SimTK ReLaunch: Back at the Cutting Edge

What does it take to make a great biocomputing repository even better?

Way back in 2005, YouTube was brand new; FaceBook had just launched; the idea for Dropbox hadn’t yet been hatched; and GitHub wasn’t even a glimmer on the horizon. So when SimTK launched that year as a place for the physics-based simulation community to share files and code and control privacy at different access levels, it was offering something quite new and unique.

 

“SimTK was really cutting edge at that time in terms of enabling sharing and collaboration,” says Joy Ku, PhD, SimTK project manager who also served as Director for Simbios, the National Center for Biomedical Computing that established SimTK. But after 10 years, the site is ready for an upgrade as well as some new functionality to put it back at the cutting edge, Ku says. “The Internet and scholarly publishing have changed dramatically, and we’re reinventing SimTK to take advantage of new technologies—new ways of interacting with and using the Web—and new paradigms in research dissemination to help accelerate research.”

 

Some new features, such as social networking capabilities to enhance collaboration, are already up and running. Others, such as opportunities to reproduce simulations in the cloud, and integrated functionality with GitHub and other valuable online resources, are planned for the coming year. New project pages include more information to help determine whether or not a particular resource would be useful, such as when a project was last updated and how many times it has been downloaded. “We want to make it easier for people to make intelligent decisions about the resources they download and use,” Ku says.

 


SimTK’s Enduring Appeal

In the years since its launch, SimTK has grown considerably. It now has more than 47,000 members and hosts more than 800 projects—despite the fact that other services now offer some of SimTK’s functionality.

 

The relaunched SimTK is available both for personal computer and mobile devices.What explains the site’s enduring appeal? For many, it’s the resources posted for downloading—models, simulations and software—that represent years and years of work. “Being able to download musculoskeletal joint models, run them and analyze them decreases barriers to entry to the discipline because people can use the models rather than redeveloping them,” says Ahmet Erdemir, PhD, director of the Computational Biomodeling Core at the Cleveland Clinic.

 

SimTK also offers some unique and difficult-to-generate datasets for download, including the one used for the Grand Knee Challenge, a modeling and simulation competition held each year for the past six years. The competition makes available to the community the most complete knee datasets anywhere on the Web. “In terms of human movement analysis, we collected and posted everything including the kitchen sink,” says B.J. Fregly, PhD, professor of computational biomechanics at the University of Florida, who ran the challenge. Participants in the challenge used the SimTK public forum to post questions; and the site’s mass emailing capability came in handy as well. “It’s one-stop shopping,” Fregly says. The knee data has been downloaded by 700 unique users. “People all over the world are using these data. It’s not just for the competition.”

 

SimTK also provides a free alternative to building a new research Web site for each of your projects. Erdemir, who has launched all his projects on the site since 2007, appreciates not having to create and maintain a centralized location for posting software, models and documentation. “SimTK offers a better chance of long-term sustainability. And it’s more public-friendly, accessible and streamlined,” he says. “The site also tracks downloads, which is useful in grant applications to show the impact on the community,” he says.

 

In addition, Erdemir uses SimTK for open development of models and software. For example, OpenKnee has been completely open from the outset. “We disseminate early and frequently, which requires time and effort, but SimTK provides that infrastructure,” he says.

 

Another advantage: By posting their projects, graduating students can ensure that their work is re-used. “I make my students put their source code, data and some readme files on SimTK before they graduate,” Fregly says. “That way a future student can go in and pick up where they left off. It makes continuity of projects easier.”

 


Social Networking with SimTK

Until now, SimTK has operated primarily as a hub-and-spoke system: A small subset of members contributed resources to the site and a large group of members downloaded them without interacting with each other. “We want to see it become a more interwoven network,” Ku says.

 

To that end, SimTK has implemented a few social networking tools. For example, the “Follow” button, one of the most recently added features, allows members to track a project either privately or publicly. The latter option places the members’ names on a list of followers that anyone can explore. “Now you’re able to interact with anyone who expresses an interest in the project, not just the project leads and key developers,” Ku says. “It’s a way to build the community and promote collaboration.”

 

The site also highlights recommendations of other projects to visit based on the project category, keywords, and the viewing behavior of other site visitors. This feature is already encouraging visitors to explore the other projects on SimTK: In the first year after it was implemented, total monthly project visits more than doubled (from 31,000 to 63,000) and 42 percent of project visits were made through the recommendation system. Ku hopes such features will also motivate visitors to host their own projects on the site.

 


Reproducibility in the Cloud

One major challenge of physics-based simulation is reproducibility—ensuring that researchers using the same data and software can get the same results.

 

To address this problem, Ku and Erdemir are working on offering members a cloud-based way to reproduce published results on SimTK. “We’re hoping to further lower the barrier to entry for modeling and simulation,” Erdemir says.

 

The feature enables users to launch a simulation by simply selecting a server, a model, and a specific software version from dropdown menus. When the results are available either for download or for browsing online, the user receives a notification. As a test case, Erdemir has created a template for running such simulations of OpenKnee. The interface allows users to run a simulation, perhaps apply a different load to the knee, and run a new simulation. Ku and Erdemir hope the cloud-based option will be up and running before the end of the year.

 


Plug and Play Capability

In the coming year, SimTK will also include the ability to plug-and-play with other online applications. For example, several SimTK projects use GitHub as a way to collaborate on their source code. They might also use another site to track bugs and then they use SimTK to share the software. But SimTK could be the hub that provides ways to pipe information to and from these multiple places, Ku says. Some of the developers of the site’s largest projects on SimTK, such as OpenSim, OpenMM and SimVascular, are eager for this improvement. “Users and contributors alike will have one place to go to get quick updates; communicate; know where the project is headed,” Ku says.

 


SimTK: Past, Present and Future

SimTK was novel in 2005 when it started out, Ku says, but 10 years on, “technology and our users’ needs have changed, so SimTK is changing, too,” she says. Ku hopes the features now being added to SimTK will put it back at the forefront—well ahead of whatever other new new things might come along—and keep it relevant for the community of researchers that flock to its pages.

 

For a sneak peek of the new SimTK site, visit https://simtkalpha.stanford.edu.

 

 



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