May 01

Germination Space:
A Place to Think Big

2018 Call for Participation
An experimental approach to germinate transformative research questions
Issued May 2018

I. Introduction and Program Goals

The emergence of Engineering-Driven Medicine (EDM) has created the opportunity for the integration of engineering, physical sciences, and medicine to develop technologies that will revolutionize healthcare and help to address big, unanswered questions in medicine. Addressing these questions and technological needs in a way that has the potential for substantial and sustained impact will require complex, multiple-faceted solutions which call for innovative, transformative research. The most vital step in pursuing transformative research comes at the formulation of the research questions.
In the meantime, more and more federal, state, and non-profit funding organizations are starting to emphasize the societal and economic impact of academic research through investing in high-impact, transformative research. It becomes ever more important for SUNY researchers to explore methods for effectively formulating research questions, establishing dynamic and engaging research collaborations, and developing innovative research approaches that will increase the competitiveness of SUNY researchers’ proposals and ultimately achieve significant research advancements.
The Germination Space program will provide SUNY researchers with the opportunity to join a group of interdisciplinary peers to formulate and refine transformative research questions through a series of in-person and online interactions. The program aims to support researchers in challenging traditional assumptions; exploring uncharted areas; and germinating high-impact, transformative research questions targeted at major societal challenges.
Germination Space

The Germination Space is an experimental program dedicated to exploring methods for effectively generating research questions – specifically transformative research questions that hold the potential to address significant societal challenges. Whether motivated by curiosity of knowledge or the pursuit of specific solutions, transformative research questions:

  • Tend to be open questions without apparent, definitive answers;
  • Do not set any initial constraints, such as disciplinary boundaries, availability of resources, etc.; and
  • Challenge both stated and hidden assumptions.

The Germination Space will build on a multiple-iteration and cyclical process comprised of formulating, reflecting upon, and redefining research questions.

  • Formulating initial research questions: What motivates the question, and what outcome is expected if the question is answered?
  • Reflecting upon research questions: Challenging both stated and hidden assumptions as well as constraints of the question, and exploring what existing knowledge and technologies can be leveraged.
  • Redefining research questions: Understanding the needs of the key stakeholders and examining if the research question is relevant to a societal challenge. The research question will then be redefined based on information and insights acquired from all three stages.

Through participation in this program, selected researchers will work with interdisciplinary peers to refine their own research questions by identifying and challenging fundamental assumptions and limitations in traditional disciplinary views.

II. Program Details

Through a series of live workshops and virtual collaboration, Stony Brook participants will iterate through a cyclical process of question formulation and refinement. Participation in the program requires a commitment to attend all on-campus sessions and complete all remote collaboration work for a given cycle. Participation is open to any Stony Brook University, PI-eligible researcher who can commit to being present on campus for the dates below for Stony Brook University:

Program: September 2018 – December 2018
Workshop A: September 28, 2018
Workshop B: October 19, 2018
Workshop C: November 30, 2018

Based on researchers’ responses to the call for participation (process below), selected researchers will be invited to a series of three on-campus, ideation workshops. As part of this process, the selected researchers will form collaborative research groups. Between workshops, researchers will explore feasibility and refinement via online collaboration. Participation is mandatory for all three on-campus workshops. Participants will generate and refine research questions, subsequently developing collaborative research proposals over the course of the semester and will be expected to provide white paper summaries of the refined proposals shortly after the completion of the final workshop. Seed funding is contingent upon the submission of these white paper summaries.
Seed funding grants of $10,000 each – with funds provided by Stony Brook University– will be provided to each of the collaborative groups to pursue the development of their proposals. Please note that there is a maximum of 5 groups that may be formed among the selected participants. Participants will then be provided support from the Office of Proposal Development to submit formal external proposals within ~12 months of completing the program.

III. Responding to this CFP

This Call for Participation (CFP) seeks to recruit researchers committed to pursuing potentially high-impact, transformative research questions that push traditional disciplinary boundaries. Participants must be willing to constructively contribute to challenging and refining both their own research questions and those of their interdisciplinary peer groups. Researchers from all backgrounds are needed
to address these large questions and all Stony Brook University, PI-eligible researchers are encouraged to apply. Please note that researchers are being asked to apply – and will be considered as – individuals. Please do not submit applications as a group. Collaborative research groups will be formed out from the individual applicants who are selected to participate in this program.

A. Applicants must submit a 1-page narrative, plus cover, as described below. Documentation must be submitted by 5pm, May 21, 2018.

Cover Page – The cover page (one page) must include:

  • Campus name;
  • Name and detailed contact information for the applicant (title, email address, phone number);
  • Brief statement of research expertise; and
  • Statement of commitment to attend all on-campus workshops

Narrative – The submitted narrative (one page) must include three sections:

  1. Clear, brief summary of researcher’s motivation for taking part in the Germination Space program and commitment to participate in full process
  2. Keyword summary of current research interests
  3. Explanation of the researcher’s current research interests and their relevance to the challenges of Engineering-Driven Medicine

Biosketch – The two-page biosketch (NSF format) must include:

  • Name, Job Title, Professional Address, Telephone Number, and E-mail address (*no personal information, e.g., home address, home phone, marital status, etc., should be included);
  • Professional Preparation: A list of individual’s undergraduate and graduate education and postdoctoral training, including institution, location, major/area, degree, and year;
  • Appointments: A list of individual’s academic/professional appointments in reverse chronological order;
  • Publications: A list of up to five recent publications closely related to the proposed areas; and
  • Synergistic Activities: A list of up to five examples of collaborative research activities, and other relevant research achievements.

B. If the response is positive, selected applicants will be invited to take part in the Fall 2018 cycle. Confirmation will be due within 7 days of invitation.

IV. Due Dates
CFP Response Deadline: May 21, 2018, by 5pm. Materials and questions should be submitted via email to

Commitment Deadline for invited applicants (notified no later than June 15, 2018): June 22, 2018.

  • After confirming participation, researchers will receive materials to prepare for first workshop by September 1, 2018.
  • Attend Workshop A: September 28, 2018
  • Attend Workshop B: October 19, 2018
  • Attend Workshop C: November 30, 2018

The Germination Space is part of an experimental effort to improve idea generation and refinement, funded by the National Science Foundation (EFRI-1745897/1745891) to Drs. Grace Wang and Phillip Ortiz at SUNY System Administration and Drs. Kemper Lewis and Ryan Muldoon at the University at Buffalo. Project costs are covered by NSF.

Seed funding will be provided by the Stony Brook University Office of the Vice President for Research.

Oct 18

Penguins are noisy, as any visitor to an aquarium knows. Penguins may be noisy in others ways too, according to a new study published in Nature Communications. Scientists have long used Adélie penguin populations to monitor the health of the Southern Ocean and to understand how major factors such as fishing and climate change impact the oceans and the animals that rely on them. Now an extensive analysis of all known data on Adélie penguin populations over the last 35 years has found that only a small fraction of year-to-year changes in Adélie penguin populations can be attributed to measurable factors such as changes in sea ice.

A new study reveals that it is difficult for scientists to understand fluctuations of Adélie penguin populations in Antarctica from year-to-year.

Instead, most of the short term fluctuations in the number of penguins breeding has no known cause; such ‘noise’ in the system is likely due to a host of marine and terrestrial factors that have not, or cannot, be measured at the majority of sites where penguins breed.

 “In many ways, our study shows that watching Adélie penguin abundance may be like watching the stock market—short term fluctuations may be exceptionally hard to predict and may not signal any change in the fundamental health of the system,” explains senior author Heather Lynch, Associate Professor of Ecology & Evolution at Stony Brook University.

“Therefore, adaptive management of marine resources, whereby we stand ‘at the ready’ to adjust our conservation strategy as new data are collected, may be as difficult, and as risky, as trying to time the stock market. Instead, our results suggest that to the extent Adélie penguins are used as a barometer of ecosystem health, the true dynamics may emerge only very slowly.”

This finding, detailed in the paper “Pan-Antarctic analysis aggregating spatial elements of Adélie penguin abundance reveals robust dynamics despite stochastic noise,” is important because it means that tracking abundance at individual colonies, one of the cornerstones of monitoring the health of the Antarctic ecosystem, may not provide a reliable signal on short time scales.

“By analyzing the data, we found that relatively little of the year-to-year variability in Adélie penguin abundance could be linked to something in the environment we can actually measure,” said lead author Dr. Christian Che-Castaldo, a postdoctoral researcher in the Department of Ecology & Evolution at Stony Brook University. “Precipitation at the site is one factor we know is likely to drive some of this unexplained variation, but like many other potential factors, it’s not one we can easily measure in Antarctica.”

Heather Lynch

“This doesn’t mean that monitoring isn’t important, only that we may have to adopt an even more conservative strategy for conserving marine resources. In the face of so much uncertainty, we may not detect a real decline until it’s already too late,” Dr. Lynch explained.

Adélie penguins are one of four species of penguins with significant breeding populations in the Antarctic. Adélie penguins are the most well studied of all penguin species and, being distributed around the entire coastline of the Antarctic continent, are often considered the “canaries in the coal mine” for anthropogenic threats like fishing and climate change.

In this study, the authors analyzed data from all 267 Adélie penguin populations in Antarctica stretching back to 1979, using data collated from the scientific literature under the auspices of a NASA-funded tool called the Mapping Application for Penguin Populations and Predicted Dynamics (MAPPPD).

They used a statistical technique known as hierarchical Bayesian modelling to accommodate the fact that most Adélie penguin breeding locations are surveyed only rarely. Finding a statistically-rigorous way to ‘fill in’ missing data was key to the effort, since it allowed the research team to look at the population dynamics of penguins at larger spatial scales than has been possible in the past.

Dr. Lynch emphasized that not only did the research uncover more details about the increase in Adélie penguin populations over the last three decades, but it suggests that monitoring more breeding colonies sporadically, rather than fewer sites consistently, may provide more timely and more reliable information for policymakers, despite short term fluctuations common in Adélie colonies.

The study also illustrates a new method of tracking Adélie penguin populations throughout the entire continent rather than at selected study sites where the majority of the data are actually collected. They hope to study other penguin species in Antarctica using the same method.

“The findings, overall, provide clear guidance on how to extract the most information from our monitoring efforts, and highlight the benefits of working across disciplines for effective conservation,” added co-author Dr. Jenouvrier at WHOI.

Co-investigators of the research included scientists from the Woods Hole Oceanographic Institution in Woods Hole, Ma.; the National Center for Atmospheric Research in Boulder, Co.; the Department of Natural Resource and Environmental Science in Reno, Nv.; the University of South Florida in St. Petersburg, Fla.; and the Centre d’Edudes Biologiques de Chize in France.

This work was funded by the National Aeronautics and Space Administration (NASA) Ecosystem Forecasting program and by the National Science Foundation’s Office of Polar Programs.

Sep 21

A team of researchers in the Department of Computer Science was recently awarded $3.5M by the Office of Naval Research to support “debloating,” a process that could help guard against security breaches that threaten the privacy and integrity of personal data.

Professors R. Sekar, left, and Michalis Polychronakis, in the classroom

Debloating is the process of removing and streamlining code, thus enhancing software performance as well as security. As part of the researchers’ debloating project, titled “Multi-layer Software Transformation for Attack Surface Reduction and Shielding,” Professors R. Sekar and Michalis Polychronakis will leverage recent advances they have made in binary code analysis and transformation to remove code bloat and tighten security of today’s software.

“Our project is based on the experience and insight gained from our prior research in this area,” said Polychronakis, a cybersecurity expert who joined the Department of Computer Science as an assistant professor in 2015. “To keep it well-managed and to optimize effectiveness, we specifically targeted three main areas: code analysis foundations, debloating and dynamic attack surface reduction, and software shielding,”

The funding is particularly timely in light of recent news that one of the country’s largest credit reporting agencies, Equifax of Atlanta, was the victim of hacking on a scale that has not been seen in years, exposing Social Security numbers and driver’s license numbers of 143 million U.S. citizens.

So why has cybersecurity become such a problem?

One issue arises from the latest software development practices, which can turn out new programs and products for advanced speed and convenience in record time. Unfortunately, the increased coding, or “code bloat,” creates a larger attack surface with a proliferation of security vulnerabilities, just waiting for hackers. These recent advances in software development often result in the need for constant system updates or bug fixes.

But failure to implement these fixes can result in breaches — some of which, like the Equifax hack, can result in the mass exposure of private data.

“This is the absolute worst digital data breach in recorded history,” said Radu Sion, professor in the Department of Computer Science, and founder of Stony Brook’s National Security Institute. “Not only is its magnitude staggering, but its implications are bordering on disastrous and are likely to haunt us for decades.”

Radu Sion of Stony Brook’s National Security Institute

This is because the type data leaked are much more important than email account login info or targeted phishing results, Radu said. As a culture dependent on technology and thus more coding across our digital infrastructure, we have left ourselves vulnerable because we value growth in the market over stronger security, he explained.

“The attack surface will be reduced by removing unnecessary code and restricting capabilities of remaining code,” said Sekar, who received his PhD from Stony Brook in 1991. “We plan to disrupt unintended data flows that are often used in exploits and freeze data that does not need to be modified during operation.”

New protection mechanisms will help shield software against exploitation while significantly advancing control-flow containment, code isolation and diversification, Sekar added.

“Professors Sekar and Polychronakis’ transformative work is critical to addressing the issues we face in today’s era of exponential technological growth,” said Fotis Sotiropoulos, dean of the College of Engineering and Applied Sciences (CEAS). “I congratulate them on this recognition from the Office of Naval Research, and thank them for their important contributions to the College and to Stony Brook University.”

This funding comes to Stony Brook through an Office of Naval Research Broad Agency Announcement that seeks “innovative scientific and technological solutions to address U.S. Navy and Marine Corps” challenges. The Department of Computer Science, part of CEAS, has received nearly $7 million in research awards this summer. According to Samir Das, the department chair, cybersecurity research conducted through Stony Brook’s National Security Institute represents more than 60 percent of the summer research funding.“Unfortunately, this is not the last breach to expect,” Sion said.

About the Researchers

R. Sekar is a graduate of the Department of Computer Science at Stony Brook, earning his PhD in 1991. His research focus is on software and systems security, and on solving practical problems and building real systems including software vulnerability mitigation, malware, intrusion detection, and management of distributed systems.

Michalis Polychronakis joined the Department of Computer Science as an assistant professor in 2015 and earned his PhD in computer science from the University of Crete, Greece. Before joining Stony Brook, he was an associate research scientist at Columbia University. His research focuses on network and system security, network monitoring and measurement, and online privacy.

Oct 13

See our Current Limited Competitions available now! Please contact us with any questions. 

Jun 07
We offer walk in hours each week to assist with education plans, mentoring plans, dissemination plans, NSF broader impact statements, COEUS, budgets, resource sharing plans, and data management plans
Go to top