Picture This: Molecular Maya Puts Life in Life Science Animations

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1 Piture This: Moleular Maya Puts Life in Life Siene Animations [ Data Visualization ] Based on the Autodesk platform, Digizyme plug-in proves aestheti and eduational effetiveness. BY KEVIN DAVIES In 2010, a reporter sat in a Life Tehnologies hotel suite admiring a promotional video illustrating one of the ompany s latest researh projets a single-moleule sequening system featuring enzymes tethered to fluoresing quantum dots. The video was impressive not merely for pushing the boundaries of sequening tehnology, but equally for showasing some powerful prodution qualities in 3D animation and rendering that, until reently, would have seemed the provenane of a Pixar movie. That video was produed by a Boston ompany alled Digizyme ( founded in 1999 by Gaël MGill as a side business while he worked on his Ph.D. at Harvard Medial Shool. Sine then, Digizyme has beome a respeted soure for eduational and promotional animations, simulations and videos for many diverse life siene appliations. The visual ommuniation of siene that s where my passion is, says MGill. He reognized early on that graphi design, animation and visualization tools were needed by several industries, not least his fellow sientists. Clients inlude aademis as well as bioteh, pharma, medial devie ompanies, along with siene A mitohondrial moleular landsape depiting signaling proteins in apoptosis (reated by Digizyme for Cell Signaling Tehnology). museums, and publi television stations. After a hiatus to run the ompany full time after his postdotoral fellowship, MGill joined the Harvard Medial Shool faulty five years ago in the Center for Moleular and Cellular Dynamis, where his researh fouses on how visualization impats researh and eduation. He is also reating a new graduate program to train students in biovisualization approahes. Most ompanies offering animation tools are staffed by visual speialists or animators with a strong artisti bakground ollaborating 12 JANUARY 2012 Visit Us at

2 with sientists. There are some great ompanies in this spae, but what sets us apart is that we re sientists, says MGill. Everyone at Digizyme is dually-trained as a sientist-animator, sientist-artist, or sientist-programmer. As a result, our visualizations are diretly informed by the primary literature and based on raw data. At Digizyme, MGill reruits twin-threat staff with a siene graduate degree as well as strong artisti talent. The ompany has reated stereosopi movies for siene museums, ustom projets for pharma lients inluding Amgen, J&J, Novartis, Life Tehnologies, and Genenteh, as well as ompleted work for several major hospitals, researh institutes, and universities. M- Gill is also the Digital Media Diretor and a ollaborating author for E.O. Wilson s Life on Earth digital biology textbook. Going Hollywood The software that powers the Digizyme platform is Maya, a suite developed by Autodesk, whih is a modeling, animation, simulation, and rendering appliation widely used in media and entertainment irles to reate video game haraters and environments and speial effets for feature films. Of ourse, suh software was never intended to display life sienes data. What are we doing with Hollywood software? says MGill. There s been billions of dollars invested in films to reate powerful software suites, suh as Maya. MGill says that urrent biosiene researh features an inredible rihness of datasets that is just overwhelming. We see visualization as the key to knowledge integration it offers a powerful and flexible platform to import and synthesize data from various fields data that would not otherwise interat. One example would be to reate an intraellular landsape using ryoem tomography data to map the loation of proteins in a ell. This map ould be populated with atomi resolution protein strutures, and then set in motion and simulated using various algorithms inluding Brownian dynamis. This begs the question: What software do I use for this sort of thing? It doesn t urrently exist, but it s something that interests many sientists. Our approah is to modify and adapt existing animation tools from Hollywood platforms like Autodesk Maya to advane toward that goal. MGill s team built a new layer of ode to make Autodesk s Maya more biologially relevant, resulting in a plug-in toolkit alled Moleular Maya (mmaya). (see, A Better World ) Moleular Maya fouses the modeling, animation, rendering, and simulation apabilities of Maya in the ontext of biologial animations and strutures. For example, instead of modeling DNA from srath, it provides a diret link to a sientifi database that downloads data diretly into Maya and automatially reates the 3D model. MGill and his team are also developing tools in mmaya to rig maromoleules to failitate biophysially-aurate animations as well as to build moleular environments. >> Visit Us at JANUARY

3 << Moleular Maya is written in languages with renowned strutural biologist Stephen (inluding Python and MEL Maya Embedded Language) that allow other researhers to surfae of HIV, MGill reated an animation Harrison, who speializes in proteins on the extend its apabilities. We ve reated a series that depits how a viral surfae protein gp41 of free, open-soure sripts that lets anybody spears the target ell membrane and refolds on type in a protein ID, say, and with a lik, have itself to drive membrane fusion and failitate this diretly onnet to the Protein Data Bank so they an model, manipulate and animate a protein within seonds, says MGill. This aessibility ame to light in the reent IGEM (International Genetially Engineered Mahine) world jamboree, where student teams from around the world used syntheti biology priniples to design novel ellular iruits and hybrid proteins. For a student team trying to design something in a forward engineering approah, the design piee is not just making a pretty piture, it an be an integral part of the oneptualization and Digizyme models the ellular entry of a reovirus. experimental approah, says MGill. For the past few years, he has been involved with viral infetion. Proteins aren t stati, they re this ompetition by hosting seminars and offering workshops to help students use Maya and tional hange annot be depited with the typi- shape shifters, says MGill. gp41 s onforma- Moleular Maya. (Autodesk has also sponsored al linear interpolation morphing tehniques. IGEM the past three years.) It undergoes a helial transition and refolds ompletely. And trying to ommuniate suh a Not Just Pretty Pitures ritial and unusual onformational hange in a MGill undersores the ritial role that visualizations an play in experimental researh. I ve MGill s group helped Harrison visualize standard researh paper was next to impossible. worked with olleagues at Harvard Medial gp41 s unique onformational hange and, in the Shool where the proess of reating a visualization an hange one s understanding of the that hopefully failitates drug disovery. Un- proess, ommuniate the mehanism in a way protein, says MGill. derstanding the speifi mehanism of how gp41 In one projet arried out in ollaboration refolds may drive better approahes to drug >> 14 JANUARY 2012 Visit Us at

4 A Better World The life sienes ommunity might appear a little staid next to some of Autodesk s other marquee lients, inluding James Cameron, Frank Gehry, Disney, and Boeing. Not so, insists Patrik Byrne, diretor of business development for the Californian ompany that elebrates its 30th anniversary in Our mission is helping ustomers imagine, design and reate a better world, says Byrne. The prinipal ustomers are in arhiteture/engineering, manufaturing and media/entertainment. Within the latter group, Autodesk has been building a produt development group to extend Maya into life sienes. It sits in our media and entertainment team, beause Maya was developed for media professionals, says Byrne. But why life sienes? When we look at the range of industries we re in, the onept of design workflows is transparent aross all industries. Whether you re in one of those industries, our tools enable you to be more effiient, more iterative and more reative. And when we look at aademi researh, we see an interesting plae, says Byrne. Without muh ado from us, people like Gael have taken Maya and used it as a platform to develop visualization tools for their industries. We want to extend and enable that. One of the keys to Maya s popularity is not just the modeling, texturing and rendering apability, but its extensible nature. Users an write their own plug in, whih an be omplex or very simple. For students and aademi users, Autodesk offers free aess to the software for three years in a termedfree liense ( om/). As you re perfeting your skill, let s make sure you have aess to the tools to perfet your raft, says Byrne. Byrne sees three prime opportunities for Maya in the life sienes: first, as a platform for innovative tools; seond, use in siene eduation urriula; and third, helping sientists in industry visualize and ommuniate researh to a wider marketplae. There is some strong ompetition in the marketplae, inluding an open-soure produt alled Blender, and its derivative Bio-Blender, but Byrne sees the market expanding. Support of the IGEM ompetition, for example, puts Maya in the hands of a global student body eager to harness the software in various syntheti biology appliations. Byrne says he is proud of the MIT group, whih won the 2011 IGEM prize in the health/mediine ategory, enabling ells to autonomously regenerate. Visit Us at JANUARY

5 << disovery or vaine development, he says. Another example is Shawn Douglas (Wyss Center, Harvard Medial Shool), a former visualization student of MGill s and now a leading figure in the field of DNA Origami designing novel DNA moleules to fold in vitro to reate biologially useful entities. Douglas Maya plug-in, Cadnano ( greatly simplifies DNA origami projets and brings the power and ease of use of typial modeling tools in Maya to this rapidly growing field. We re now ollaborating to have both plug-ins mmaya and Cadnano work together inside Maya, says MGill. Cadnano figures out how to reate the geneti sequenes that, when mixed in a test tube, fold into the shape of an objet modeled in Maya. It s magi a great example of how a design tool an transform a proess that previously took weeks or months to navigate. Visualization researh isn t just about making movies but also about understanding how to design the most effetive movie to impat a target audiene. Says MGill: We re very interested in understanding how design hoies how we represent or animate a proess an have an impat on the effetiveness of a movie, espeially in the ontext of eduational animations. We strive to reate animations and interatives that have a high pedagogial impat on students, not just animations that are engaging and aesthetially pleasing. In one reent projet, hundreds of students assessed four different styles of animating a simple moleular interation: a hormone binding to a ell surfae reeptor. MGill and his 3D visualization tehniques prove a valuable tool for teahing moleular biology. ollaborators tested students before and after viewing these animations as well as monitored their reations using eye-traking methods. Typial medial animations often impart deision-making properties to moleular entities as if moleules know where they are going. This ouldn t be further from the truth! says MGill. He aknowledges that reating animations that depit both the stohasti nature of the moleular world while keeping students attention on the mehanism and speifiity of an interation is quite a design and tehnial hallenge. MGill has reated an eduational web site alled moleularmovies.om. It has three setions: one is a Showase of some of the best online ell and moleular animations, organized by sientifi topi. A Learning setion ontains MGill s teahing urriulum at Harvard Medial Shool, available free. And third is the Toolkit setion, where researhers an download Moleular Maya. 16 JANUARY 2012 Visit Us at

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