2016 - MMBioS

Details: Published: Tuesday, 18 October 2016 14:57

Modeling with BioNetGen Gives MMBioS Team Insight into How Immune System Decides to Attack — or Let Be

Friend or Foe?

A mix of computer modeling and laboratory experiments has helped reveal how the body differentiates “friend from foe.” Using their BioNetGen computer tool for simulating biochemistry, MMBioS members and colleagues have painted a sharper picture of how T cells, the advance scouts of the immune system, decide when to protect bodily tissues from immune attack—and when to lead the attack. The finding may guide future efforts to control human diseases like diabetes and cancer.

When T cells—a type of white blood cell—encounter other cells in the body, “they have to decide what kind of a response to make,” says James Faeder, project co-leader of MMBioS’s Technology Research and Development Project 2 Team and associate professor of computational & systems biology, University of Pittsburgh. “Is that a threat, or is it something benign? Depending on their assessment of a possible threat they can either become activated, immune-boosting cells that kill pathogens, or they can tamp down those responses.”

Details: Published: Wednesday, 05 October 2016 16:04

MCell 3.4 Released

MCell version 3.4 has been released. For more information on MCell and to download version 3.4, see the MMBioS software page.

Details: Published: Friday, 05 August 2016 15:12

Bahar participates as an invited speaker at the White House for the National Strategic Computing Initiative

A snapshot from multiscale simulations of dopamine signaling (by Cihan Kaya, in collaboration with Faeder, Sorkin, Sejnowski and Bahar labs)

Dr. Ivet Bahar was invited to participate in a workshop and give a talk at the White House for the National Strategic Computing Initiative (NSCI).

On July 29, 2015, the President issued an Executive Order creating the NSCI, a whole-of-Nation effort to maximize the benefits of high-performance computing (HPC).

The workshop brought together 75 leaders from industry, academia, and government to discuss opportunities of HPC and solutions to the challenges faced. Dr Bahar participated in the meeting as one of the three invited speakers from academia. She presented her perspective on what is the state-of-the-art in computational biology using her NIH-funded Biomedical Technology and Research Center’s focus as a lens, and discussed current challenges that could be addressed by exascale computing through NSCI. The title of her talk was, “Exascale Computing for Multiscale Modeling and Big Data in Biology”.

Details: Published: Wednesday, 20 July 2016 14:44

Congratulations to our recent graduates

Two MMBioS team members recently completed their Ph.D. work.

Rory Donovan

Congratulations to Dr. Rory Donovan, who successfully defended his thesis, “Efficient Sampling in Stochastic Biological Models” on May 31. Rory joined CPCB following his MS in Physics at U. of Washington, and his BA in Physics at Reed College, and was advised by CPCB co-Director Dr. Daniel Zuckerman.

Rory came back to Pittsburgh to defend his thesis, as he had already begun his position as a postdoctoral fellow in the lab of Dr. Nathan Price at the Institute for Systems Biology in Seattle. In addition to celebrating his PhD, we are also eagerly awaiting news of the arrival of his first child!

Jose Juan Tapia-Valenzuela

Congratulations to Jose for successfully defending his dissertation, “A study on systems modeling frameworks and their Interoperability”. Jose was a member of the Faeder lab during his time at CPCB, and now will continue to work with Jim.

Details: Published: Friday, 01 July 2016 18:57

Zuckerman and Faeder Receive R01 Grant

Zuckerman (top) and Faeder (bottom)

Dr. Daniel Zuckerman (PI), in collaboration with Dr. Lillian Chong (PI) and Dr. James Faeder (Co-I), was awarded an NIH R01 grant for $1.3 million over 4 years. The grant is titled “High-Performance Weighted Ensemble Software for Simulation of Complex Bio-Events”.

In response to a call from NIH, the aims are to provide open-source software to enhance the power of simulations at any scale (e.g. molecular, cellular) for a potentially large user base. Thus, the primary impact will be to facilitate key segments of the burgeoning field of computational biomedical research. Additionally, research to be performed directly by the investigators is designed to yield insights into cancer and neurological processes with potential to enhance drug design efforts.

Details: Published: Friday, 17 June 2016 17:05

Murphy & Wülfing receive grants from new international collaboration program

Murphy (top) and Wülfing (bottom)

MMBioS investigators Bob Murphy (Carnegie Mellon University) and Christoph Wülfing (University of Bristol) have just received grants from a new program encouraging collaboration between U.S. and U.K. investigators. The program, run jointly by the U.S. National Science Foundation (NSF) and the U.K. Biotechnology and Biological Sciences Research Council, allows the investigators to submit a single proposal that is reviewed by only one of the agencies: if it scores highly, the second agency simply accepts the recommendation of the first. The project builds on initial work funded by NSF and subsequent work done through MMBioS that led to a recent major paper in Science Signaling. The project will involve analyzing fluorescence microscope movies to create spatiotemporal maps of proteins involved in signaling by T cells, a key component of the immune system. The maps will be combined with data on cell-wide protein phosphorylation and used both to infer potential signaling complexes, and to estimate the apparent affinities and potential causal relationships amongst proteins involved in T lymphocyte signaling.

Details: Published: Wednesday, 04 May 2016 15:36

Drs Ayoob and Liu Promoted

Dr. Joseph C. Ayoob has been promoted to Associate Professor in the department of Computational and Systems Biology at the University of Pittsburgh. Joe has been with the department since July 2009 and has done invaluable work with our educational programs and scientific outreach.

Dr. Bing Liu has been promoted to Research Assistant Professor in the department of Computational and Systems Biology at the University of Pittsburgh. Bing has been with the Bahar lab since 2013. He works to develop computational modeling, simulation and analysis techniques to study the dynamics of biological systems.