Faster than the Speed of Life: Accelerating Developmental Biology Simulations with GPUs and FPGAs
@inproceedings{Hesam2018FasterTT,
title={Faster than the Speed of Life: Accelerating Developmental Biology Simulations with GPUs and FPGAs},
author={Ahmad Hesam},
year={2018}
}Life scientists are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex models. BioDynaMo is an open-source biological simulation platform that aims to alleviate them from the intricacies that go into development. Life scientists are able to base their models on top of BioDynaMo’s highly optimized core execution engine. At the core of all biological simulations is the mechanical interactions between possibly millions of objects. In…
Figures and Tables from this paper
figure 2.1 
figure 2.2 
figure 2.3 
figure 2.4 
figure 2.5 
figure 3.1 
figure 3.3 
figure 3.4 
figure 3.5 
figure 3.6 
figure 3.7 
figure 3.8 
figure 3.9 
figure 4.1 
table 4.1 
figure 4.10 
figure 4.11 
figure 4.12 
figure 4.2 
table 4.2 
figure 4.3 
figure 4.4 
figure 4.5 
figure 4.6 
figure 4.7 
figure 4.8 
figure 4.9 
table 5.1 
figure 5.1 
table 5.2 
figure 5.2 
table 5.3 
figure 5.3 
figure 5.4 
table 5.4 
figure 5.5 
table 5.5 
figure 5.6 
figure 6.1
References
SHOWING 1-10 OF 20 REFERENCES
An optimization approach for agent-based computational models of biological development
- Computer ScienceAdv. Eng. Softw.
- 2018
Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system
- Computer ScienceJ. Parallel Distributed Comput.
- 2013
GPU Virtualization and Scheduling Methods
- Computer ScienceACM Comput. Surv.
- 2017
An extensive and in-depth survey of GPU virtualization techniques and their scheduling methods is presented and a perspective on the challenges and opportunities for virtualization of heterogeneous computing environments is delivered.
The BioDynaMo Project: Creating a Platform for Large-Scale Reproducible Biological Simulations
- Computer ScienceArXiv
- 2016
Challenges and lessons learnt during the early stages of the software development process are described, in the context of implementation issues and the international nature of the collaboration.
Data-Intensive Modelling and Simulation in Life Sciences and Socio-economical and Physical Sciences
- Computer ScienceData Science and Engineering
- 2017
This DSE special issue collects contributions originating from the coordinated work of the ‘‘modelling’’ working groups WG3 and WG4 across the first two years of the ICT COST Action IC1406 High-Performance Modelling and Simulation for Big Data Applications (cHiPSet).
Self-construction in the context of cortical growth
- Biology
- 2013
This thesis explores the biological development of the neocortex as a model for selfconstructing systems with a model that contains the essential elements of biological self-construction, but is sufficiently tractable to be simulated.
Simulating cancer growth with multiscale agent-based modeling.
- BiologySeminars in cancer biology
- 2015
Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects
- BiologyPLoS Comput. Biol.
- 2013
This result is the first comprehensive demonstration of the principles of self-construction whereby the cortical architecture develops, and makes several testable predictions concerning cell migration and branching mechanisms.
Cramming More Components Onto Integrated Circuits
- Computer ScienceProceedings of the IEEE
- 1998
The future of integrated electronics is the future of electronics itself. The advantages of integration will bring about a proliferation of electronics, pushing this science into many new areas.…