Today’s cutting-edge research often requires sophisticated, expensive tools, as well as expertise in using and maintaining them. In many scientific fields, it has become impractical, uneconomical, and unproductive for researchers to continue going it alone.

Material Sciences Professor Jennifer Dionne (top right) with researchers (from left to right) Pari Moradifar, Andrew Barnum, and Briley Bourgeois, interacting on Titan Environmental Transmission Electron Microscope (ETEM) in the Stanford Nano Shared Facilities (SNSF). (Image credit: Andrew Brodhead)

For this reason, Stanford has created dozens of distinct shared instrumentation facilities over the years, as well as new investments in shared resources for computing and data storage as part of the Long-Range Vision. In another important step toward supporting collaborative science, the university is announcing new funding to continue growing its Shared Research Platforms. The platforms seek to ensure easy, affordable access for faculty, researchers, and students campus-wide to capable instrumentation coupled with high-quality data computation and storage.

For fiscal year 2023, the university budget that Provost Persis Drell recently presented at the Faculty Senate will invest over $15 million to address a list of instrumentation priorities identified in concert with Stanford community members. These priorities include upgrading lab equipment, boosting staffing, and increasing educational outreach to facility users. An additional $5 million or so will go towards improving data resources. The funds will secure key new hardware and software for the Stanford Research Computing Center (SRCC), as well as hire staff dedicated to enhancing user experiences.

“With this investment in world-class equipment and facilities, Stanford is boosting frontier innovation,” said Jennifer Dionne, an associate professor of material science and engineering and senior associate vice provost for research platforms/shared facilities. Dionne is also the leader of the instrumentation-focused arm of the Shared Research Platform initiative, called C-ShARP (The Community of Shared Research Platforms).

The shared facilities are also meant to serve as interactive workspaces where the Stanford research community can come together. “The scale of challenges the world is facing demands a convergence of interdisciplinary ideas,” Dionne said. “Shared facilities can serve as a ‘watering hole’ where users not only benefit from the tools available but have opportunities to dynamically collaborate.”

David Studdert, a professor of health policy and of law and acting vice provost for research, has been working alongside Dionne as the leader of the data-resources arm of the Shared Research Facilities initiative. “We’re looking at the full life cycle of a research project,” said Studdert, “from the time data comes in the door or is generated, through computation and storage, all the way through to archiving and efficiently sharing the data with collaborators around the world.”

Studdert said that the newly announced investments respond to the paramount needs identified through a faculty survey and about 18 months of discussions with Stanford community users.

“If you work with data, as thousands of researchers on campus do every day, you care about data acquisition, computation, and storage,” he added. “But you also want access to technical expertise and support, as well as efficient ways to obtain, move, share, and archive research data. The new investments in shared data resources are directed at these key areas.”

Advancing research

Georgios “Yiorgo” Skiniotis is one of many faculty whose research is poised to potentially benefit from enhanced investment in shared research platforms at Stanford. When Skiniotis joined Stanford in 2017, part of his recruitment included a commitment to building a cutting-edge platform for cryo-electron microscopy (cryo-EM). This resource soon evolved to be a service center for the university, now known as the Stanford cryo-Electron Microscopy center (cEMc) for which Skiniotis serves as the scientific director.

Cryo-EM is a groundbreaking microscopy technique that involves flash-freezing biomolecules or cells and using a beam of electrons to visualize their structure. “It had become clear that cryo-EM was going to be the next big thing, and its use has indeed exploded just in the last several years,” said Skiniotis, who is a professor of molecular & cellular physiology, of structural biology, and of photon science.

His group uses cEMc to study the structure and function of G protein coupled receptors, the largest family of cell surface receptors in humans that represent outstanding drug targets for countless diseases. Improved understanding of this crucial class of receptors promises to lead to the development of highly efficacious drugs with minimal side effects.

Thanks to its suite of sophisticated instrumentation and specialized staff trained to assist investigators with using the equipment, the cEMc has evolved into a shared facility supporting a community of researchers not just in biology, but also engineering, materials science, and myriad other fields. “The facility allows for the cross-fertilization of different disciplines, and that leads to innovation,” said Skiniotis. In the years ahead, maintaining the facility’s edge will require continued investment from the university.

Another proponent of a shared research platform at Stanford is Srabanti Chowdhury, an associate professor of electrical engineering and a senior fellow at Stanford’s Precourt Institute for Energy. Her lab focuses on energy-efficient, compact system architectures for electronics.

“We are in an era where we are extremely hungry for energy efficiency because our dependency on electronics is growing and shows no signs of saturation,” Chowdhury said. “The only way we can think about a roadmap forward is by developing electronics that are ultra-efficient in both energy and size and highly versatile.”

Chowdhury and colleagues do much of their experimental work involving the fabrication and testing of gallium nitride semiconductors at the Stanford Nanofabrication Facility (SNF) and the Stanford Nano Shared Facilities (SNSF). Their research relies on custom-made and highly precise tools. “It is impossible for any single researcher to maintain these expensive tools by themselves,” said Chowdhury. “That is why a shared concept is so extremely important – it allows us to create a hub of excellence at Stanford.”

Moving into the data vanguard

Nigam Shah, a professor of medicine (biomedical informatics) and of biomedical data science, expects to benefit from the new investments to Stanford’s shared data resources. Shah’s research aims to leverage the tremendous amounts of data collected across millions of patients’ electronic health records (EHRs) to help guide better medical decisions.

“The crux of the idea is, can we learn to treat the next patient better based on all the previous patients we’ve seen?” Shah said.

One particular project involves pairing imaging data with EHRs to improve predictions of long-term complications of pulmonary embolisms, a common and serious medical condition where a blood clot lodges in the lungs. In collaboration with the Center for Artificial Intelligence in Medicine & Imaging (AIMI), which Shah co-directs, the effort trains algorithms to parse and analyze huge volumes of data. For their massive computing time needs, which cannot be met on campus, Shah and colleagues have had to turn to costly commercial cloud services. “Having a community-shared resource that is university-sponsored and is our hardware, where we’d not be running the meter by the minute, so to speak, to perform this research would be of tremendous value,” said Shah.

Russell Poldrack, the Albert Ray Lang Professor of Psychology, hopes the enhancements to Stanford’s shared data resources will help reduce his team’s dependence on external sources for its computational needs. Poldrack’s research centers on understanding human behavior by using functional magnetic resonance imaging (fMRI) to decipher the brain’s activity patterns. Great quantities of data are generated in the process, which are then compared to data sets from other institutions to generate insights about the human mind. Both are very computationally intensive tasks.

“Stanford is one of the leading institutions in the world for all sorts of computational science, so we should have world-leading computing infrastructure,” Poldrack said. “This new investment in shared data resources will help get us there.”

Dionne hopes that the Shared Research Platforms initiative will be an asset for every researcher on campus and help their science flourish.

“With the infrastructure we’re building in shared instrumentation and data resources,” she said, “we are catalyzing discovery and accelerating solutions.”