MMBioS Welcomes Two New External Advisory Board Members

It is with great pleasure that MMBioS and Dr. Ivet Bahar announce two new additions to the External Advisory Board.

Dr. Linda Petzold joins us from the University of California at Santa Barbara where she is currently a Distinguished Professor in the Department of Mechanical Engineering and the Department of Computer Science (Chair 2003-2007), and the Director of the Computational Science and Engineering Graduate Emphasis at the University of California Santa Barbara.  She is a member of the US National Academy of Engineering and a Fellow of ACM, ASME, SIAM and AAAS.  

Dr. Petzold was named the UCSB Faculty Research Lecturer for 2011, was awarded the SIAM/ACM Prize for Computational Science and Engineering in 2013, received an Honorary Doctorate from Uppsala University in 2015, was awarded the SIAM Prize for Distinguished Service in 2016, and was awarded the IEEE Sydney Fernbach Prize in 2018.  Dr. Petzold’s current research focuses on modeling, simulation and data analytics of multiscale systems in biology and medicine.

 

Stacey D. Finley, Ph.D., joins us from the University of Southern California where she is currently an Associate Professor in the Department of Biomedical Engineering. She is the holder of the Gordon S. Marshall Early Career Chair and the Director of the Center for Computational Modeling of Cancer. Dr. Finley additionally has a joint appointment in the Mork Family Department of Chemical Engineering and Materials Science and the Department of Biological Sciences (Quantitative and Computational Biology section). She is also a member of the Norris Comprehensive Cancer Center.

Dr. Finley received her Bachelor’s degree in Chemical Engineering from Florida A & M University. Her graduate studies were completed in 2009 in Chemical Engineering at Northwestern University and involved using computational tools to predict and estimate the feasibility of novel biodegradation pathways. Her postdoctoral studies at Johns Hopkins University focused on computational modeling of VEGF signaling pathways. She was awarded postdoctoral fellowships from the NIH National Research Service Award and the UNCF/Merck Science Initiative. Dr. Finley’s current research applies a systems biology approach to develop molecular-detailed computational models of biological processes related to human disease.

We look forward to working with the both of you! Please join us in welcoming Drs. Finley and Petzold to the MMBioS community!

We would also like to thank Drs. Harel Weinstein and Mark Ellisman for their service and valuable contributions to MMBioS during your tenure as External Advisory Board members.

Shawn Brown joins MMBioS Executive Committee

We are delighted to announce that Dr. Shawn Brown joined the MMBioS team and will also serve as a member of the Executive Committee. Mr. Brown was recently selected as the next director of the Pittsburgh Supercomputing Center (PSC). Brown’s work uses high performance computing, informatics and computational modeling to advance research in scientific fields, including neuroscience and public health. Shawn joined the PSC from McGill University in Montreal where he served as the Chief Technology Officer of the Neurohub Project and Associate Director of Research Software Development at the McGill Centre for Integrative Neuroscience. While at McGill, he led the development of the infrastructure of two large-scale platforms, Neurohub and CBRAIN, which use high-performance computing, machine-learning and artificial intelligence to analyze diverse datasets to advance neuroscience and mental health research. This marks Brown’s return to PSC. While at PSC from 2005-2017 he developed six computational platforms for public health research and published research on obesity prevention, infectious diseases and vaccine strategies. He also served as a faculty at the Department of Biostatistics at Pitt Graduate School of Public Health. Welcome to our team Shawn, we are excited to have you join the MMBioS team!

TECBio REU Pioneers Successful Virtual Program

Amidst the uncertainty and turmoil that beleaguered the early months of 2020, the TECBio Research Experience for Undergraduates (REU) program at the University of Pittsburgh had to make the difficult decision of whether or not to proceed with their annual summer research program. Preparations had to be made and longstanding playbooks had to be completely re-written, but it was decided that the program would continue so we could serve our students (honor our commitments to them, or something like that). Naturally, one of the biggest changes would be the move to an online/virtual platform. 

During the planning process, Dr. Joseph Ayoob began efforts to coordinate with REU programs nationwide to build a network of support and cooperation amongst the handful of them that were also considering holding virtual programs. Bi-weekly meetings were held throughout the summer where inter-program communications avenues were paved and information was shared for the mutual benefit of all involved. In the end, this group enabled and supported ~30 programs to provide research opportunities for students.  

The plans for TECBio had finally coalesced into a more cohesive vision for the summer and, on May 25, 2020, the first Virtual TECBio REU program began with the opening orientation. Though there were many challenges, the students and their faculty mentors and labmates, managed to discover new ways of communicating and working together on their research projects. As one TECBio student noted, "It was an enriching experience, despite the fact that we had to adapt to a new modality, everything went smoothly." The student committee groups (which are comprised of TECBio student volunteers and are organized into Social, T-Shirt, Ambassador, and Mentoring Committees respectively), helped to oversee further adaptations to the new virtual format through new and creative ways of fostering interaction and engagement. Overall, both students and faculty expressed their happiness with how the research and program progressed. For the first time, virtual reality was utilized (in the form of Oculus Quest headsets) for a seminar talk as well as the final poster session, which took place entirely in a large VR gallery room. The use of this technology was universally applauded by everyone in the program and helped foster a feeling of connectedness despite the distances. 

Despite the obstacles presented for this year's program, it concluded as a success with many students reporting significant gains in their confidence and ability as researchers, and all of them expressing gratitude that they were able to participate in a meaningful experience during these uncertain times. One TECBio student, Caleb Armstrong, summarized his experience thusly, "This REU gave me a thorough insight into what being a graduate student is like from many aspects, including research, learning, and social activities. Before this opportunity, I had barely any research experience, or even any idea what graduate school was really like; now, I feel properly prepared (and confident enough) to pursue research as a career and a passion."

 

We would like to make you aware of this year's remote (online) workshop:

HANDS-ON WORKSHOP ON COMPUTATIONAL BIOPHYSICS
Workshop Dates: October 12 - 15, 2020
Application Deadline: September 25, 2020
For more details, or to apply visit:
https://mmbios.pitt.edu/workshops/2020-workshops?id=239

The Hands-On Workshop on Computational Biophysics is a joint-effort between The NIH Center for Macromolecular Modeling & Bioinformatics at UIUC [www.ks.uiuc.edu] and The National Center for Multiscale Modeling of Biological Systems (MMBioS) [mmbios.org]. Drs. Ivet Bahar (Pitt) and Emad Tajkhorshid (UIUC) will lead the instruction for this interactive 4-day event. The workshop will cover a wide range of physical models and computational approaches for the simulation of biological systems using NAMD, VMD, and ProDy. Space is limited and applications will be accepted until September 16th. This workshop is jointly supported by MMBioS, an NIH Biomedical Technology and Research Resource and the NIH Center for Macromolecular Modeling & Bioinformatics.

The agenda for the workshop will be updated and posted on the meeting website:
https://mmbios.pitt.edu/workshops/2020-workshops?id=239

Dr. Ivet Bahar has been elected a member of The National Academy of Sciences

Dr. Ivet Bahar is among the exceptional scientists elected this year to the The National Academy of Sciences (NAS). NAS membership is a widely accepted mark of excellence in science and is considered one of the highest honors that a scientist can receive. Dr. Bahar has been elected “in honor of outstanding contributions to computational biology.” She is a pioneer in structural and computational biology, having developed widely-used elastic network models for protein dynamics.  These models reveal cooperative motions that are intrinsically favored by 3D protein architectures to allow substrate-binding, allosteric regulation, and supramolecular machinery, thus computationally bridging structure and function. Dr. Bahar adapted fundamental theories and methods of polymer statistical mechanics to biomolecular structure and dynamics. She pioneered a modified version of the classical Rouse model, to examine the collective dynamics of proteins modeled as elastic network models (ENMs). ENMs have three strengths: simplicity, ability to yield a unique solution for each structure, and efficient applicability to supramolecular complexes/assemblies. Her theory and methods have withstood numerous tests since their inception, and established fundamental concepts in molecular biology: the role of entropy-driven fluctuations defined by 3D contact topology in optimizing biomolecular interactions; the evolutionary pressure for robustly maintaining structural dynamics to support flexible mechanisms of actions – not only structure to ensure stability; the ability of proteins to exploit their structure-encoded dynamics to adapt to promiscuous interactions and mutations as demonstrated in numerous applications, including neurotransmitter transporters in recent years. Recent application to chromosomal dynamics provided insights into the physical basis of gene co-expression and regulation events. Dr. Bahar is a Distinguished Professor and the founding John K Vries Chair of the Department of Computational and Systems Biology, University of Pittsburgh School of Medicine; and co-founder of an internationally-acclaimed PhD program in Computational Biology, CPCB, jointly offered by the University of Pittsburgh and  Carnegie Mellon University.

NAS is a private, non-profit society of distinguished scholars established in 1863, which aims to provide independent, objective advice to the nation on matters related to science and technology. Approximately 500 current and deceased members of the NAS have won Nobel Prizes. This year’s election of 120 members and 26 international members brings the total number of active NAS members to 2403, and the total number of international members to 501. Members of NAS are elected at the annual meeting in April in recognition of their distinguished and continuing achievements in original research. You can read their official press release in National Academy of Sciences Elects New Members.  

Congratulations Dr. Bahar!

MMBioS Cell Modeling Virtual Workshop: June 22 - 26, 2020

*Due to the associated travel restrictions related to the spread of COVID-19, and to safeguard workshop participants, we have decided to restructure the Cell Modeling Workshop into a "virtual workshop."  Applicants will be updated with more details soon. We regret the inconvenience for this change and appreciate your patience as we deal with these exceptional circumstances.

We are proud to announce our latest workshop:

CELL MODELING WORKSHOP
Dates: June 22 - 26, 2020
Application deadline: May 15, 2020

For more details, or to apply visit:

https://mmbios.pitt.edu/workshops/2020-workshops
 

The Cell Modeling workshop will cover theory and practice for the design and simulation of cell models focused on diffusion-reaction systems such as neurotransmission, signaling cascades, and other forms of biochemical networks. During the workshop, participants will learn how to use the tools developed by MMBioS to create, run, and analyze models of cellular microphysiology and apply them to their own research questions. In particular, the workshop will focus on: 1) The latest version of the MCell simulation environment, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces. 2) Novel tools to construct and simulate rule-based models using the BioNetGen software 3) The CellOrganizer system for creating image-derived models of cell shape and intracellular organization that can be used to compare cell populations and as the basis for cell simulations and 4) The newest version of CellBlender, our MCell model creation and visualization framework. The attendees are encouraged to bring ideas/data for their own simulation projects.

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