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PhysiCell workshop training
Tools | 13 Nov 2019 | Contributor(s):: Randy Heiland
Provide a general purpose PhysiCell app for training.
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PhysiCell biorobots simulation
Tools | 12 Nov 2019 | Contributor(s):: Randy Heiland, Paul Macklin
2D sim of director, worker, and cargo cells.
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Nanosphere Electrostatics Lab Tutorial
Online Presentations | 11 Nov 2019 | Contributor(s):: Jayanath Chamindu Sandanuwan Kadupitiya Kadupitige, Ballard, Joshua Brendan
Accurate knowledge of ionic structure & dynamics is critical to study nanoparticle dynamics. Nanoparticles are polarized in most solvents. Simulating the dynamics of ions near polarizable nanoparticles is challenging: Need to solve Poisson equation at every timestep....
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Motility Training App for PhysiCell
Tools | 17 Oct 2019 | Contributor(s):: Furkan Kurtoglu, Aneequa Sundus, Kali Nicole Konstantinopoulos, Drew Willis, Mary Chen, Randy Heiland, Paul Macklin
Training application for "Motility" concept in PhysiCell.
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Perspectives on High-Performance Computing in a Big Data World: Part D - Learning Model Details and Agent-Based Simulations
Online Presentations | 17 Oct 2019 | Contributor(s):: Fox, Geoffrey C.
This lecture completes the discussion of MLforHPC. It covers Learning Model Details and Agents and Time-Series Case Studies.
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Perspectives on High-Performance Computing in a Big Data World: Part E - Challenges and Opportunities, Conclusions
Online Presentations | 17 Oct 2019 | Contributor(s):: Fox, Geoffrey C.
This lecture covers the computer science issues raised in this talk. The conclusions note that HPDC/HPC is essential; it is good to work closely with industry with student Internships and Collaborations; the Global AI and Modeling Supercomputer GAIMSC is a good framework with an HPC Cloud linked...
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Perspectives on High-Performance Computing in a Big Data World: Part C - MLaroundHPDC/HPC and MLAutotuning
Online Presentations | 10 Oct 2019 | Contributor(s):: Fox, Geoffrey C.
This is the first part of the discussion of MLforHPC. It includes MLAutotuning (Using ML to configure or autotune ML or HPC simulations and MLaroundHPC (Learning outputs from inputs).
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Perspectives on High-Performance Computing in a Big Data World
Courses | 30 Sep 2019 | Contributor(s):: Fox, Geoffrey C.
This course was deleivered at ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC).High-Performance Computing (HPC) and Cyberinfrastructure have played a leadership role in computational science even since the start of the NSF computing centers program. Thirty...
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Perspectives on High-Performance Computing in a Big Data World: Part B - More on the Evolution of Interests and Communities
Online Presentations | 30 Sep 2019 | Contributor(s):: Fox, Geoffrey C.
This part contains several topics. It discusses the importance of industry in several facets of the field: SysML conference, clouds, MLPerf, the Global AI Supercomputer. The nature of data science and data engineering jobs. We emphasize the need for HPC. We finish by introducing MLforHPC (AI for...
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Motility Training App
Tools | 20 Sep 2019 | Contributor(s):: Furkan Kurtoglu, Aneequa Sundus, Kali Nicole Konstantinopoulos, Mary Chen, Drew Willis, Randy Heiland, Paul Macklin
Training application for "Motility" concept in PhysiCell.
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Tellurium
Tools | 26 Aug 2019 | Contributor(s):: Somogyi, Andy T
1.0
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Perspectives on High-Performance Computing in a Big Data World: Part A - Data on the Evolution of Interests and Communities
Online Presentations | 13 Aug 2019 | Contributor(s):: Fox, Geoffrey C.
This lecture has an overall outline of the 5 part presentation. It covers trends seen from conferences and journals -- the number of papers, attendees and h5index. Then we look at relevant Google Trends. Cyberinfrastructure related activities are less buoyant than those for AI and ML.
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Cloud-hosted Mathematical Models: Links between Education, Research, and Outreach
Presentation Materials | 01 Aug 2019 | Contributor(s):: Paul Macklin
To address the challenges facing undergraduate research, we tested lab structure that can scalably involve undergraduates in cutting-edge mathematical biology research. Teams of two-to-four undergraduates are jointly mentored by a graduate student (or senior personnel) and the lab’s...
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AMIGOS - Hypoxia
Tools | 25 Apr 2019 | Contributor(s):: Furkan Kurtoglu, John Metzcar, Kali Nicole Konstantinopoulos, Timothy M Mahajan, Randy Heiland, Paul Macklin
Modeling Tumor in Hypoxic Condition
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Replication Competent Oncolytic Virus expressing secretable trimeric TRAIL: hypothesis testing
Tools | 23 Apr 2019 | Contributor(s):: Adrianne Jenner, Paul Macklin
Using PhysiCell to simulate a replication competent oncolytic virus expressing secretable trimeric TRAIL which induces apoptosis in nearby cells
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Replication Competent Oncolytic Virus in Epithelial cell layer
Tools | 18 Apr 2019 | Contributor(s):: Adrianne Jenner, Paul Macklin
PhysiCell simulation of a replication competent oncolytic virus release from two veins, diffusing through a layer of epithelial cells.
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CompuCell3D - Bacterium Macrophage
Tools | 17 Apr 2019 | Contributor(s):: Juliano Ferrari Gianlupi, Somogyi, Andy T
Simulation of macrophage chasing bacterium
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Polyvalent Nanoparticle Binding Simulator
Tools | 16 Apr 2019 | Contributor(s):: Nilsson, Lauren, JCS Kadupitiya, Vikram Jadhao
Simulates the binding of ligand-decorated nanoparticles to cell membrane driven by ligand-cell-receptor attraction
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(CC3D v3 - old) CompuCell3D Vascular Tumor
Tools | 16 Apr 2019 | Contributor(s):: Juliano Ferrari Gianlupi, Somogyi, Andy T
Simulate 3D vascular tumor with CompuCell3D
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PhysiCell: liver tissue mechanobiology
Tools | 15 Apr 2019 | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin
An ABM simulating the impact of tumor-parenchyma biomechanics on liver metastatic progression with PhysiCell