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Managing genomic variant calling workflows with Swift/T [article]

Azza Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal Fadlelmola, Daniel Katz, Katherine Kendig, Matthew Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew Weber, Jennie Zermeno (+2 others)
2019 bioRxiv   pre-print
With the above features, users have a powerful and portable way to scale up their variant calling analysis to run in many traditional computer cluster architectures. https://github.com/ncsa/Swift-T-Variant-Calling  ...  The use of Swift/T conveys two key advantages: (1) Thanks to the embedded ability of Swift/T to transparently operate in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment  ...  and cons of Swift/T for bioinformatics workflows 301 Swift/T is a powerful and versatile language that offers many advantages for production 302 large-scale bioinformatics workflows.  ... 
doi:10.1101/524645 fatcat:r4s3zppzo5d7dkqveimwlx5w5u

Managing genomic variant calling workflows with Swift/T

Azza E. Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal M. Fadlelmola, Daniel S. Katz, Katherine Kendig, Matthew C. Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew R. Weber, Justin M. Wozniak (+3 others)
2019 PLoS ONE  
Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud.  ...  The code for our implementation of a variant calling workflow using Swift/T can be found on GitHub at https://github.com/ncsa/Swift-T-Variant-Calling, with full documentation provided at http://swift-t-variant-calling.readthedocs.io  ...  Chicago Swift/T developer team during the implementation, testing, and scalability efforts in this project.  ... 
doi:10.1371/journal.pone.0211608 pmid:31287816 pmcid:PMC6615596 fatcat:rr25otjjrjbl3bnz4i7uh5mdsi

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow [article]

Jonathan Ozik, Nicholson Collier, Justin Wozniak, Charles Macal, Chase Cockrell, Samuel Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An, Paul Macklin
2017 bioRxiv   pre-print
Results: In this paper, we introduce a high throughput computing (HTC) framework that integrates a mechanistic 3-D multicellular simulator (PhysiCell) with an extreme-scale model exploration platform (  ...  Conclusions: While key notational and computational challenges remain, mechanistic agent-based models and high-throughput model exploration environments can be combined to systematically and rapidly explore  ...  The Extreme-scale Model Exploration with Swift (EMEWS) framework [31] is built on the the generalpurpose parallel scripting language Swift/T [46] , and is used to generate dynamic, highly concurrent  ... 
doi:10.1101/196709 fatcat:uk4522iosraf5mlthxpkodnnym

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow

Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Charles Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An, Paul Macklin
2018 BMC Bioinformatics  
Results: In this paper, we introduce a high throughput computing (HTC) framework that integrates a mechanistic 3-D multicellular simulator (PhysiCell) with an extreme-scale model exploration platform (  ...  Conclusions: While key notational and computational challenges remain, mechanistic agent-based models and high-throughput model exploration environments can be combined to systematically and rapidly explore  ...  Exploration with Swift): A framework for model exploration using the Swift/T parallel scripting language; HPC (high performance computing): Solution of large and complex problems by parallelization over  ... 
doi:10.1186/s12859-018-2510-x fatcat:kqohcccqw5c4dedyg5uoiyqrga

Learning-accelerated discovery of immune-tumour interactions

Jonathan Ozik, Nicholson Collier, Randy Heiland, Gary An, Paul Macklin
2019 Molecular Systems Design & Engineering  
This work was completed in part with resources provided by the Laboratory Computing Resource Center at Argonne National Laboratory (the Bebop cluster), and the University of Chicago (the Beagle supercomputer  ...  EMEWS is built on the general-purpose parallel scripting language Swift/T, 38 which provides the capability of running multi-language tasks on anywhere from desktops to petascale plus computing resources  ...  The points to evaluate for each iteration are passed from the ME algorithms to the Swift/T workflow for evaluation via the queues.  ... 
doi:10.1039/c9me00036d pmid:31497314 pmcid:PMC6690424 fatcat:swq7voamjzg2vb7kxkeelt2bi4

Learning-accelerated Discovery of Immune-Tumour Interactions [article]

Jonathan Ozik, Nicholson Collier, Randy Heiland, Paul Macklin
2019 bioRxiv   pre-print
We present an integrated framework for enabling dynamic exploration of design spaces for cancer immunotherapies with detailed dynamical simulation models on high-performance computing resources.  ...  Our framework combines PhysiCell, an open source agent-based simulation platform for cancer and other multicellular systems, and EMEWS, an open source platform for extreme-scale model exploration.  ...  This work was completed in part with resources provided by the Laboratory Computing Resource Center at Argonne National Laboratory (the Bebop cluster), and the University of Chicago (the Beagle supercomputer  ... 
doi:10.1101/573972 fatcat:ftdxzyzuungu3lij5hmdmcktk4

DAPT: A package enabling distributed automated parameter testing

Ben Duggan, John Metzcar, Paul Macklin
2021 Gigabyte  
Managing that testing for large scale parameter sweeps (grid searches), as well as storing simulation data, requires multiple, potentially customizable steps that may vary across simulations.  ...  While high-performance computing (HPC) has become increasingly available, models can often be tested faster with the use of multiple computers and HPC resources.  ...  ACKNOWLEDGEMENTS We would like to thank Daniel Murphy and Brandon Fischer for helping with the design and initial testing of DAPT.  ... 
doi:10.46471/gigabyte.22 fatcat:j7o3t5ycyjhozmspjeuley4fqq

Parallel computing in genomic research: advances and applications

Daniel de Oliveira, Kary Ocaña
2015 Advances and Applications in Bioinformatics and Chemistry  
Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC  ...  However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological  ...  Author contributions All authors contributed toward data analysis, drafting and revising the paper and agree to be accountable for all aspects of the work.  ... 
doi:10.2147/aabc.s64482 pmid:26604801 pmcid:PMC4655901 fatcat:qyslams5evftjm7euma5vg2rtq

VECMAtk: A Scalable Verification, Validation and Uncertainty Quantification Toolkit for Scientific Simulations [article]

D. Groen, H. Arabnejad, V. Jancauskas, W. N. Edeling, F. Jansson, R. A. Richardson, J. Lakhlili, L. Veen, B. Bosak, P. Kopta, D. W. Wright, N. Monnier (+14 others)
2020 arXiv   pre-print
platform from the desktop to current multi-petascale computers.  ...  examples from seven different domains such as conflict modelling and environmental sciences.  ...  middleware agnosticism, along with single scale and multiscale modelling.  ... 
arXiv:2010.03923v2 fatcat:zmzbqjonzfdkjpr6tg6pvl3syu

VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations

D Groen, H Arabnejad, V Jancauskas, W N Edeling, F Jansson, R A Richardson, J Lakhlili, L Veen, B Bosak, P Kopta, D W Wright, N Monnier (+14 others)
2021 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
platform from the desktop to current multi-petascale computers.  ...  examples from seven different domains such as conflict modelling and environmental sciences.  ...  , along with single scale and multiscale modelling.  ... 
doi:10.1098/rsta.2020.0221 pmid:33775151 pmcid:PMC8059654 fatcat:ncbubshtj5echo3bspdiuxs5yy

Microsimulation Model Calibration using Incremental Mixture Approximate Bayesian Computation [article]

Carolyn Rutter, Jonathan Ozik, Maria DeYoreo, Nicholson Collier
2018 arXiv   pre-print
We demonstrate IMABC by calibrating a MSM for the natural history of colorectal cancer to obtain simulated draws from the joint posterior distribution of model parameters.  ...  IMABC begins with a rejection-based approximate Bayesian computation (ABC) step, drawing a sample of parameters from the prior distribution and simulating calibration targets.  ...  In addition, because calibration to summary statistics requires simulation of a large number of model evaluations, each with a large number of agents, we plan to explore ways to improve the efficiency  ... 
arXiv:1804.02090v3 fatcat:5jwg7zbp7bbklowx27xk2cwkwa

D1.3 Life Sciences Use Case: Requirements, Scenario Definitions and Initial Evaluation Report

Project Consortium Members
2020 Zenodo  
Moreover, we present a model exploration technique that allows us to study the s [...]  ...  These simulations are being scaled up by several orders of magnitude by parallelising the code in a hybrid OpenMP-MPI implementation, aiming to scale up simulations of cancer cell 3D spheroids up to a  ...  desktop to large-scale model exploration withSWIFT/T.  ... 
doi:10.5281/zenodo.4034037 fatcat:kmcmrsgeerfzhmwzv2ogqylmbq

D1.2 Initial Agent-Based Model

Project Consortium Members
2020 Zenodo  
Furthermore, to scale our simulations we need to parallelize our MSM. With that in mind we have started by parallelizing the environment component, which has the smallest time scale.  ...  Lastly, we present a model exploration technique that allows us to define the structure and hierarchy of the model's parameters and to evaluate its sensibility to the parameters' perturbation.  ...  Extreme-scale Model Exploration with Swift/T (EMEWS), uses the generalpurpose parallel scripting language Swift (Armstrong et al., 2014) to generate highly concurrent simulation workflows.  ... 
doi:10.5281/zenodo.4034022 fatcat:a4prlxmlpvdyznhlvxqfzhjfyq

Distributed in-memory data management for workflow executions

Renan Souza, Vitor Silva, Alexandre A. B. Lima, Daniel de Oliveira, Patrick Valduriez, Marta Mattoso
2021 PeerJ Computer Science  
Complex scientific experiments from various domains are typically modeled as workflows and executed on large-scale machines using a Parallel Workflow Management System (WMS).  ...  To evaluate our proposal, we develop d-Chiron, a WMS designed according to SchalaDB's principles. We carry out an extensive experimental evaluation on an HPC cluster with up to 960 computing cores.  ...  ACKNOWLEDGEMENTS The experiments were carried out using the Grid5000 testbed from Inria. The authors would also like to thank Pedro Paiva Miranda for his help during the development of d-Chiron.  ... 
doi:10.7717/peerj-cs.527 pmid:34013039 pmcid:PMC8114816 fatcat:lg2cmuwsgvdzzk3mowg7e5doea

BioExcel-2 Deliverable 2.1 – State of the Art and Initial Roadmap

Adam Hospital, Stian Soiland-Reyes, Josep Lluís Gelpí, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier
2019 Zenodo  
This deliverable is presented as a follow-up to the BioExcel-1 D2.1 deliverable, describing the new state of the art of technologies, methods and tools applicable to the computational biomolecular field  ...  Workflow managers, especially the ones focused on the HPC and exascale supercomputers are also reviewed, presenting a collaboration with the Molecular Science Software Institute (MolSSI).  ...  Parsl and its predecessors, Swift/K and Swift/T, have enabled a wide variety of applications: simulations (supercooled glass materials, protein and biomolecular structures and interactions), climate model  ... 
doi:10.5281/zenodo.4604607 fatcat:u3yplgrepzfytda2zwzu37phge
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