MMBioS News

News about MMBioS and MMBioS team members.


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MMBioS Leader Speaks on the Boom in Machine Learning

stackTerry Sejnowski, computational neuroscientist at the Salk Institute for Biological Studies, president of the Neural Information Processing System (NIPS) Foundation and project co-leader for the MMBioS TR&D2 project, was interviewed at the NIPS Conference in December about growth in machine learning. See what he had to say.


MMBioS Renewed

We are happy to announce that MMBioS has been renewed for five years by the NIH's National Institute of General Medical Sciences (NIGMS).  


Making a Difference by Daring to be Different

photo-for the webThe life and career of Ivet Bahar, MMBioS PI and Director, has been profiled by the Biophysical Society.

See the article at


tec-bio logoWe are pleased to announce that our partner outreach program, the Training and Experimentation in Computational Biology (TECBio) Research Experiences for Undergraduates (REU) program ( has been recommended for a 4-year renewal by the National Science Foundation. TECBio provides a graduate-level research experiences to a diverse group of students, who are mentored in part by our MMBioS Investigators. We look forward to a continued successful partnership with this important program for our nascent scientists.  



MMBioS Having a Big Impact

stackAs MMBios enters its 5th year, we took some time to reflect on the impact that our Resource has had.  We are bolstered by the extensive use of our technologies and software by investigators both inside and outside of MMBioS.  To date, over 120 publications have acknowledged the MMBioS award, and these high quality papers have already been cited over 550 times!  We look forward to the advances that lie ahead and to the sustained impact of MMBioS! 



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

T-Cell Receptor SignalingFriend 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.”


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.



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

Dopamine signaling simulation

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”.



Congratulations to our recent graduates

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

Rory Donavan

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!

Juan Jose Tapia Valenzula

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.



Zuckerman and Faeder Receive R01 Grant

Dan Zuckerman
James Faeder

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.


Murphy & Wülfing receive grants from new international collaboration program

Bob Murphy
Christoph Wülfing

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.



Drs Ayoob and Liu Promoted

Joseph Ayoob

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.

Bing Liu

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.





Mary Cheng and the Power of Computational Biology: Biology in 3D


An Interview with Assistant Professor Mary Cheng, on her recent work on dopamine transporter dynamics, by Cell Press, highlighting recent paper published in Structure (see Cheng MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter Structure pii: S0969-2126)

Read Interview from Cell Press



Terrence Sejnowski Receives Swartz Prize

sejnowskiThe Society for Neuroscience (SfN) will award the Swartz Prize for Theoretical and Computational Neuroscience to Terrence Sejnowski, PhD, of the Salk Institute for Biological Studies. Dr. Sejnowski is also a member of the MMBioS Executive Committee and co-leader of the TR&D2 project.  The $25,000 prize, supported by The Swartz Foundation, recognizes an individual who has produced a significant cumulative contribution to theoretical models or computational methods in neuroscience.

Read the press release from SfN



Murphy and Faeder organize NIMBioS Working Group for Spatial Cell Simulation

The National Institute for Mathematical and Biological Synthesis has announced support for a working group on Spatial Cell Simulation based on a proposal by Bob Murphy and Jim Faeder, both of whom are project leaders in MMBioS. Systems biology emphasizes the creation of mathematical or computational models of biological systems such as cells and tissues, as a means both to integrate all available information and to make predictions about unmeasured mechanisms or behaviors. The working group will address critical challenges currently faced in creating mathematical/computational simulations of the inner workings and dynamics of eukaryotic cells that reflect realistic cell architecture, especially for accurately simulating changes in cell shape and organization over time.

The issues to be addressed include methods for simulation that can consider dynamic cell and organelle shapes and positions and methods for learning joint probability distributions for thousands of cellular components. The working group will meet 2-3

times per year to develop new approaches to these problems, implement them in software, develop proposals for future funding of such research, and develop training materials for biomedical researchers. The first meeting will be December 1-3, 2015.

Scientists interested in contributing to the effort are encouraged to contact the organizers at This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it..



Bahar and MMBioS Featured in Genetic Engineering & Biotechnology News

Dr. Ivet Bahar comments on the MMBioS collaboration in a Genetic Engineering & Biotechnology News article: Read More.



MCell 3.3.0 Released

MCell version 3.3.0 has been released.  For more information on MCell and to download version 3.3.0, see the MMBioS software page.



MMBioS PI Dittrich and Collaborators Receive CRCNS Funding

MMBioS PI Markus Dittrich and collaborators Stephen Meriney (University of Pittsburgh) and Thomas Blanpied (University of Maryland) have been awarded CRCNS funding from the NINDS for their proposal entitled "Transmitter Release Site Organization in Plasticity and Disease at the NMJ".



Bahar Lab and MMBioS Research Highlighted

Cheng 100The  implications and wide impact of the research undertaken by MMBioS and the Bahar lab are highlighted in an article in International Innovation,  a research report which covers health and biology research and development being conducted worldwide.

Read the full article



Clay Reid Featured in New York Times

FigIX.1CClay Reid, Senior Investigator at the Allen Institute for Brain Science and an MMBioS collaborator, is featured in a recent New York Times article, "The Brain's Inner Language."  The article is part of The Mapmakers, a science series at the paper dealing with the human mind.



MMBioS PI Ivet Bahar Receives Distinguished Research Award

photo-for the webIvet Bahar, MMBioS PI and Director, has been honored with a 2014 Chancellor's Distinguished Research Award from  University of Pittsburgh Chancellor Mark Nordenberg.

See the announcement at's-teaching-research-and-service-awards-announced.



MMBioS Featured at Biophysical Society Meeting

openingA short video on MMBioS was featured at the 58th annual meeting of the Biophysical Society.  The meeting was held February 15 - 19, 2014, in San Francisco, California. 

See the video.



New Release of MCell

MCellMCell version 3.2.1, containing bug fixes and enhancements, has just been released.   For more information about MCell and to download version 3.2.1, see the MMBios software page.



Major New Release of CellOrganizer 2.0

Example cell image generated by CellOrganizer showing the nuclear membrane (red), cell boundary (blue) and individual lysosomes (yellow).A major new release of the CellOrganizer system for creating image-derived models of cell shape and organization has just been published. The software is a major focus of research supported by the NIH through the National Center for Multiscale Modeling of Biological Systems (MMBioS). It creates statistical, generative models of cell and nuclear shape, microtubule patterns, and vesicular organelles that can be used as the basis for cell simulations (another focus of MMBioS). Generative models capture not just a description of a pattern but the ability to produce new examples of that pattern (analogously to the way in which humans capture models of letters or spoken words not just by describing them but by learning to produce new examples). Support for CellOrganizer has also come from NIH grants GM075205 and GM090033.


Salk scientist Terrence Sejnowski elected to American Academy of Arts and Sciences 

sejnowskiLA JOLLA, CA—Salk researcher Terrence J. Sejnowski, professor and head of the Computational Neurobiology Laboratory, has been elected a Fellow of the American Academy of Arts and Sciences, a distinction awarded annually to global leaders in business, government, public affairs, the arts and popular culture as well as biomedical research.

Sejnowski is world renowned as a pioneer in the field of computational neuroscience and his work on neural networks helped spark the neural networks revolution in computing in the 1980s. His research has made important contributions to artificial and real neural network algorithms and applying signal processing models to neuroscience.

Read Full Article:



Neuroimaging Resource Powers-up with new Cloud Computing Capability

A valuable resource for MMBioS researchers is now "in the cloud".


A library of tools for analyzing brain images and related data has moved to the “cloud,” potentially enabling faster and cheaper analysis and hypothesis-testing.

Read Full Article



Follow the Money: Big Grants in Biomedical Computing


The clear winner: Big Data 

MMBios Featured in Biomedical Computation Review, highlighting Big Data by "Bridging Gaps in Multiscale Modeling"

Several biomedical computing projects received big money in the fall of 2012. If there’s one clear winner, it’s “Big Data”: three of the grants focus on building new computational infrastructure and tools for dealing with massive biological datasets. A fourth grant focuses on building new tools for multiscale modeling.

Read Full Article




NIH Awards $9.3 Million to Establish Biomedical Technology Research Center 

PITTSBURGH, Nov. 30, 2012 – The University of Pittsburgh School of MedicineCarnegie Mellon University (CMU), the Pittsburgh Supercomputing Center (PSC) and the Salk Institute for Biological Studies (Salk) have been awarded a five-year, $9.3 million grant from the National Institutes of Health (NIH) to establish the Biomedical Technology Research Center (BTRC) that will develop computational tools for modeling and simulating biological systems from the tissue level down to the molecular level.
By filling in the missing pieces between modeling efforts at disparate scales of structural biology, cell modeling and large-scale image analysis, this new collaborative initiative seeks to identify the molecular and cellular mechanisms that control neurotransmission and signaling events, which in turn could lead to the development of novel treatments for nervous system disorders.