Friday, February 22, 2019

Ripping threads: a new workstation

Before we get started, if you'd rather see the super short version with mostly just pictures, check out my Instagram profile instead. Okay, on with the post. I recently purchased and assembled a new PC! Reason 1: My previous home workstation was purchased a little over 9 years ago. Reason 2: I'll be making computer animations that are fairly demanding with respect to computer hardware.

Yes, it was past time for me to build a new computer. Over the years, I have made some additions and replacements here and there to my old machine; I chronicled one such upgrade in this tongue-in-cheek blog post. However the core of my old computer has been a constant and stalwart workhorse and has enabled me to apply to, complete, and make use of a Master's of Science in Biomedical Communication. It's a bittersweet parting.

Part of the reason (beyond the expense) it took so long to upgrade is because purchasing a computer comes with so many decisions: Windows, Mac, or Linux? Laptop or desktop? Pre-assembled or self-assembled? Intel or AMD? NVidia or AMD? Water-cooled or air-cooled? How much RAM? Everything fits in the case, yes? How about that Samsung NVMe boot drive: Pro or Evo? And do you really need a USB type C port on the front of the case? No, but calculus involving shipping times, availability, cost, colors, side panels, so yes I have one. The list is nigh endless.

I'm not going to discuss pros and cons or rationalize all the decisions I made. I am confident that I did sufficient research and made decisions that were right for me, which are not going to be the choices that anyone else should necessarily make. I try hard not to be a fanboy for any company (I'll admit my chief failing in this regard is Redshift3D). I don't think brand loyalty is worth very much for consumers of hardware, though it's worth a tremendous amount for companies. Food for thought.

So (five paragraphs in), let's cut to the good stuff. All the components arrived in exciting boxes. The case shipped later, so I opted to assemble the guts outside the case in the meantime to make sure I didn't have any dead components.
Like Christmas morning
I cleared off my desk (it's never this tidy), stole my wife's MacBook for on-the-fly support and troubleshooting, and grabbed my iFixit toolkit (a worthwhile birthday splurge).
The streetcar print was a secret santa gift. I love it/hate it.
I grounded myself with an anti-static wrist strap (not pictured) and placed the ROG Strix x399-E motherboard on its box to use as a non-zapping workbench.
It's convenient that so much gaming hardware is perfectly functional for workstations.
Then it was time to install the CPU. I chose the AMD Threadripper 2920x, with 12 cores, 24 threads, 3.5GHz base clock, and this post's namesake. For me it's a good balance of single- and multi-threaded performance and price. Screwing it down was a sweat-inducing nightmare though. I had to press hard way beyond comfort to get the tiny screws to catch. Installing the 64GB of Corsair RAM was comparatively easy, with 4 empty slots for adding more in the future. Yes, I use a lot of RAM hungry applications. There's simply never enough.
This smallish piece of silicon came in the most dramatic packaging I've ever opened.
Next is the "hard drive". In this case it's a tiny (half-terabyte) stick of non-volatile flash memory. Computer technology has come so far. The Samsung 970 series of NVMe SSDs is a very popular choice. I'm using this to hold my operating system (Windows 10 Pro) and all my applications (too many to list, sorry not sorry).
I broke one of the stand-off posts, I think. Ah well, not critical I'm sur&#,%20&..#^@.......
I stuck with air-cooling for this build; I'm not quite convinced of the merits of water-cooling (even AIOs) just yet. Noctua has built great coolers for me in the past, and this giant hunk of metal looks to be another excellent cooler. I meticulously followed the thermal paste application guidelines; indeed I measured out and drew reference circles on that piece of paper in the image, to verify my pea-sized dots of paste.
Fans are available in beige and brown. No, beige AND brown.
As mentioned previously, I'm using a GPU render engine called Redshift to create my images, so a decently powerful NVidia graphics card is a must. This one is the RTX 2070, and I also added the GTX 970 from my old computer (not pictured).
Blower-style. That's not a joke, that's what it is.
I have to power all those components somehow! I wanted high efficiency and enough headroom to potentially add more graphics cards in the future, so the Corsair HX-1000 (1000W) seemed a good reliable choice.
The computer component most likely to explode, kill you, catch on fire, or all of the above. Buy reliable.
And… with held-breath, I poked the start button. And lights came on! And fans spun! And the BIOS showed up on my monitor! I checked a few things, flashed the BIOS to the most recent version so that my processor was properly supported, and shut it down again.
The CPU fan started and stopped a bunch and freaked me out.
Cut to a few days later when my case arrived. Actually it got dropped at a postal outlet many blocks away so I lugged it home in the snow because I'm cheap and don't like taxis and don't have Uber/Lyft and whatever. And exercise is good. The Fractal Design Define R6 Blackout without side-window with USB-C top panel (there are a lot of different configurations) was my choice of case and I'm pleased with it. It's a very understated and quiet black metal box. One would hardly know there's anything happening under my desk right now.
It's bigger than it looks. But I didn't go crazy and get a Corsair 1000D.
I finished the assembly inside the case and made sure the system still booted. It did, yay!
If you see blue and red, your computer's not dead.
After installing and updating Windows, drivers, and some applications, I moved my hard drives from my old computer to the new system (2 SSDs and 2 HDDs) and did a bunch of cable management. I've been using this new machine for the past few weeks, getting everything installed and configured, and I must say I am very happy with the new system. I haven't pushed it too hard yet beyond some initial benchmarks and mini projects, so the biggest noticeable difference so far has simply been the noise. It is so much quieter than my old machine, it's hard to believe.

And that's it! I'll need to upgrade my monitors and mouse (circa 2007-2008) next, but that can wait another few months or years.

I hope with this post I struck the right balance of detailed enough but not boring. If you're down here instead of on Instagram, then perhaps it was okay. I'm happy to answer any and all questions via blog comments, Twitter, Instagram, Email (stuart at biocinematics d0t com), or wherever. You know: "Stuart, you simply must tell me, is your VRAM GDDR6 or HBM2???"

Teaser: My next post will the last one on this blog. What? Why? How? Wherefore? Come back next week!

Thank you for reading.
Stuart

Friday, February 15, 2019

Knots and Robots

I've made various promises to share some recent work, and it's high time I follow-up on that. Over the past few years, I've done a number of freelance animation and illustration jobs, mainly for Professor David Leigh, who runs a Chemistry laboratory at the University of Manchester.

On several occasions I've been privileged to be able to work alongside this research group, who perform intriguing research in the field of molecular robots and molecular knots (What are those? See below for some more explanation). My contributions have been primarily visual analogies of the science behind their work.

I designed editorial illustrations to generate interest in the research and for use as cover images of the journals in which the research is published. I shared one example in my previous post and here's another example on the subject of molecular knots:

An eight-crossing molecular knot and some ions
What's a molecular knot? And why tie one? It's essentially a looped molecule that isn't just a loop. So… it loops through itself at least a few times. There's an interesting (to me) mathematical field of knots, where different kinds of knots are classified based on numbers of crossings–and I probably shouldn't get too far down this rabbit hole. So why create a molecular knot? In my mind, it's about finding novel ways of chemically synthesizing new structures, which could be useful in materials science, manufacturing, and nanotechnology.

It seemed logical to depict this particular molecule as a knotted rope, and I went with a nautical theme, including a central chloride ion represented as a Japanese glass fishing float. To get the right feeling of a heavy, thick rope, I spent a long time working with displacement maps to get the right texture, and I scattered loose hairs with a MASH network.


The illustration didn't end up on the cover of Science, sadly (these choices are made by the publisher for various reasons), but it did show up on various sites, from Forbes to NPR and was an "Image of the Day" for The Scientist and apparently appears in the 2019 Guinness Book of World Records, for the entry "Tightest knotted structure".

Following the creation of an illustration, I was often tasked with developing short animations to be used in presentations of the research. This knot synthesis animation was a huge technical challenge, but a rewarding project.


If I remember correctly, I ended up using three or four different rope rigging setups to create the necessary behaviours as the lengths of rope assembled themselves.

A technical mess looking like the proverbial Gordian Knot
One of the hardest parts, as you might imagine, was the binding action and getting the rope "tendrils" to wrap around each other; I had to carefully measure how far each rope-end was from its neighbours to get the action correct.


In addition to the "knot" work, I also ended up doing a few "molecular robot" pieces. One robot that the lab developed was capable of moving a cargo molecule from one binding site to another, controlled purely by the addition of different chemicals, such as certain acids and bases.


But what does this robot actually look like? Well, we can't observe molecules of this size directly, but here's the chemical structure, showing all the atoms that comprise it.

You can see why I used a lot of hexagon motifs
The lab developed this concept further and designed a programmable molecular robot with a similar structure to the one above. This new molecule can synthesize different stereoisomers, driven once again by different chemical reagents. What are stereoisomers? They are sets of related molecules that differ only in the 3D orientation of atoms. So think of one molecule having an atom sticking out the front, and its "stereoisomer" partner has the corresponding atom sticking out the back.


I had an early concept for a delivery system for the atoms (shown as colored balls in the video), which I think is kind of fun, but we ended up with a simpler concept where the atoms just fly to the tables.


I also had fun designing the peripheral apparatuses (apparati?) to fit with the mechanical theme:

Substrate entry...
... and chemical product exit

I will conclude this lengthy post here (granted much has happened in the last couple years). Thanks for reading all the way down here. Next week I'll share some details about my new workstation, which may be of interest to some?

Finally, an optional "Call to Action": If you'd like to help me out tremendously, subscribing to my Biocinematics channel and liking the most recent two videos (if indeed that aligns with your feelings towards them) would be massively appreciated. If you have already have a Google account or Gmail account, you don't need to sign up for anything new or take any extra steps. If you'd like to go the extra mile, you could share this YouTube channel with friends or family who might be interested in educational science-y stuff.

Thanks again for reading and supporting me,

Stuart

Friday, February 8, 2019

And now for something (almost) completely different

Hello again! It's been a little while. Okay, two and a half years.

Way back in 2016, I started working at AXS Studio (see announcement from my previous post). As a technical artist / technical director, I worked on: illustrations, including one for Scientific American; animations, including clips for a PBS documentary; and interactive projects, including a multiplayer VR game about repairing DNA as nanobots. I also worked on a lot of technical aspects: designing effects and rigs, managing a render farm, programming animation tools, fixing broken assets, and many more.

Over the past couple of years, I also worked freelance on a number of animations and images for Professor David Leigh (http://catenane.net/), which I will share more about in a follow-up post next week. In the meantime, you can see some of the work on my website (www.biocinematics.com)This is an illustration that was created for Nature (submitted for the cover, but sadly not used as such) in which a programmable molecular machine is depicted as a robotic arm. The molecule can produce different stereoisomers depending on the sequence of chemical inputs.

Programmable molecular robot

Over the last few months, I came to the difficult decision to leave AXS Studio and pursue some self-directed work. Why? There are a number of reasons: some personal and family-related, others professional. Ultimately, I decided the time was right to try something (almost) completely different.

Since before this blog started (nearly 10 years ago!) I've been passionate about using animation and computer visualization to teach people about molecular biology. That has not changed, and now more than ever, that's exactly what I want to do. However, the format, platform, technology, and job description will be new to me. More on that in a moment. I realized that to educate and inspire people (especially young people) and help them engage in biology, I need to forego the client-work and studio-work models typically used in the field of biomedical illustration/animation. There's a lot I'd like to explore within science education, so at least for the next year, I'm giving myself free reign to create whatever I feel will best express the ideas I have about biology, education, and animation.

Well, that sounds very lofty and vague, but what am I actually going to do? Some of it is TBD, that's kind of what "free reign" means. But here's the elevator pitch:
I will be making videos about biology.
They will be a combination of 2D and 3D animation, with maybe some video footage. Let's call it "mixed media".
They won't all be the same format, length, style, structure, or content.
They will be on YouTube, all freely accessible for everyone that has open internet access.
They will be less about facts and more about concepts. I want to promote understanding more than knowledge of trivia.
They will be fun and maybe sometimes a little funny.

Also:
I will continue to publish tutorials, though I expect to migrate them to a second channel in the near future.
I will be creating editorial molecular illustrations on Instagram and my website.
I will continue to post on this blog.
I will be learning a lot of new things (see below).
I will likely work on the occasional freelance client project.
I will likely have some other interesting side projects on the go. We'll see what comes up.

I know, that looks like a lot. It is a lot. It's ambitious and risky, and I could fall down and embarrass myself and have to find another "real job" and that's okay. It's really okay. This is a journey I need to take regardless of where it leads, and I'm incredibly excited to start down these paths.

Is there anything else new?
Yes, I built myself a new computer. I'll write a blog post about it down the road. It's awesome and fun and I haven't had a new workstation at home since TWO-THOUSAND-AND-NINE. Yes, that's right, since the year this blog started.

I'm going to be doing a lot of reading and research in molecular biology - to refresh my undergraduate knowledge, to fill in some gaps, and to deepen my understanding of physical biology, biochemistry, and related disciplines. My bookshelf is now overstuffed with textbooks.

And I'm going to be using a lot of new software. Some of it I've used a little, some a moderate amount, and some none at all. Here's my current pipeline plan:
Reference management: Zotero
Writing: Sublime
Storyboarding: Storyboarder
Modeling: ZBrush/Houdini/Blender
Animation/FX: Houdini
Texturing: Photoshop/ZBrush
Rendering: Redshift
Compositing: Fusion
Motion Graphics/Titles: AfterEffects/Illustrator
Editing/Grading: DaVinci Resolve
SFX/Music: Ableton Live/DaVinci Resolve

Where's Maya in this mix? For various reasons, I am gracefully disembarking from the Autodesk and Adobe trains. By gracefully, I mean I'm taking a giant leap and trying to remember how to do a tuck-roll. It's true, I will be making some use of my Adobe CS6 collection, but I think the time has come to step away from Maya. It's been fun, and I may come crawling back, but this is another area in which I need to assert some independence and do what I believe is right for me. Wow, that got a little personal. Moving on…

Initial Redshift test in Houdini
Houdini and Fusion/DaVinci Resolve are the big new ones for me. They both have steep learning curves, but there are several reasons I think they are good choices for content creation for me. It's a bit premature to get into all of that now, but I'm sure I'll end up talking about it in the future.

This has been, by necessity, a fairly long post, so I'll try to wrap it up here.

Thanks for reading, and I hope you'll stay in touch as my new adventures begin.
Stuart

Ah… maybe a very brief and slightly awkward FAQ:
Q: Sorry if I missed it, but are you planning to earn money? YouTube is a hard ecosystem to succeed in.
A: Yes, I know. I will be experimenting with various revenue streams, but regardless of financial success, I'm in this for at least a year. I'll be doing the occasional client gig on the side, but my focus is to create the animations that I feel most passionate about.

Q: I want to support your efforts, what's the best way for me to do that?
A: Aw, thanks! For now, I'd love for you to subscribe to my Biocinematics YouTube channel and connect with me on the social media platforms you regularly use (Twitter: @biocinematics, Instagram: @biocinematics, Facebook: @biocinematics - consistency is good).

Q: I mean, is there any way to support you financially?
A: What, really? That's super kind. I couldn't possibly… *shuffles feet*. No, nothing yet, but stay tuned. Keep an eye on the social media platform of your choice, and I will be sure to make some noise once there are more things in place. Give it a little time though, there's a chance you won't want to "buy what I'm selling" after all…

Q: Is the post title a Monty Python reference?
A: ……………. Ni!