Other Training Activities
MMBioS supports these training activities in conjunction with the University of Pittsburgh and Carnegie Mellon University.
CPCB - The Joint CMU-Pitt Ph.D. Program in Computational Biology
TECBio REU - Training and Experimentation in Computational Biology. An NSF and DOD Research Experiences for Undergraduates program
CompBio Academy - The Computational Biology Research Summer Academy for high school students.
Cell Modeling Workshop Evaluation Questions
Cell Modeling Workshop Evaluation Questions
- The cell modeling workshop was very valuable for my current/future research
- I would recommend the Cell Modeling Workshop to my colleagues
- The instructors and teaching assistants were well prepared
- The instructors and teaching assistants were helpful and assisted me with my problems and questions
- The online tutorials were useful (www.mcell.org/tutorials)
- The presentation was clear and well structured
- The lecture taught me the basics of building MCell Models
- I expect that MCell modeling will be important to my current or planned research projects
- Ease of use of CellBlender/RuleBender
- I expect that CellBlender/RuleBender will be important to my current or planned research projects
- Clarity of Presentations on CellBlender/RuleBender
- How much you learned from the presentations on CellBlender/RuleBender
- Usefulness of CellBlender/RuleBender to your current or planned research projects
Hands-on Workshop Evaluation Questions
Hands-on Workshop in Computational Biophysics Evaluation Questions
We survey attendees at the conclusion of each workshop so that we can constantly improve our offerings. Here is a list of topics that attendees to the Hands-on Workshop in Computational Biophysics are asked to evaluate:
Outcomes
- The Workshop broadened my understanding of concepts and principles in the field of Computational and Theoretical Biophysics.
- The Workshop improved my ability to carry out original research in the field of Theoretical and Computation biophysics.
- The workshop improved significantly my computational skills.
- The workshop taught me techniques directly applicable to my career.
- The material presented in the workshop was relevant to my research.
Lectures
- The instructor's knowledge of the subjects was good.
- The instructors explained the material well.
- The instructors provided real-world examples.
- The lectures were coordinated between instructors.
- Lectures incorporated recent developments in the field.
- The range of lectures captured the overall essentials of the field.
- The level of the lectures was appropriate.
- The underlying rationale of the techniques presented was clear.
- The instructors stimulated my intellectual curiosity.
- The daily Q&A period was beneficial.
- The Tuesday presentations by participants were a valuable addition to the Workshop.
Hands-On Sessions
- The hands-on sessions were important for the learning process in the Workshop.
- The concrete examples in the hands-on tutorials increased my understanding of the lectures.
- The hands-on sessions were long enough.
- The hands on sessions were coordinated with the lectures.
- TAs were well-prepared to answer questions.
- There were sufficient instructions to proceed with the hands-on assignments.
- There were enough TAs /instructional staff to help the participants.
- The tutorial options accommodated the differing interests of the participants.
- The tutorial options accommodated the differing expertise of the participants.
Environment and Technical Resources
- The software used in the Workshop ran well on my (Windows, Mac, Linux) laptop.
- The lecture room was conductive to learning.
- The projection was sufficient for lectures.
- The Hampton Inn provided sufficient accommodations.
Communication and Dissemination
- Instructors were readily available for Q&A outside the lecture periods.
- The Workshop web site was informative about the event.
- The emails about setting up laptops for the Workshop were helpful.
- The organizational emails before the workshop were helpful.
Overall Satisfaction
- The Workshop was well organized.
- The balance between lectures and hands-on sessions was optimal.
- The Workshop addressed my research needs.
- Overall, the Workshop met my expectations.
- I would recommend this Workshop to others.
EAB Meeting Fall 2015
External Advisory Board Meeting
For NIH Biomedical Technology & Research Resource (BTRR) on
“MMBioS: High Performance Computing for Multiscale Modeling of Biological Systems BTRR”
School of Computer Science, Carnegie Mellon University, Room 8102, Gates Hillman Center
Agenda
Wednesday Sept 16 |
|
8pm |
Dinner with the EAB Members, BTRR Leadership & Symposium Speakers |
Thursday Sept 17 – EAB Meeting |
|
8:15 am |
Hotel guests pick up by designated MMBioS members |
8:25 am–8:55 am |
Breakfast |
8:55 am—9:05 am |
Welcome – Introduction (Ivet Bahar) - Download presentation |
9:05 am – 10:20 am |
TR&D1 + associated DBPs/C&SPs 9:05 – 9:35 Ivet Bahar (Pitt) - ProDy, coMD, DBP1, CSPs1, 2, 16-18 - Download presentation 9:35 – 9:50 Dan Zuckerman (Pitt) - WE and applications - Download presentation 9:50—10:00 Ingo Greger (Cambridge, UK) - Download presentation 10:00 – 10:20 Q&A |
10:20am-10:40am |
Coffee Break |
10:40 am – 12:05 pm |
TR&D2 + associated DBPs/C&SPs 10:40-11:10 Jim Faeder (Pitt) – TR&D2 Aims with DBP3 - Download presentation 11:10-11:20 Tom Bartol (Salk) with Mary Kennedy (Caltech/remotely)-DBP2 - Download presentation 11:20-11:35 Tom Bartol (Salk) - CellBlender & CSP6 - Download presentation 11:35-11:45 Steve Meriney (Pitt) CSP4 - Download presentation 11:45-12:05Q&A |
12:05pm– 1:05pm |
Lunch Break |
1:05 pm – 2:25 pm |
TR&D3 + associated DBPs/C&SPs 1:05-1:15 Gustavo Rohde (CMU) - Aim 1. Optimal Transport work - Download presentation 1:15-1:40 Bob Murphy (CMU) – Aim 1. CellOrganizer update/CSPs 7,8,11,12,13 - Download presentation 1:40-1:50Christoph Wuelfing (Bristol) - DP4 - Download presentation 1:50-2:05Art Wetzel (PSC) - Aims 2 and 3 - Download presentation 2:05-2:15 Clay Reid (Allen Brain Inst) - DBP5 - Download presentation 2:15-2:25 Q&A |
2:25 pm – 2:50 pm |
Training & Dissemination 2:25-2:50 Markus Dittrich (PSC) |
2:50 pm – 4:00 pm |
Coffee Break, Discussion and Poster Session 7th Floor Atrium of GHC |
4:00 pm – 5:00 pm |
Business Meeting of EAB Members Room 8102 |
4:00 pm – 5:00 pm |
Simultaneous Meeting of EC Members Room GHC 6501 |
5:00 pm – 6:30 pm |
Joint Meeting Between EAB Members & BTRR EC Members Room 8102 |
6:30pm |
Departure for 7pm Dinner with EAB Members, BTRR Leadership, Mini Symposium Speakers & Invited Other Investigators (Pick up mini symposium speaker, Sykulev from Wyndham en route to dinner) Reservation made at Eleven, 1150 Smallman St, Pittsburgh PA 15222 |
Subcategories
Tutorial presentations given by MMBioS investigators are listed on this page.
Many software packages developed by MMBioS partners include online tutorials; see the listing for each package on the Software page.
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Research Highlights
The Bahar (TR&D1) and Sorkin (DBP3) labs published an article in the Journal of Biological Chemistry, selected as one of JBC's "Editors' Picks. Our results demonstrate a direct coupling between conformational dynamics of DAT, functional activity of the transporter and its oligomerization leading to endocytosis. The high specificity of such coupling for DAT makes the TM4-9 hub a new target for pharmacological modulation of DAT activity and subcellular localization. (Read more)
Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation
Comparison with RNA-seq expression data reveals a strong overlap between highly expressed genes and those distinguished by high mobilities in the present study, in support of the role of the intrinsic spatial dynamics of chromatin as a determinant of cell differentiation. (Read more)
Nanoscale co-organization and coactivation of AMPAR, NMDAR, and mGluR at excitatory synapses
Work by TR&D2 Investigators and collaborators provide insights into the nanometer scale organization of postsynaptic glutamate receptors using a combination of dual-color superresolution imaging, electrophysiology, and computational modeling. (Read more)
Parallel Tempering with Lasso for model reduction in systems biology
TR&D3 Investigators and collaborators develop PTLasso, a Bayesian model reduction approach that combines Parallel Tempering with Lasso regularization, to automatically extract minimal subsets of detailed models that are sufficient to explain experimental data. On both synthetic and real biological data, PTLasso is an effective method to isolate distinct parts of a larger signaling model that are sufficient for specific data. (Read more)
Image-derived models of cell organization changes during differentiation and drug treatments
Our work on modeling PC12 cells undergoing differentiation into neuron-like morphologies (under C&SP11, completed) has been published in Molecular Biology of the Cell. We have also made the large dataset of 3D images collected in that study available through Dryad. (Read more)
Monoamine transporters: structure, intrinsic dynamics and allosteric regulation
T&RD1 investigators Mary Cheng and Ivet Bahar published an invited review article in Nature Structural & Molecular Biology, addressing recent progress in the elucidation of the structural dynamics of MATs and their conformational landscape and transitions, as well as allosteric regulation mechanisms. (Read more)
Trimerization of dopamine transporter triggered by AIM-100 binding
The Bahar (TR&D1) and Sorkin (DBP3) labs explored the trimerization of dopamine transporter (DAT) triggered by a furopyrimidine, AIM-100, using a combination of computational and biochemical methods, and single-molecule live-cell imaging assays. (Read more)
Pre-post synaptic alignment through neuroligin-1 tunes synaptic transmission efficiency
TR&D2 investigators and collaborators describe organizing role of neuroligin-1 to align post-synaptic AMPA Receptors with pre-synaptic release sites into trans-synaptic “nano-columns” to enhance signaling.(Read more)
Inferring the Assembly Network of Influenza Virus
In an article in PLoS Computational Biology, MMBioS TR&D4 members Xiongto Ruan and Bob Murphy collaborated with Seema Lakdawala to address this question of the assembly network of the Influenza virus.(Read more)
Our findings highlight an important mechanism by which proteins genetically implicated in Parkinson’s disease (PD; PINK1) and frontotemporal dementia (FTD; VCP) interact to support the health and maintenance of neuronal arbors.(Read more)
Improved methods for modeling cell shape
In a recent paper in Bioinformatics, Xiongtao Ruan and Bob Murphy of TR&D4 addressed the question of how best to model cell and nuclear shape.(Read more)
New tool to predict pathogenicity of missense variants based on structural dynamics: RHAPSODY
We demonstrated that the analysis of a protein’s intrinsic dynamics can be successfully used to improve the prediction of the effect of point mutations on a protein functionality. This method employs ANM/GNM tools (Read more)
New method for investigating chromatin structural dynamics.
By adapting the Gaussian Network Model (GNM) protein-modeling framework, we were able to model chromatin dynamics using Hi-C data, which led to the identification of novel cross-correlated distal domains (CCDDs) that were found to also be associated with increased gene co-expression. (Read more)
Structural elements coupling anion conductance and substrate transport identified
We identified an intermediate anion channeling state (iChS) during the global transition from the outward facing (OF) to inward facing state (IFS). Our prediction was tested and validated by experimental study conducted in the Amara lab (NIMH). Critical residues and interactions were analyzed by SCAM, electrophysiology and substrate uptake experiments (Read more)
Integrating MMBioS technologies for multiscale discovery
TR&D teams driven by individual DBPs are naturally joining forces, integrating their tools to respond to the needs of the DBP, and creating integrative frameworks for combining structural and kinetic data and computing technologies at multiple scales. (Read more)
Large scale visualization of rule-based models.
Signaling in living cells is mediated through a complex network of chemical interactions. Current predictive models of signal pathways have hundreds of reaction rules that specify chemical interactions, and a comprehensive model of a stem cell or cancer cell would be expected to have many more. Visualizations of rules and their interactions are needed to navigate, organize, communicate and analyze large signaling models. (Read more)
Integration of MCellR into MCell/CellBlender
Using spatial biochemical models of SynGAP/PSD95, MMBioS investigators were able to merge the MCellR code-base with the MCell code-base and validate its utility and correctness of this sophisticated technology now easily accessible through the MCell/CellBlender GUI. (Read more)
Causal relationships of spatial distributions of T cell signaling proteins
The idea is to identify a relationship in which a change in the concentration of one protein in one cell region consistently is associated with a change in the concentration of another protein in the same or a different region. We used the data from our Science Signaling paper reported last year to construct a model for T cells undergoing stimulation by both the T cell receptor and the costimulatory receptor. (Read more...)
BioNetGen modeling helps reveal immune system response decision
To attack or to let be is an important decision that our immune systems must make to protect our bodies from foreign invaders or protect bodily tissues from an immune attack. Using modeling and experiments, we have painted a sharper picture of how T cells make these critical decisions. (Read more)
Tools for determining the spatial relationships between different cell components
An important task for understanding how cells are organized is determining which components have spatial patterns that are related to each other.Read more
Pipeline for creation of spatiotemporal maps
Using a combination of diffeomorphic methods and improved cell segmentation, we developed a CellOrganizer pipeline for use in DPB4 to construct models of the 4D distributions of actin and 8 of its regulators during the response of T cells to antigen presentation. Read more
Multi-scale Hybrid Methodology
The hybrid methodology, coMD, that we have recently developed [1] has been recently extended to construct the energy landscape near the functional states of LeuT (Fig 1) [2]. This is the first energy landscape constructed for this NSS family member. Read more
Insights into the cooperative dynamics of AMPAR
Comparative analysis of AMPAR and NMDAR dynamics reveals striking similarities, opening the way to designing new modulators of allosteric interactions. Read more
Improved Sampling of Cell-Scale Models using the WE Strategy
The WE strategy for orchestrating a large set of parallel simulations has now been extended to spatially resolved cell-scale systems. The WESTPA implementation of WE has been used to control MCell simulations, including models built using a BioNetGen-CellOrganizer pipeline for situating complex biochemistry within spatially realistic cell models. Read more
Anatomy and Function of an Excitatory Network in the Visual Cortex
MMBioS researcher Greg Hood’s collaboration with Wei-Chung Allen Lee of Harvard University and R. Clay Reid of the Allen Institute for Brain Science concerning the reconstruction of an excitatory nerve-cell network in the mouse brain cortex at a subcellular level using the AlignTK software has been published in Nature. Read more
Molecular Mechanism of Dopamine Transport by hDAT
Dopamine transporters (DATs) control neurotransmitter dopamine (DA) homeostasis by reuptake of excess DA, assisted by sodium and chloride ions. The recent resolution of DAT structure (dDAT) from Drosophila permits us for the first time to directly view the sequence of events involved in DA reuptake in human DAT (hDAT). Read more
Synaptic Facilitation Revealed
An investigation of several mechanisms of short-term facilitation at the frog neuromuscular junction concludes that the presence of a second class of calcium sensor proteins distinct from synaptotagmin can explain known properties of facilitation. Read more
Sparse Graphical Models of Protein:Protein Interactions
DgSpi is a new method for learning and using graphical models that explicitly represent the amino acid basis for interaction specificity and extend earlier classification-oriented approaches to predict ΔG of binding. Read more
Advancing Parallel Bio-simulations
A new non-Markovian analysis can eliminate bias in estimates of long-timescale behavior, such as the mean first-passage time for the dissociation of methane molecules in explicit solvent. Read more