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Keio University Researchers Wow ISMB Crowd With New 3D Front End for E-Cell Platform

VIENNA – After more than a decade of development, the E-Cell Project at the Keio University Institute for Advanced Biosciences in Japan is beginning to attract a heightened level of attention, thanks to a new front end for the platform.
Kazuharu Arakawa, research associate and a team leader at Keio University, debuted the new system, called E-Cell 3D, at two separate venues during the 15th annual Intelligent Systems for Molecular Biology conference, held here this week: the Bioinformatics Open Source special interest group meeting held prior to ISMB and in a software demonstration session during the main conference. Both demonstrations drew standing-room only crowds.
The E-Cell Project kicked off in 1996 with the goal of developing a comprehensive computational platform for whole-cell simulation. Now, with E-Cell 3D, the effort has pushed its simulation capabilities into the third dimension via a new interface that enables researchers to model cellular systems with 3D graphics.
The E-Cell 3D visualization engine, which was inspired by other scientific disciplines, such as chemistry, that have done 3D modeling, automatically lays out the model in 3D space, while the underlying E-Cell Simulation Environment simulates the time-course progression of the molecular components in the cell.

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E-Cell 3D was developed with Apple’s Quartz graphics API and the OpenGL 3D software development kit. The software works with Windows or Linux, but really hums in conjunction with Mac OS X — a fact that wasn’t lost on Apple representatives at the ISMB. The company quickly scooped up E-Cell 3D to demonstrate the visualization capabilities of the computers set up at its booth.
Arakawa said that the E-Cell 3D website had been accessed more than 425 times between the time the software was introduced at BOSC on July 17 and the afternoon of July 23, though he pointed out that that did not necessarily equal an outright number of downloads. He was not sure what percentage of hits were actual downloads.
Meanwhile, a promotional video produced by Arakawa’s brother and shown at the conference — an upbeat, irreverent YouTube commercial — had been downloaded “about 1,000 times.”
Under the Hood
Arakawa said that Apple’s Quartz Composer is the “main visual component” for E-Cell 3D. “That environment doesn’t require users to write any lines of code, but instead they can use … a graphical modeling environment,” he said.
The interface is designed as a sphere, and researchers can connect subcellular components, represented in processing units called “patches,” in the sphere in order to model them in 3D.
Arakawa said that the Keio team developed the software to take advantage of graphics processing cards as well as CPUs. Processing on a CPU alone “requires too much power for this kind of real-time rendering, so we had to make many of the patches using open GL — [the] main graphics library — and we have made custom patches optimized that are … processed more by the GPU than the CPU,” he said.
According to Arakawa, “the most frequently asked question is, ‘Does it require a high-end graphics card?’ It does not. We did the optimization at the software level.” He said users typically see rendering at about 20 frames per second, “even on the MacBooks, which aren’t equipped with the graphic card.”
Arakawa said that “intuitive visualization” is the driver behind E-Cell 3D, which is designed for either the standard mouse-and-keyboard, or for a Bluetooth-enabled wand-like device, which can also serve as a way of highlighting, and thus accelerating, colors and concentration levels of the components or proteins within a cell.
Flight Pattern Inspiration
Arakawa’s co-developer, Nozomu Yachie, a PhD student at Keio University, said that E-Cell 3D’s constellation-like appearance was “inspired by a flight simulation map of the US.”

“This is the first time we’ve presented [E-Cell 3D] outside of Japan.”

At the BOSC demo, Arakawa’s demonstration stood out mostly for its visualization features — the ability to “see” the interior of a cell, not only in 3D, but in interactive colors that fade from red to blue depending on the concentration of biomolecules. 
“This is the first time we’ve presented [E-Cell 3D] outside of Japan,” said Arakawa
Arakawa said he isn’t interested in commercializing the software.
“I want to stay in science, and I think it’s crucial to have everything open so it can have the traceability … so every scientist can trace back [to] the algorithm that’s inside the software and maybe test it if they want to,” he said.
He added that he and Yachie tried to make the demonstration as scientific as possible, despite its obvious crowd appeal.
What’s Next?
Now, a primary goal for the software is to bridge the E-Cell Simulation Environment’s stochastic and deterministic algorithms.
Arakawa said what sets E-Cell apart from other simulation platforms — aside from the new 3D front end — is that “[unlike] other simulators … it can handle multiple … algorithms at the same time.”
Currently most simulations are either stochastic or deterministic, not both. He said that while deterministic modeling works well for most types of metabolic models, “if you are doing gene expression … [its concentrations] are so small that they behave stochastically, so you have to do stochastic simulation.”
Converging the two approaches, Arakawa said, is the next challenge for the E-Cell Project.
For more information or to download the software, visit: or  

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