OpenWorm: Difference between revisions

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{{Short description|Science project with the goalSimulation of simulating a roundworm}}

{{Multiple issues|

{{update|date=April 2019}}

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'''OpenWorm''' is an international [[open science]] project for the purpose of [[simulation|simulating]] the roundworm ''[[Caenorhabditis elegans]]'' at the [[cell (biology)|cell]]ular level.<ref>{{cite news |url=https://www.theregister.co.uk/2014/05/05/nematode_fanciers_open_their_worm_to_a_kickstarter/ |title=What's that PARASITE wriggling inside my browser? Nematode fanciers open their worm to a Kickstarter |work=The Register |date=5 May 2014 |first=Richard |last=Chirgwin}}</ref><ref>{{Cite journal |first1=Andrey |last1=Palyanov |first2=Sergey |last2=Khayrulin |first3=Stephen D. |last3=Larson |first4=Alexander|last4=Dibert|date=2012-01-01|title=Towards a virtual C. elegans: A framework for simulation and visualization of the neuromuscular system in a 3D physical environment|journal=In Silico Biology|language=en|volume=11|issue=3|doi=10.3233/isb-2012-0445|issn=1386-6338|pmid=22935967|pages=137–147|url=https://www.researchgate.net/publication/235326413}}</ref><ref>{{Cite journal|last1=Gewaltig|first1=Marc-Oliver|last2=Cannon|first2=Robert|date=2014-01-23|title=Current Practice in Software Development for Computational Neuroscience and How to Improve It|journal=PLOS Computational Biology|language=en|volume=10|issue=1|pages=e1003376|doi=10.1371/journal.pcbi.1003376|issn=1553-7358|pmc=3900372|pmid=24465191|bibcode=2014PLSCB..10E3376G |doi-access=free }}</ref> Although the long-term goal is to model all 959 cells of the ''C. elegans'', the first stage is to model the worm's [[Animal locomotion|locomotion]] by simulating the 302 [[Neuron|neurons]] and 95 [[Muscle cell|muscle cells]]. This bottom up simulation is being pursued by the OpenWorm community.

As of 2014, a [[physics engine]] called [[Sibernetic]] has been built for the project and models of the neural [[connectome]] and a muscle cell have been created in [[NeuroML]] format. A 3D model of the worm [[anatomy]] can be accessed through the web via the OpenWorm browser. The OpenWorm project is also contributing to develop [[Geppetto (software)|Geppetto]],<ref>[http://www.geppetto.org Geppetto]</ref> a web-based multi-algorithm, multi-scale simulation platform engineered to support the simulation of the whole [[organism]].<ref>{{cite web |url=https://venturebeat.com/2014/04/30/openworm-is-going-to-be-a-digital-organism-in-your-browser/ |title=Openworm is going to be a digital organism in your browser |date=30 April 2014 |last=Takahashi |first=Dean |work=VentureBeat}}</ref>

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[[File:Adult Caenorhabditis elegans.jpg|thumb|right|An adult ''Caenorhabditis elegans'' worm]]

''C. elegans'' has one of the simplest nervous systems of any organism - its [[hermaphrodite]] type possesses only 302 neurons. Furthermore, the structural [[connectome]] of these neurons is fully worked outmapped. There are fewer than one thousand cells in the whole body of a ''C. elegans'' worm, and because ''C. elegans'' is a [[model organism]], each has a unique identifier and comprehensive supporting literature. Being a model organism, the genome is fully known, along with many well characterized mutants readily available, and a comprehensive literature of behavioural studies. With so few neurons and new [[3D optical data storage|2-photon]] calcium [[microscopy]] techniques, it should soon be possible to record the complete neural activity of a living organism. The manipulation of neurons via [[Optogenetics|optogenetic]] methods, in tandem with the foregoing technical capacities, has provided the project an unprecedented position - now able to fully characterize the neural dynamics of an entire organism.

The efforts to build an ''[[in silico]]'' model of ''C. elegans'', although a relatively simple organism, have burgeoned the development of technologies that will make it easier to model progressively more complex organisms.

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In 2005 a Texas researcher described a simplified ''C. elegans'' simulator based on a 1-wire network incorporating a digital Parallax Basic Stamp processor, sensory inputs and motor outputs. Inputs employed 16-bit A/D converters attached to operational amplifier simulated neurons and a 1-wire temperature sensor. Motor outputs were controlled by 256-position digital potentiometers and 8-bit digital ports. Artificial muscle action was based on Nitinol actuators. It used a "sense-process-react" operating loop which recreated several instinctual behaviors.<ref>{{cite conference |first=Paul |last=Frenger |title=Simple C. elegans Nervous System Emulator |conference=Houston Conference for Biomedical Engineering Research |date=2005 |page=192}}</ref>

These early attempts of simulation have been criticized for not being biologically realistic. Although we have the complete structural connectome, we do not know the [[synaptic weight]]s at each of the known synapses. We do not even know whether the synapses are [[Inhibitory synapse|inhibitory]] or [[Excitatory synapse|excitatory]]. To compensate for this the Hiroshima group used machine learning to find some weights of the synapses which would generate the desired behaviour. It is therefore no surprise that the model displayed the behaviour, and it may not represent true understanding of the system.{{Citation needed|date=December 2023}}

==Open science==