Theodore Alexandrov,
Universität Bremen
Getting 3D Molecular Snapshots Using Imaging Mass Spectrometry
3D imaging mass spectrometry is a novel label-free bioanalytical technique for 3D spatially-resolved analysis. We show how it can bring insight into pathology and microbiology.
Chandrajit Bajaj,
University of Texas
Computational Science Challenges for the 3D Virtual Cell
Translating computational tools into meaningful results for scientific discovery requires a combined expertise in mathematical modeling, algorithm design and computer architecture, in addition to experimental verification and validation details associated with the particular quantity of interest.
Donald Blumenthal,
University of Utah
Drug Action and Cell Signaling in a 3D Virtual Cell
We use small-angle scattering to study the structural organization and global conformational dynamics of signaling enzymes and signaling complexes.
Blake Borgeson,
University of Texas at Austin
Mapping Animal Protein Complexes: Scaling Up
Using mass spectrometry to analyze high-resolution biochemical separations from human and other animals, we are constructing high-confidence maps of protein complexes with exceptional coverage.
Wah Chiu,
Baylor College of Medicine
Cryo-Electron Tomography of Cells
Cryo-electron tomography is an imaging tool for frozen-hydrated cells. The computational challenges of these 3-D data include segmentation, feature identification, annotation and subvolume data processing.
Tim Clark,
Massachusetts General Hospital; Harvard Medical School
Where is the evidence for that statement? Formal semantic representation of biomedical argumentation and supporting data
I will discuss our work on problems of evidence traceability, and availability of data and methods for reuse, using formal models of biomedical argument structure.
Phillip Compeau,
University of California, San Diego
Rosalind: Learning Bioinformatics through Programming
An introduction to Rosalind, a free website similar to Project Euler helping students learn bioinformatics through programming challenges of increasing algorithmic and biological complexity.
Markus Covert,
Stanford University
A Computational Whole-Cell Model Predicts Genotype From Phenotype
I'll discuss how we've recently built a comprehensive whole-cell model of a bacterium, what we're learning from it, and where we'll go from here.
Pieter Dorrestein,
University of California, San Diego
Capturing conversations of cell populations through a million little dots
This presentation will describe a mass spectrometry approach for the mapping of the structural universe of molecules.
Mark H. Ellisman,
University of California, San Diego
Challenges and Opportunities for Efforts to Create Accessible Atlases of Visible Virtual Cells
Recent advances have made it feasible to image and reconstruct the detailed microscopic structure of an entire cell with sufficient resolution to allow the direct visualization of macromolecules in situ. More
Yolanda Gil,
University of Southern California
Discovery Informatics: Intelligent Systems For Science Innovation
The emerging discipline of Discovery Informatics catalyzes research in artificial intelligence, machine learning, and social computing to innovate science processes and accelerate discoveries.
James Glazier,
Indiana University
From Molecules to Tissues: Multiscale Modeling from a Multicellular Viewpoint
CompuCell3D is an open-source multiscale model development environment for simulating embryonic development, homeostasis and developmental diseases that takes a cell-behavior out perspective, connecting subcellular reaction kinetics, cell behaviors, multicell interactions and continuum tissue mechanics.
David Goodsell,
The Scripps Research Institute
Visualizing the Molecular Structure of Cellular Environments
The scientific support and visualization process will be described for a series of illustrations that present the molecular structure of a living cell.
Erich Huang,
Duke Institute for Genome Sciences & Policy
clearScience: Effacing the Boundary Between Doing and Communicating Science
clearScience is about RESTful APIs for not only accessing scientific data and code, but stringing them together into compelling scientific communication.
Peter Hunter,
University of Auckland
The VPH/Physiome Project
The VPH/Physiome Project uses biophysically and anatomically based multiscale modeling, with opensource software and model repositories based on model and data encoding standards.
Graham Johnson,
University of California, San Francisco
cellPack: A Virtual Mesoscope to Model and Visualize Structural Systems Biology
The cellPack framework contains software to model, analyze, visualize, database and collect feedback for iterative community improvement of mesoscale cellular volumes modeled with molecular detail.
Natarajan Kannan,
University of Georgia
Modeling complex signaling systems using semantic web applications
Ontologies provide a unique framework for conceptualizing data in ways computers can read and humans can understand. In this talk, I will highlight the need for focused ontologies to investigate complex signaling systems such as protein kinases.
Peter Karp,
SRI International
Literate Modeling
Curation is critical to systems biology. Modeling is data intensive and should be coupled with a database. Good mathematics does not imply a good modeling software tool.
Thomas Knudsen,
Environmental Protection Agency
Virtual Embryo: Computational Embryology And Predictive Toxicology
EPA's Virtual Embryo project is helping scientists understand how chemical exposure affects a developing embryo using modern computational toxicology, novel experimental techniques, and sophisticated computer models.
Leslie Loew,
University of Connecticut Health Center
The Virtual Cell Project
VCell is a software environment, built on a database, for modeling signaling, transport and electrophysiology. It performs stochastic and deterministic simulations in image-based 3D geometries.
Maryann Martone,
University of California, San Diego
Taking a global view of data and e-scholarship: Perspectives from FORCE11 and the Neuroscience Information Framework
I will discuss the potential power of collaborative, on-line frameworks for building communities, models and advancing science, informed by my experiences in the Neuroscience Information Framework and Future of Research Communications and E-Scholarship (FORCE11) projects.
Andrew McCulloch,
University of California, San Diego
Multi-Scale Modeling of the Cardiac Myocyte
I will give an overview of approaches and tools used by our group, our colleagues in the National Biomedical Computational and the International Cardiac Physiome community to multi-scale modeling of the heart with emphasis on the cardiac myocyte. I will also identify challenges and opportunities for the future.
Martin Meier-Schellersheim,
National Institutes of Health
Simulating Cellular Signaling Pathways Embedded into Realistic Morphologies
I will discuss the challenges associated with simulating detailed molecular reaction-diffusion networks within realistic models of cellular morphologies.
Marcel Oberlaender,
Max Planck Institute for Biological Cybernetics
Simulation of sensory-evoked signal flow in 3D reconstructions of anatomically realistic network models
Recent progress in embedding full-compartmental neuron models into anatomically realistic neural networks and recovering in vivo measurements by simulating sensory-evoked excitation.
Lucila Ohno-Machado,
University of California, San Diego
Sharing software and data
Are researchers ready for a radical change, where a scientific discovery will no longer be credited to a single individual, or a small group of individuals?
Arthur Olson,
The Scripps Research Institute
Interacting with the Molecular Cell
New technologies including 3D printing and Augmented Reality may expand the way we interact with complex molecular data.
Bernhard Palsson,
University of California, San Diego
Computing with ME
Genome-scale metabolic (M) models have been in use since the late 1990's. About 10 years later genome-scale models describing protein expression (E) were developed. Today several integrated metabolic-expression (ME) models have been developed. ME-models simultaneously account for metabolism and expression and they compute a much wider array of cellular phenotypic functions than M-models. Such computations will be described in this talk.
Steven Peltier,
University of California, San Diego
Multiscale Microscopy and Tools for Processing Big Data
An overview of NCMIR activities that intersect the aims of 3DVC, including technologies for acquiring, refining, managing, analyzing, and sharing big data.
Bing Ren,
University of California, San Diego
Charting the 3D Genome Landscape
New results have shed lights on the chromosome folding principles and relationships between nuclear organization of DNA and gene regulation.
Daniel Russel,
University of California, San Francisco and Google
Integrative Modeling of the Structure and Dynamics of Assemblies
IMP is an extensible platform for building structural and structural dynamics models of assemblies in the cell that are consistent with the available experimental data. (http://www.integrativemodeling.org)
Hebert Sauro,
University of Washington
Building sustainable and vibrant communities
In this talk I will cover some of the theoretical and computational approaches used to build models of biochemical networks. I will draw on examples from the literature and my own work to illustrate successful efforts and future areas of interest to the modeling community.
Terry Sejnowski,
University of California, San Diego
MCell: A 3D Monte Carlo Model Of A Virtual Cell
MCell simulates the diffusion and biochemical reactions within cells using Monte Carlo techniques and can be used to study cell signaling pathways.
Nigam Shah,
Stanford University
Using Ontologies for Reasoning in a Virtual Cell
I will discuss the use of ontologies for validating models of biological processes in a virtual cell as well as review the current set of public ontologies that can be used for that task.
James Sluka,
Indiana University
The Cell Behavior Ontology: Defining the Existential Qualities of Cells
The Cell Behavior Ontology (CBO) describes the behaviors (growth, chemotaxis, adhesion, etc.) and physical qualities of cells as well as computational models of multicellular systems.
Maciej Swat,
Indiana University
Towards Virtual Tissues - multi-cell modeling using CompuCell3D
I will cover CompuCell3D-based approach for implementing predictive tissue-scale, multi-cell simulations of development, homeostasis and disease of tissues.
Susan Taylor,
University of California, San Diego
PKA: Assembly of dynamic macromolecular signaling complexes
To understand how the PKA subunits are assembled into tetrameric holoenzyme complexes anchored to scaffold proteins requires the integration of interdisciplinary tools that include structural biology, NMR, biophysics, and chemistry as well as computational tools.
Anita de Waard,
Elsevier Labs
A Proposal to Create Incidental Collaboratories for Experimental Data
To better assess the complexity and diversity of living systems, I propose building an ‘incidental collaboratory’ that allows comparisons between entities, interactions and experimental observations.
Wei Wang,
University of California, San Diego
Proteomic identification of methyllysine and quantitative modeling of its recognition
Identification of methylated peptides in the human protoeme using an integrated approach and deciphering the recogniztion mechanisms of methyllysine using a quantitiative model.
Ross Whitaker,
University of Utah
Image-Based Modeling and Simulation for Biomedical Analysis and Discovery
This talk describes a variety of algorithms and open-source software tools that constitute a processing pipeline for using 3D image data in physiological simulations.
Nancy Wilkins-Diehr,
University of California, San Diego
The Science Gateway Institute
The impact of scientific web portals is a fraction of what it could be. I present plans for a Science Gateway Institute to change this.
This project has been funded by a grant (#1216893) from the National Science Foundation
UC San Diego has been awarded this grant for planning activities leading to a design for an NSF S2I2 Institute for Translational Systems Biology (ITSB) that emphasizes biological 3-dimensional (3D) structures from molecule to cell and addresses the sustainability challenge.
