will bring.

Later,
Stuart

A lyrical tribute to BMC

Okay, I'll post up some materials from my MRP shortly, cause I'm done! But first I wanted to just put some lyrics on the page, cause why not.
Presenting: "A Tribute to BMC" to the tune of Paul Simon's Kodachrome (YouTube below, if you're not in the know, and if you are, you can still hit play and sing along). //comments (not lyrics) prefaced with double slashes.

A Tribute to BMC

When I think back on all the stuff I learned in grad school  //*ahem* stuff
It's a wonder I can think at all
And though my lack of fine art knowledge
Hasn't hurt me none
I critique the paintings on the wall

Bee Em Cee-ee-ee  //This is phonetic
You give us those nice bright colors
You give us the research methods
Makes you draw everyone's anatomy, oh yeah  //Provided they stand still
I got a Mac computer  //I don't, I have an ASUS, Corsair, Lian Li, Intel, Windows PC
I love to use the Photoshop
So summer, don't take my BMC away  //Or do, this is just a song

If you took all the art I made
When I was younger
And some of it looks decent, don't you think?  //Operative word: some
I know they'd never match
My sweet communications
And everything looks great in pen and ink  //Hyperbole

BMC  //This sounds the same as the phonetic spelling above
You give us that final gather  //Ambient occlusion would've been great, but... syllables
You give us the verts of Maya
Makes you put particles in all your shots, oh yeah
I got Adobe software  //A lot.
I love to break the picture plane
So summer, don't take my BMC away

Summer, don't take my BMC away (x3)

Summer, don't take my BMC //Sing it out!
Summer, don't take my BMC
Summer, don't take my BMC away

Summer, don't take my BMC
Got to find a job, you see
Summer don't take my BMC away

Summer, don't take my BMC
Summer, don't take my BMC away