- Published on January 24, 2017
We are pleased to announce that our partner outreach program, the Training and Experimentation in Computational Biology (TECBio) Research Experiences for Undergraduates (REU) program (www.tecbioreu.pitt.edu) 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.
- Published on January 24, 2017
MMBioS Having a Big Impact
As 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!
- Published on October 18, 2016
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.”
- Published on October 05, 2016
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.
- Published on August 05, 2016
Bahar participates as an invited speaker at the White House for the National Strategic Computing Initiative
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”.
- Published on July 20, 2016
Congratulations to our recent graduates
Two MMBioS team members recently completed their Ph.D. work.
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.
- Published on July 01, 2016
Zuckerman and Faeder Receive R01 Grant
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.
- Published on June 17, 2016
Murphy & Wülfing receive grants from new international collaboration program
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.
- Published on May 04, 2016
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.
- Published on November 25, 2015
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)
- Published on October 22, 2015
Terrence Sejnowski Receives Swartz Prize
The 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.
- Published on September 04, 2015
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.
- Published on June 10, 2015
Bahar and MMBioS Featured in Genetic Engineering & Biotechnology News
- Published on May 11, 2015
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.
- Published on October 06, 2014
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".
- Published on March 14, 2014
Bahar Lab and MMBioS Research Highlighted
The 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.
- Published on February 25, 2014
Clay Reid Featured in New York Times
Clay 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.
- Published on February 24, 2014
MMBioS PI Ivet Bahar Receives Distinguished Research Award
Ivet 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 http://www.chronicle.pitt.edu/story/chancellor's-teaching-research-and-service-awards-announced.
- Published on February 19, 2014
MMBioS Featured at Biophysical Society Meeting
A 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.
- Published on February 12, 2014
New Release of MCell
MCell 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.
- Published on September 30, 2013
Major New Release of CellOrganizer 2.0
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.
- Published on May 02, 2013
Salk scientist Terrence Sejnowski elected to American Academy of Arts and Sciences
LA 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: http://www.salk.edu/news/pressrelease_details.php?press_id=611
- Published on April 04, 2013
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.
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.