March 08 2016, Adv. Eng. Software, DOI: 10.1016/j.advengsoft.2016.03.002
A prerequisite for simulating the biophysics of complex biological tissues and whole organisms are
computational descriptions of biological matter that are flexible and can interface with materials of
different viscosities, such as liquid. The landscape of software that is easily available to do such work is
limited and lacks essential features necessary for combining elastic matter with simulations of liquids.
Here we present an open source software package called Sibernetic, designed for the physical simulation
of biomechanical matter (membranes, elastic matter, contractile matter) and environments (liquids,
solids and elastic matter with variable physical properties). At its core, Sibernetic is built as an extension
to Predictive–Corrective Incompressible Smoothed Particle Hydrodynamics (PCISPH). Sibernetic is built
on top of OpenCL, making it possible to run simulations on CPUs or GPUs, and has 3D visualization
support built on top of OpenGL. Several test examples of the software running and reproducing physical
experiments, as well as performance benchmarks, are presented and future directions are discussed.
August 10 2016, F1000Research 5:1946 (2016), DOI: 10.12688/f1000research.9315.1
The growth of the software industry has gone hand in hand with the development of tools
and cultural practices for ensuring the reliability of complex pieces of software.
These tools and practices are now acknowledged to be essential to the management of
modern software. As computational models and methods have become increasingly common
in the biological sciences, it is important to examine how these practices can accelerate
biological software development and improve research quality. In this article, we give a
focused case study of our experience with the practices of unit testing and test-driven
development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans.
We identify and discuss the challenges of incorporating test-driven development into a
heterogeneous, data-driven project, as well as the role of model validation tests, a
category of tests unique to software which expresses scientific models.
July 18 2015, BMC Neuroscience., DOI: 10.1186/1471-2202-16-S1-P141
November 03 2014, Front. Comput. Neurosci., DOI: 10.3389/fncom.2014.00137
OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans)
emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational
models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and
test hypotheses. The modeling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue
simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of
integrative modeling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm
collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.
July 11 2013, Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. DOI: 10.3389/conf.fninf.2013.09.00032
The C. elegans connectome (White et al., 1986) is currently the most detailed connectome data set at the neuronal circuit level that is publicly available. Represented as a network graph, it consists of edges that distinguish between gap junctions and chemical synapses, weighted by synapse count, with nodes that represent neurons whose identities are unambiguous and well known.
We have found exploration of the C. elegans connectome using hive plots to lead to the discovery of interesting qualitative structure that was previously not obvious, enabling this structure to be further pursued quantitatively using complex network mathematics.
July 8 2013, BMC Neuroscience 2013, 14(Suppl 1):P209 DOI:10.1186/1471-2202-14-S1-P209
OpenWorm is an international collaboration with the aim of producing an integrative computational model of Caenorhabditis elegans to further the understanding of how macroscopic behaviour of the organism emerges from aggregated biophysical processes. A core component of the project involves the integration of electrophysiological modelling and predictive-corrective incompressible smoothed particle hydrodynamics (PCISPH) to model how neuronal and muscle dynamics effect the nematode's behaviour.
Aug 2012, In Silico Biology, 11(3):137-147 DOI:10.3233/ISB-2012-0445
The nematode C. elegans is the only animal with a known neuronal wiring diagram, or "connectome". During the last three decades, extensive studies of the C. elegans have provided wide-ranging data about it, but few systematic ways of integrating these data into a dynamic model have been put forward. Here we present a detailed demonstration of a virtual C. elegans aimed at integrating these data in the form of a 3D dynamic model operating in a simulated physical environment. Our current demonstration includes a realistic flexible worm body model, muscular system and a partially implemented ventral neural cord. Our virtual C. elegans demonstrates successful forward and backward locomotion when sending sinusoidal patterns of neuronal activity to groups of motor neurons. To account for the relatively slow propagation velocity and the attenuation of neuronal signals, we introduced "pseudo neurons" into our model to simulate simplified neuronal dynamics. The pseudo neurons also provide a good way of visualizing the nervous system's structure and activity dynamics.
September 11 2012 - Neuroinformatics 2012 Abstract Book
We have merged and extended the C. elegans connectome (Varshney et al., 2006) and a three-dimensional cellular anatomy model (Grove & Sternberg, 2011) in the context of the OpenWorm project, an open source project to build a data integration and simulation framework for the C. elegans.
September 4 2011 - Neuroinformatics 2012 Abstract Book
Computational biology is asserting itself as an important approach to understanding complex biological systems.
In order to be able to effectively manage the complexity that comes with integrating and maintaining coarse-grained architectures, tools, digital information artifacts and code-bases, it is important for computational biology to fully embrace software engineering methodologies and best practices and follow the lead of the simulation based research in the physical sciences.
Taking cues from pioneering projects in computational neuroscience that are addressing this problem (MOOSE, http://j.mp/gSZZNF, Clones; http://j.mp/gzC5CP), we describe our approach to the integration of close-to-the-metal massively parallel simulations with high-level abstractions through the use of design patterns, including emerging paradigms for GPU-based parallel programming.