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—itsorganism - 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—nowposition - 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==

{{Unsourced|section|date=December 2023}}

The OpenWorm community is committed to the ideals of [[open science]].<ref>[https://royalsocietypublishing.org/doi/10.1098/rstb.2017.0382 Royal Society website, ''OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans'', article by Gopal P. Sarma et al dated September 10, 2018]</ref> Generally this means that the team will try to publish in open access journals and include all data gathered (to avoid the [[file drawer problem]]). Indeed, all the biological data the team has gathered is publicly available, and the five publications the group has made so far are available for free on their website. All the software that OpenWorm has produced is completely free and open source.

By mid-2024, twenty publications made by the group are available for free on their website.<ref>[https://openworm.org/publications.html OpenWorm website, ''Publications'', retrieved September 18, 2024]</ref> All the software that OpenWorm has produced is completely free and open source.<ref>[https://openworm.org/downloads.html OpenWorm website, ''Downloads'', retrieved September 18, 2024]</ref><ref>[https://openworm.org OpenWorm website, retrieved September 18, 2024]</ref>

OpenWorm is also trying a radically open model of scientific collaboration. The team consists of anyone who wishes to be a part of it. There are over one hundred "members" who are signed up for the high volume technical mailing list. Of the most active members who are named on a publication there are collaborators from Russia, Brazil, England, Scotland, Ireland and the United States. To coordinate this international effort, the team uses "virtual lab meetings" and other online tools that are detailed in the resources section.

OpenWorm is also trying a radically open model of scientific collaboration. The team consists of anyone who wishes to be a part of it. There are over one hundred "members" who are signed up for the high volume technical mailing list. Of the most active members who are named on a publication there are collaborators from Russia, Brazil, England, Scotland, Ireland and the United States. To coordinate this international effort, the team uses "virtual lab meetings" and other online tools that are detailed in the resources section.

To coordinate this international effort, the team uses "virtual lab meetings" and other online tools that are detailed in the resources section.<Ref>[https://www.frontiersin.org/journals/computational-neuroscience/articles/10.3389/fncom.2014.00137/full Frontiers website, ''OpenWorm: an open-science approach to modeling Caenorhabditis elegans'', article by Balázs Szigeti et al, dated November 3, 2014]</ref>

== References ==