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Winter Interactive nanoBIO Workshop
04 Feb 2021 | | Contributor(s):: Ballard, Joshua Brendan (editor)
The Winter Interactive nanoBIO Workshop will walk students and researchers through how to understand a variety of biological problems using simulations based on cloud-based tools on nanoHUB or other easy to use platforms.
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Deep Learning for Time Series Illustrated by COVID-19 Infection Studies
04 Feb 2021 | | Contributor(s):: Geoffrey C. Fox
We show that one can study several sets of sequences or time-series in terms of an underlying evolution operator which can be learned with a deep learning network.
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How Simple Cell-Cell Interactions Lead to Complex Multicellular Dynamics
04 Feb 2021 | | Contributor(s):: Paul Macklin
In this talk, we use agent-based simulation models to simulate (1) individual cell behaviors, (2) cell-cell interactions, and (3) cell-environment interactions to show how simple rules can give rise to complex multicellular phenomena. We showcase and explore free, interactive online tools to...
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Cancer Games: Interactive Simulation of the Effect of Resource Limitation on Cancer Somatic Evolution using nanoHUB CompuCell3D
04 Feb 2021 | | Contributor(s):: James A Glazier
In this interactive mini-workshop we will use a very simple model of cancer somatic evolution and resource limitation based on one originally proposed by Heiko Enderling.
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Shape-changing Nanoparticles for Nanomedicine Applications
04 Feb 2021 | | Contributor(s):: Vikram Jadhao
I will describe the nanoHUB tool “Nanoparticle Shape Lab” that enables simulations of the shape deformation of charged nanoparticles for a broad variety of nanoparticle material properties including nanoparticle surface charge, pattern, elasticity and solution conditions such...
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Biology of COVID-19 Attack on Epithelial Cells, understood from a Modeling and Simulation Perspective
04 Feb 2021 | | Contributor(s):: Paul Macklin
n this session, we describe a community-driven effort to iteratively develop a multiscale, spatially-resolved open source model of SARS-CoV-2 dynamics and immune response in tissues.
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U-Net Convolutional Neural Networks for Image Segmentation: Application to Scanning Electron Microscopy Images of Graphene
01 Feb 2021 | | Contributor(s):: Aagam Rajeev Shah
This tutorial introduces you to U-Net, a popular convolutional neural network commonly developed for image segmentation in biomedicine. Using an assembled data set, you will learn how to create and train a U-Net neural network, and apply it to segment scanning electron microscopy images of...
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A Vaccine Model for COVID-19
25 Jan 2021 | | Contributor(s):: Kali Nicole Konstantinopoulos, James A Glazier (editor), Josua Oscar Aponte-Serrano (editor)
Simulate the introduction of a vaccine in the COVID-19 pandemic, focused on the US.
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PhysiCell 3D tumor
20 Jan 2021 | | Contributor(s):: Randy Heiland, Paul Macklin, Koudoro, Serge, Javier Guaje
Simulate a 3D spheroid cancer tumor with PhysiCell
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Influenza In Host Kinetics Model
19 Dec 2020 | | Contributor(s):: Hanna, Tyler Scott, James A Glazier, Josua Oscar Aponte-Serrano
Module explaining the in-host viral kinetics of IAV under different conditions.
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Cycle Training App for PhysiCell
18 Dec 2020 | | Contributor(s):: Furkan Kurtoglu, Aneequa Sundus, Kali Nicole Konstantinopoulos, Drew Willis, Mary Chen, Randy Heiland, Paul Macklin
Training application for "Cycle" concept in PhysiCell.
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Winter Interactive nanoBIO Workshop
10 Dec 2020 |
The Winter Interactive nanoBIO Workshop will walk students and researchers through how to understand a variety of biological problems using simulations based on cloud-based tools on nanoHUB or other easy to use platforms. Each session will include some background material to understand the nature...
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Saliva-Based Testing for COVID-19
22 Nov 2020 | | Contributor(s):: Mohit Verma
The Verma lab is developing a molecular test for SARS-CoV-2 that detects the RNA and produces a color change in less than one hour. Using saliva as the sample, this test is easier to use at the point-of-care.
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Three-Type Multicellular Simulation Lab
09 Nov 2020 | | Contributor(s):: Paul Macklin, Randy Heiland
An analog of the 3-body problem: modeling 3 interacting cell types in a dynamic environment
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PhysiBoSS simulation of COVID19 infection
27 Oct 2020 | | Contributor(s):: Vincent Noel, Miguel Ponce de Leon, Anna Niarakis, Laurence Calzone, Alfonso Valencia, Arnau Montagud
PhysiBoSS-COVID: the Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework
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Photosynthetic Protein Spectroscopy Lab
19 Oct 2020 | | Contributor(s):: Safa Ahad, Chientzu Lin, Michael Earl Reppert
This tool parses PDB structures of photosynthetic proteins to identify pigments, calculate inter-pigment interactions, and simulate optical spectra for the complex.
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Amide I Vibrational Spectroscopy Lab
24 Sep 2020 | | Contributor(s):: Michael Earl Reppert, Jacob Hnatusko Wat
This tool allows users to upload/fetch protein databank files, visualize the protein structure, and calculate Amide I vibrational spectra for the protein.
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Molecular Spectroscopy
12 Aug 2020 | | Contributor(s):: Michael Earl Reppert
Front-end for content of Purdue course CHM676 (Molecular Spectroscopy).
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PhysiCell model for tumor hypoxia
07 Aug 2020 | | Contributor(s):: Lima Da Rocha, Heber, Paul Macklin, Furkan Kurtoglu
Multicellular simulation in 2-D of tumor hypoxia.
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COVID-19 data analysis
07 Aug 2020 | | Contributor(s):: Randy Heiland, Paul Macklin
Perform data analysis in a Jupyter notebook using data from the pc4covid19 tool.