Literature DB >> 31239603

FROM DESKTOP TO LARGE-SCALE MODEL EXPLORATION WITH SWIFT/T.

Jonathan Ozik1, Nicholson T Collier1, Justin M Wozniak1, Carmine Spagnuolo2.   

Abstract

As high-performance computing resources have become increasingly available, new modes of computational processing and experimentation have become possible. This tutorial presents the Extreme-scale Model Exploration with Swift/T (EMEWS) framework for combining existing capabilities for model exploration approaches (e.g., model calibration, metaheuristics, data assimilation) and simulations (or any "black box" application code) with the Swift/T parallel scripting language to run scientific workflows on a variety of computing resources, from desktop to academic clusters to Top 500 level supercomputers. We will present a number of use-cases, starting with a simple agent-based model parameter sweep, and ending with a complex adaptive parameter space exploration workflow coordinating ensembles of distributed simulations. The use-cases are published on a public repository for interested parties to download and run on their own.

Entities:  

Year:  2017        PMID: 31239603      PMCID: PMC6592281          DOI: 10.1109/WSC.2016.7822090

Source DB:  PubMed          Journal:  Proc Winter Simul Conf        ISSN: 0891-7736


  11 in total

1.  MULTI-OBJECTIVE MODEL EXPLORATION OF HEPATITIS C ELIMINATION IN AN AGENT-BASED MODEL OF PEOPLE WHO INJECT DRUGS.

Authors:  Eric Tatara; Nicholson T Collier; Jonathan Ozik; Alexander Gutfraind; Scott J Cotler; Harel Dahari; Marian Major; Basmattee Boodram
Journal:  Proc Winter Simul Conf       Date:  2020-02-20

2.  Application of Distributed Agent-based Modeling to Investigate Opioid Use Outcomes in Justice Involved Populations.

Authors:  Eric Tatara; John Schneider; Madeline Quasebarth; Nicholson Collier; Harold Pollack; Basmattee Boodram; Sam Friedman; Elizabeth Salisbury-Afshar; Mary Ellen Mackesy-Amiti; Jonathan Ozik
Journal:  IEEE Int Symp Parallel Distrib Process Workshops Phd Forum       Date:  2021-06-24

3.  Too Good to Be True? Evaluation of Colonoscopy Sensitivity Assumptions Used in Policy Models.

Authors:  Carolyn M Rutter; Pedro Nascimento de Lima; Jeffrey K Lee; Jonathan Ozik
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2022-04-01       Impact factor: 4.090

4.  An antigenic diversification threshold for falciparum malaria transmission at high endemicity.

Authors:  Qixin He; Mercedes Pascual
Journal:  PLoS Comput Biol       Date:  2021-02-19       Impact factor: 4.475

5.  Sequentially calibrating a Bayesian microsimulation model to incorporate new information and assumptions.

Authors:  Maria DeYoreo; Carolyn M Rutter; Jonathan Ozik; Nicholson Collier
Journal:  BMC Med Inform Decis Mak       Date:  2022-01-12       Impact factor: 3.298

6.  An Evolutionary Algorithm to Personalize Stool-Based Colorectal Cancer Screening.

Authors:  Luuk A van Duuren; Jonathan Ozik; Remy Spliet; Nicholson T Collier; Iris Lansdorp-Vogelaar; Reinier G S Meester
Journal:  Front Physiol       Date:  2022-01-26       Impact factor: 4.755

7.  Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth.

Authors:  Miguel Ponce-de-Leon; Arnau Montagud; Charilaos Akasiadis; Janina Schreiber; Thaleia Ntiniakou; Alfonso Valencia
Journal:  Front Mol Biosci       Date:  2022-04-06

8.  Learning-accelerated discovery of immune-tumour interactions.

Authors:  Jonathan Ozik; Nicholson Collier; Randy Heiland; Gary An; Paul Macklin
Journal:  Mol Syst Des Eng       Date:  2019-06-07

9.  Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention.

Authors:  Stacy Tessler Lindau; Jennifer A Makelarski; Chaitanya Kaligotla; Emily M Abramsohn; David G Beiser; Chiahung Chou; Nicholson Collier; Elbert S Huang; Charles M Macal; Jonathan Ozik; Elizabeth L Tung
Journal:  PLoS Comput Biol       Date:  2021-10-25       Impact factor: 4.475

10.  Modeling hepatitis C micro-elimination among people who inject drugs with direct-acting antivirals in metropolitan Chicago.

Authors:  Eric Tatara; Alexander Gutfraind; Nicholson T Collier; Desarae Echevarria; Scott J Cotler; Marian E Major; Jonathan Ozik; Harel Dahari; Basmattee Boodram
Journal:  PLoS One       Date:  2022-03-10       Impact factor: 3.240

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