Understanding the nature of signaling pathways — networks of molecules in a cell that work together to control a cell’s response to its environment — is an increasingly important part of biomedical research and helpful, for example, in enhancing our understanding of how cancer cells live or die.
In a paper, Pathways on demand: automated reconstruction of human signaling networks, published in Systems Biology and Applications, a Nature partner journal, T. M. Murali, professor in the Department of Computer Science at Virginia Tech, in collaboration with Shiv Kale, a research scientist at the Biocomplexity Institute of Virginia Tech, present a new computational algorithm called PathLinker that automatically reconstructs signaling pathways from a background network of molecular interactions.
The Office of the Vice President for Research and Innovation recognizes Anil Kumar Vullikanti, an assistant professor of computer science in the College of Engineering and the Biocomplexity Institute, who develops methods to forecast significant societal events, such as disease outbreaks.
He is a member of the Biocomplexity Institute’s Network Dynamics and Simulation Science Laboratory, which integrates informatics, analytics, and large complex system modeling across diverse domains to build synthetic information tools for real-world, stakeholder-defined problems.
Vullikanti studies dynamical systems, wireless networks, social networks, computation epidemiology, and the modeling, simulation, and analysis of socio-technical systems.
Virginia Tech Center for Autism Research experts will host a one-day seminar March 4 in Falls Church, Virginia, for scientists, professionals, educators, students, and health-care providers in the field of autism, and individuals with autism and/or their family members to learn about new insights in the disorder that affects more than 3 million Americans.
This marks the second time that Virginia Tech has hosted a public seminar in the National Capital Region focusing on novel autism research and other information about its autism center. The first seminar was held in 2014, the same year the U.S. Centers for Disease Control released startling new data on the growing prevalence of autism: That one in 68 children has some form of autism spectrum disorder (ASD), a 123 percent increase during the last decade.
Virginia Tech researchers will provide additional insight into new research involving autism.
Congratulations to Osman Balci on being honored with the 2015 ACM SIGSIM Distinguished Contributions Award.
The award recognizes individuals based on their overall contributions to the field of modeling and simulation, including technical innovations, publications, leadership, teaching, mentoring, and service to the community.
Cal Ribbens, professor and associate head of the department of computer science has been named as the new head of the department. His new position officially begins December 10.
Ribbens has been a member of the computer science department since 1987. He was named associate head for the department in 2003 and associate head for undergraduate studies in 2008. His research has focused on advancing high-performance computing and its applications for computational science and engineering, with the goal of making high-performance computing an effective tool for solving important scientific and engineering problems.
Richard C. Benson, dean of the College of Engineering who holds the Paul and Dorothea Torgersen Chair, said Ribbens emerged from a very strong field of candidates. “Cal is very well known to this department, and many other corners of the university, for his long and exemplary service as an associate head for the department,” Benson said. “I am grateful to the search committee for its great work, and especially grateful to the department heads who Cal succeeds — Dennis Kafura and Barbara Ryder. I’ve watched the department thrive under their leadership and know that it is in excellent hands moving forward.”
Ribbens has taught 19 different courses at Virginia Tech, including all levels of core computer sciences courses, an honors course and several advanced topics courses. He chaired 17 master’s committees and eight Ph.D. committees, and served on dozens of others. As associate head for undergraduate studies, he had a lead role in faculty teaching assignments and course scheduling, and graduate teaching assistant selection and assignment. Ribbens also supervised the academic advising staff and lead curriculum revisions and assessments.
“I am looking forward to this opportunity to lead a strong and growing department,” Ribbens said. “This is a very exciting time to be in computer science. Our students and faculty are working on challenging problems drawn from a remarkably wide array of application areas, and affecting virtually every aspect of life.”
Ribbens completed his undergraduate work in mathematics at Calvin College. He earned his master’s and doctoral degrees in computer science from Purdue University. He has been widely published in journals, including the Journal of Parallel & Distributed Computing, the Journal of Computational Science, and ACM Transactions On Mathematical Software.
Ribbens has served on more than 20 conference program committees and as general chair of the 17th High Performance Computing Symposium, and is founding director of the Laboratory for Scientific Computing and Applications. He played a major role in the System X supercomputer project.
As associate head, Ribbens helped guide the department through considerable change, including joining a new college and the hiring of more than 20 faculty members.
“It is an exciting time for Virginia Tech, the College of Engineering, and the Department of Computer Science, as we continue to grow in size, impact, and quality,” Ribbens said.
Three CS@VT faculty members were among the 49 computing professionals recognized this year as Association for Computing Machinery (ACM) Distinguished Members. This honor recognizes educators and researchers with at least 15 years of professional experience, who have significant accomplishments or who have made a significant impact within the computing field. Congratulations to Dr. Cliff Shaffer (ACM Distinguished Educator), Dr. C.T. Lu (ACM Distinguished Scientist), and Dr. Adrian Sandu (ACM Distinguished Scientist).
Congratulations also to one of our alumni, Dr. James “Bo” Begole (PhD, 1998), who was also named a Distinguished Scientist this year.
A team of researchers led by a Virginia Tech faculty member has received $1.25 million from the National Science Foundation to introduce computational approaches to help students learn chemistry in an environment that encourages scientific discussion.
Felicia Etzkorn, a professor of bioorganic chemistry in Virginia Tech’s College of Science, is part of the team, along with two faculty members from the University of Texas at Austin’s College of Education — Victor Sampson and Stephanie Rivale. The project will involve four teachers in the Austin, Texas area.
Tatar talked about ways to integrate computing with science, technology, engineering, and math education at a National Science Foundation Conference about Next Generation STEM Learning on Nov. 9 in Washington, D.C.
Now, with National Science Foundation support, the researchers will help teachers introduce computational approaches into eighth grade integrated science courses.
Supporting one of the primary goals of the Institute for Creativity, Arts, and Technology, the work brings together science, engineering, art, and design in an effort to transform K-12 education.
The project embeds targeted chemistry topics into computational models, supported by a framework that encourages structured scientific argumentation. Eighth grade chemistry students will learn how earth-science systems work by interacting with graphically-based computational models, or simulations. By modifying and adapting the code in these models to better represent aspects of chemical systems, they will also build computational thinking skills.
“Our goal here is for students to understand how systems work — both chemical and computational — and the important role complex systems play in our lives,” explains Tatar. “It’s difficult to describe these systems to students, so simulations provide a level of interaction with the processes. Students can actually see cause and effect and they have opportunities to think critically about the problems in the world around them.”
The team will develop four modules to be used in four eighth grade chemistry classrooms. Each module will have measurable goals related to chemistry and computational learning, as well as argumentation implementation.
For example, one module will examine atmospheric science, specifically the retention of greenhouse gas in the environment. While the results of this process can be seen, the actual process — how increased concentrations of carbon dioxide traps heat in the atmosphere — is more abstract. The simulation created by the team visually demonstrates the interactions between matter and energy, with an emphasis on thermodynamics and kinetics.
This model shows the earth and sky and features graphical representations of the heat generated by the earth and the sun’s energy. Users can add sources and sinks of carbon dioxide to the model world in the form of trees and factories. Students can easily change the production rates of the factories in the simulation’s code and immediately see the results and potential real-world impacts. For example, they could manipulate the code to determine how many trees would be needed to balance the production rates of the factories.
Using these graphically-based simulations, students can discover how initial elements on the model operate, and they can also easily inspect, change, and test the code. When a student examines the model, makes a prediction, changes the code, and then re-runs the model, the computer provides feedback.
The process of anticipating, interpreting, and testing the computer’s feedback allows the student to act as a scientist, exploring both the computational and physical world. This also helps strengthen their argumentation skills — being able to prepare, support, challenge, and refine their ideas. Before implementing any changes, the students will describe in their own words how the code will be changed, outline their plan, and justify their expectations.
Dr. Barbara G. Ryder, J. Byron Maupin Professor of Engineering, received the College of Engineering (COE) Diversity Committee Award for her commitment to diversity. Barbara’s work has improved diversity in the Department of Computer Science at Virginia Tech, region and state. This award is richly deserved and one in which all supporters of inclusion efforts can take pride in. The award was presented by Dr. Bevlee Watford, COE Associate Dean for Academic Affairs, at an AdvanceVT luncheon on November 4, 2015. Barbara said, “I am honored by this award and very much appreciate the CS faculty and staff who have contributed to the department’s recent gains in the gender diversity of its students and faculty (in fall 2015, 16.7% CS majors and 21% CS tenure-track faculty are female).”
AdvanceVT began in 2003 with a grant from the National Science Foundation to promote and enhance the careers of women in academic science and engineering through institutional transformation. Read more about Advance VT here.
NATIONAL CAPITAL REGION, Nov. 10, 2015 – An initiative supported by the National Science Foundation (NSF) will bring research universities across the southern U.S. into a partnership to develop a Big Data Regional Innovation Hub.
Virginia Tech’s Chang-Tien Lu, associate professor of computer science and associate director of the Discovery Analytics Center, is leading the university’s broad-based collaboration on the project, which will develop public-private partnerships to address big data challenges facing the region.
