Evidence map›Paper›PMID 31515016›Full record

ArticlePhysica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)2019

Monte Carlo Processing on a Chip (MCoaC)-preliminary experiments toward the realization of optimal-hardware for TOPAS/Geant4 to drive discovery.

Yogindra S Abhyankar, Sachin Dev, O S Sarun, Amit Saxena, Rajendra Joshi, Hemant Darbari, C Sajish, U B Sonavane, Vivek Gavane, Abhay Deshpande and 14 more

Abstract read
In one paragraph

Article in Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. The TOPAS tool for particle simulation, a Monte Carlo simulation tool for physics, biology and clinical research.Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) · 2020
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

24 authors.

Yogindra S AbhyankarCentre for Development of Advanced Computing (C-DAC), Pune, India.
Sachin DevOpen Health Systems Laboratory (OHSL), USA.
O S SarunCentre for Development of Advanced Computing (C-DAC), Pune, India.
Amit SaxenaCentre for Development of Advanced Computing (C-DAC), Pune, India.
Rajendra JoshiCentre for Development of Advanced Computing (C-DAC), Pune, India.
Hemant DarbariCentre for Development of Advanced Computing (C-DAC), Pune, India.
C SajishCentre for Development of Advanced Computing (C-DAC), Pune, India.
U B SonavaneCentre for Development of Advanced Computing (C-DAC), Pune, India.
Vivek GavaneCentre for Development of Advanced Computing (C-DAC), Pune, India.
Abhay DeshpandeSociety for Applied Microwave Electronics Engineering & Research (SAMEER), Mumbai, India.
Tanuja DixitSociety for Applied Microwave Electronics Engineering & Research (SAMEER), Mumbai, India.
Rajesh HarshSociety for Applied Microwave Electronics Engineering & Research (SAMEER), Mumbai, India.
Rajendra BadweTata Memorial Centre (TMC), Mumbai, India.
G K RathAll India Institute of Medical Sciences (AIIMS), Delhi, India.
Siddhartha LaskarTata Memorial Centre (TMC), Mumbai, India.
Bruce FaddegonUniversity of California San Francisco, USA.
Joseph PerlSLAC National Accelerator Laboratory, Menlo Park, USA.
Harald PaganettiMassachusetts General Hospital and Harvard Medical School, Boston, USA.
Jan SchuemannMassachusetts General Hospital and Harvard Medical School, Boston, USA.
Anil SrivastavaNational Cancer Institute (NCI), Bethesda, USA.
Ceferino ObcemeaNational Cancer Institute (NCI), Bethesda, USA.
Asheet K NathCentre for Development of Advanced Computing (C-DAC), Pune, India.
Ashok SharmaAll India Institute of Medical Sciences (AIIMS), Delhi, India.
Jeffrey BuchsbaumNational Cancer Institute (NCI), Bethesda, USA. Electronic address: jeff.buchsbaum@nih.gov.

Funding

The TOPAS Tool for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical ResearchU24CA215123 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FADDEGON, BRUCE · 2018 to 2022
$4.2M
NCI NIH HHS U24 CA215123
6 · The paper itself

Abstract

Amongst the scientific frameworks powered by the Monte Carlo (MC) toolkit Geant4 (Agostinelli et al., 2003), the TOPAS (Tool for Particle Simulation) (Perl et al., 2012) is one. TOPAS focuses on providing ease of use, and has significant implementation in the radiation oncology space at present. TOPAS functionality extends across the full capacity of Geant4, is freely available to non-profit users, and is being extended into radiobiology via TOPAS-nBIO (Ramos-Mendez et al., 2018). A current "grand problem" in cancer therapy is to convert the dose of treatment from physical dose to biological dose, optimized ultimately to the individual context of administration of treatment. Biology MC calculations are some of the most complex and require significant computational resources. In order to enhance TOPAS's ability to become a critical tool to explore the definition and application of biological dose in radiation therapy, we chose to explore the use of Field Programmable Gate Array (FPGA) chips to speedup the Geant4 calculations at the heart of TOPAS, because this approach called "Reconfigurable Computing" (RC), has proven able to produce significant (around 90x) (Sajish et al., 2012) speed increases in scientific computing. Here, we describe initial steps to port Geant4 and TOPAS to be used on FPGA. We provide performance analysis of the current TOPAS/Geant4 code from an RC implementation perspective. Baseline benchmarks are presented. Achievable performance figures of the subsections of the code on optimal hardware are presented; Aspects of practical implementation of "Monte Carlo on a chip" are also discussed.

Indexed as

Monte Carlo MethodRadiobiologyRadiotherapy Planning, Computer-AssistedTime FactorsFPGAGeant4Monte CarloSimulationTOPAS

Identifiers

PMID31515016
PMCPMC7238758

What OpenQuestion holds

Textmetadata
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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.