Have you ever dreamed of walking along a microtubule? Imagined a textbook image coming to life? Wished your data would speak to you? These dreams will become reality sooner rather than later, thanks to a new generation of scientists who are creating tools for biological data visualization and modeling. Last month I had the good fortune to attend the Sixth QCBNet workshop in Salt Lake City where experts in molecular graphics, simulation, animation, data visualization and gaming got together to share their knowledge and their vision for making data speak in new ways.
The Quantitative Cell Biology Network (QCBNet) is a project supported by the National Science Foundation (NSF) to create a network of scientists committed to the advancement of quantitative cell biology. ASCB members are involved in QCBNet at every level and the two-day meeting in Salt Lake was kicked off by ASCB member Janet Iwasa’s presentation on animating cell biology. Recounting her training in both cell biology and computer animation (including her studies at the Gnomon School of Visual Effects in Hollywood), Iwasa, who is now at the University of Utah School of Medicine, said her eclectic career has been made possible by the emerging confluence of mathematical modeling, biological illustration, and animation.
Iwasa introduced us to Molecular Flipbook, a powerful program that creates 3D molecular animations. Another highlight of the meeting was cellPack, a plugin for an advanced 3D graphics program (CINEMA 4D). Graham Johnson from the Allen Institute for Cell Science (AICS) and Ludovic Autin from the Scripps Research Institute showed us how to use cellPACK to build a model that randomly localizes proteins on the surface of a cell. Tom Goddard of the University of California, San Francisco (UCSF), and a leading developer of Chimera, taught us how to identify lamellipodia from a 3D light microscopy image of single neutrophil cell. Megan Riel-Mehan from UCSF explained how she used a similar approach to analyze and visualize massive amounts of volumetric data of fast-crawling neutrophil cells. We even used the Oculus Rift system to experience one of the many virtual reality “worlds” presented by Chris Collins from High Fidelity. One by one, each attendee had the opportunity to shadow a dynein molecule on its journey along the microtubule. How cool is that?
In between lectures and workshops, students and professors at the QCBNet workshop discussed hot topics such as the “gamification” of research, utilization of agent-based simulation in science, and building a digital cell. Many felt that the presentation of big data itself has become a major obstacle to progress in science. “Accessing large amounts of data is no longer an obstacle, but the time and expertise required to make sense of it is,” said Yale graduate student Nathan Williams. “User-friendly programs like Molecular Flipbook and cutting-edge specialized software like Chimera are breaking down this barrier.”
The information obtained from Big Data programs will not make an impact if scientists create data that cannot be transferred between researchers. According to UCSF’s Wallace Marshall, who is the Director of QCBNet, “The lack of established data standards and agreed-on algorithms means that every lab is still developing their own approaches, often on an ad-hoc basis.” A standard programming language would help scientists to transfer relevant data between programs that target different scales of biological complexity, Marshall believes.
Although quantitative cell biology is still in an embryonic state, the QCBNet workshop showcased the great progress that the field has already made. Animating and visualizing our data will not only save us time at the bench but will open up new avenues of research. Perhaps someday it will allow us to realize our goal of building a digital cell.
The next QCBNet Workshop will take place at the AICS in Seattle, WA. Susanne Rafelski of AICS and Marshall will organize the Eighth edition, which will focus on quantitative tools. QCBNet workshops are open to anyone with an interest in quantitative biology. You can register here at 9:00 am PDT on Monday, August 15. Registration is free—yes, free—including funding for travel and accommodation. Acceptance is on a first-come, first-served basis, so be online as soon as registration opens. The Salt Lake workshop’s registration filled up in the first 10 minutes.
About the Author:
Sofia Espinoza Sanchez is a graduate student in the Pollard lab at Yale University where she is studying the mechanism of Arp2/3 complex activation. She is also a co-director of the REPU program http://www.repuprogram.org.
Christina Szalinski is a science writer with a PhD in Cell Biology from the University of Pittsburgh.
