Software is an extremely valuable tool with countless applications. Need to digest spectral information from a series of images to determine the presence or absence of a target material, perhaps a cancerous tumor or explosive residue? Image processing software has you covered. Need to model how a new airplane design will take to the skies or how a Generation IV nuclear reactor will bring clean energy to cities of the future? Once again, software has your back. Heck, need help solving a differential equation for that pesky university course? Your professor may not like it, but software can help you find the answers.
Despite its usefulness, software has offered little help when it comes to designing biology. While we can confidently predict the lift and drag on a conceptual airplane wing design with 1s and 0s, we face significantly greater hurdles designing something as complex as a single cell. It is extremely difficult to characterize the numerous variables represented by cellular biochemical processes and their respective relationships to each other and the list of environmental factors affecting their function with lines of software.
Of course, some of the problems of developing software for characterizing biology stem from the fact that researchers haven’t needed such tools until very recently. It will take time, learning, and considerable resources, both human and monetary, to tackle the gap between what researchers need and what they have at their disposable. If only there were a global leader in software design tools for modeling, simulation, visualization, and optimization that could step in and help the field of synthetic biology. Hmm…
Autodesk, the creator of AutoCAD and a global leader in 3-D design software, has risen to the challenge. I recently spoke to Carlos Olguin, head of the Bio/Nano/Programmable Matter Group at Autodesk Research, about how Project Cyborg will reshape the “Design, Build, Test” cycle and forever change the way the world thinks about biology.
One platform to rule them all
What is Project Cyborg? It’s a design space for proving real-world methods and processes that is restricted beta testing at the moment, but that doesn’t limit its potential. The cloud-based meta-platform will serve as a foundation for multiple specialized design platforms. For instance, initial efforts are focused on creating design tools for four specific domains:
Tissue engineering: Also called 3-D bioprinting, Autodesk is working with Organovo on constructing functional human tissues for revolutionizing healthcare.
4D printing: A 3D printed object that performs an additional function after being manufactured, such as learning from and evolving with its environment or an IKEA chair that self-assembles after you take it out of the box.
Nanoparticles and DNA origami: Design nanorobots that will seek and destroy cancer cells or DNA scaffolds that will deliver active pharmaceutical ingredients to specific targets within the body.
Synthetic biology: Redesign a metabolic pathway virtually or, eventually, create a fully functional synthetic cell from scratch in a digital environment.
Project Cyborg can be used to target completely new design domains, such as self-assembly, and will be able to find patterns to improve design algorithms. Additionally, cross-pollination can occur between domains. Why not create DNA scaffolds that self-assemble, or harness the power of synthetic biology to build the first fully functional human liver? The possibilities are nearly endless and not limited to the examples listed.
The goal of Project Cyborg and the Bio/Nano/Programmable Matter Group is to create the tools that will allow innovative, creative work to flourish. While it may sound as if Autodesk is trying to compete with software platforms being created by startups, that isn’t how the company is approaching development. “Project Cyborg should not be viewed as a direct competitor to other technology platforms, but rather as a backbone that can guide or enhance development,” Carlos told me.
So, how, exactly, will the meta-platform enable unique solutions for synthetic biology?
Where is the tipping point?
Carlos and I discussed the limitations facing researchers looking to design biology. For one, it’s labor-intensive. Just think about what it takes to engineer a metabolic pathway. You need to create a protocol for assembling DNA, perform the actual cloning, and then analyze the success and function of the new pathway. Luckily, Carlos says most of that work can be reliably performed by software today. “Step 0 for Project Cyborg would be removing all of the labor-intensive tasks that people do today. If we did nothing else, at least that would enable synthetic biologists to work on harder problems.”
One partial solution: take advantage of the crowd. Autodesk has teamed up with J. Chris Anderson at University of Berkeley and Douglas Densmore of the Center for Integrating Design Automation Research at Boston University to develop a specialized platform for synthetic biology called Clotho, which is separate from, but compatible with, Project Cyborg. Clotho is an application environment, similar to an iPhone, for synthetic biology. Anyone can build, share, and download new apps for completing any number of lab tasks. As the platform grows and expands more apps will be available, and more challenging projects can be completed.
Data management tools from Clotho and automated assembly tools from Project Cyborg are big steps in the right direction, but creating tools that will help researchers with harder problems is the longer term goal. “Can we help scientists find answers to unknown phenomenon to predict unknown problems through simulations? We’ll need to characterize biology before that’s possible,” Carlos admitted.
The Build/Test Switcheroo
Unfortunately, the power of software is currently trumped by the complexity of biology. There are simply too many variables to corral a virtual living system into a state of high predictability with a software platform. The potential that could be unlocked is undeniable. Yet, while synthetic biology aims to manufacture things (chemicals, materials, vaccines, and other substances) with biology, there are some major differences between biology and traditional manufacturing.
Think about it: traditional manufacturing processes work by designing a prototype and calibrating its performance before designing a final product. Ford builds a handful of prototype cars for each new model, conducts every conceivable test, makes improvements, then commits to building thousands every day. The “Design, Build, Test” cycle for synthetic biology is not as efficient. Researchers must endure the same costs and sweat equity for each new iterative design as they do for the final product. It shouldn’t be that cumbersome.
What researchers really need is a “Design, Test, Build” cycle. That’s what Project Cyborg is working towards. That’s the power of software. It will take time to characterize biology and enable predictable modeling in a virtual environment, but one day in the not so distant future it will be the featured tool in every synthetic biologist’s toolbox. You’ll have to hang onto those pipettes in the meantime.1