A History and Pre-History of OpenWorm
What follows is a history of C. elegans research, of the OpenWorm Project, as well as of several similar projects.
1900: C. elegans was first described by Émile Maupas, who isolated it from soil in Algeria.
1963: Sydney Brenner, at MRC Laboratory in Cambridge, proposed using C. elegans as a model organism for scientific study. He won a Nobel prize for this work in 2002.
1986: After thirteen years of work, John White, also at MRC Laboratory in Cambridge, publishes the full C. elegans connectome.
1999: C. elegans becomes the first animal to have its genome completely sequenced. Humans follow in 2002.
1999: Ferree and Lockery publish a neural network model of chemotaxis in C.Elegans
2002: David Harel proposes complete modeling of the C. elegans as a grand challenge in computing.
2009: Boyle & Cohen publish an integrated 2D computer model of C. elegans locomotion
18 May 2014: A team from MIT develops a technique to view all C. elegans neurons at once, which may fill in a remaining data gap.
Fall of 2007: Andrey Palyanov starts the CyberElegans project.
~2007: Co-founders Giovanni Idili and Matteo Cantarelli (software engineers) have conversations about simulating the worm, but nothing comes of it at the time as they lack computational biology / neuroscience background.
June 2008: First CyberElegans publication: Palyanov A.Yu., Dibert A.A., Computer simulation of C. Elegans muscular system and neural network // In: Proc. 6-th Int. Conf. Bioinformatics of Genome Regulation and Structure (BGRS), June 22-28, 2008, p. 61.
~2009: Andrey posts the first CyberElegans video to youtube: https://www.youtube.com/watch?v=Ek49JSAiKjY
Jan 2010: Sergey Khayrulin joins Andrey on the CyberElegans project.
1 Jan 2010: In the tweet heard 'round the world, co-founder Giovanni Idili proposes what would later be called the OpenWorm project to co-founder Stephen Larson (PhD student at UCSD) at the Whole Brain Catalog:
@BrainCatalog new year's resolution: simulate the whole C.Elegans brain (302 neurons)!— Giovanni Idili (@John_Idol) January 1, 2010
Early Jan 2011: Stephen Larson puts out a call for volunteers through Whole Brain Catalog, originally oriented at finding contributors for the WBC platform. Giovanni replies to the call restating his goal of C. elegans simulation, and brings Matteo into the conversation. The 3 get together on a skype call and decide to start a project together, during this conversation Stephen proposes the name "OpenWorm" and the name sticks. Subsequent early days conversations include Timothy Busbice (who also replied to Stephen's call for volunteers and co-founded OpenWorm), Marius Buibas (UCSD at the time) and Jay Coggan (Salk Institute).
24 Jan 2011: Giovanni discovers CyberElegans, developed by Andrey Palyanov and Sergey Khayrulin (from AP Ershov Institute of Informatics, Russia) who are contacted and immediately agree to join forces with the OpenWorm team:
4 September 2011: Article: Managing Complexity in Multi-Algorithm, Multi-Scale Biological Simulations: An Integrated Software Engineering and Neuroinformatics Approach.
September 2011: OpenWorm Release 1
December 2011: OpenWorm's Blog is initiated
April 2012: OpenWorm Release 2
August 2012: Article: Towards a virtual C. elegans: A framework for simulation and visualization of the neuromuscular system in a 3D physical environment.
November 2012: OpenWorm Release 3
21 March 2013: OpenWorm Journal Club with John White, the "father of the connectome".
- First OpenWorm Conference, in Paris.
- Article: Integration of predictive-corrective incompressible SPH and Hodgkin-Huxley based models in the OpenWorm in silico model of C. elegans.
- Article: Beyond the connectome hairball: Rational visualizations and analysis of the C. elegans connectome as a network graph using hive plots.
- OpenWorm Release 4
January 2014: OpenWorm Release 5
19 May 2014: OpenWorm raises 121,000 USD via Kickstarter
24 May 2014: OpenWorm article in The Economist
Summer 2014: Two OpenWorm volunteers are sponsored by the Google Summer of Code program via the INCF.
4-6 November 2014: Second OpenWorm Conference, in London, UK.
April 2015: Amazon Web Services donates credits to the OpenWorm project.
Summer 2015: One OpenWorm volunteer is sponsored by the Google Summer of Code program via the INCF.
Projects similar to OpenWorm
Detailed spreadsheet of these models and their attributes \<https://docs.google.com/spreadsheets/d/1NclOVMRIqY_hn-aL8MdLlJrfuhDgNJyk_ChsZMjugmE/edit?usp=sharing>
~1997: NemaSys at University of Oregon A full model was planned, including body, every neuron, every synapse, and complete set of sensory modalities. Four papers were released in 1997-1998 on pieces of the model, but its ultimate ambition was not finished. Webpage link
~1998 Perfect C. elegans Project in Tokyo They released an initial report \<http://www.mitpressjournals.org/doi/abs/10.1162/106454698568495#.VDrtDfldV8E>, but no more.
~2004 Virtual C. Elegans project at Hiroshima University, Japan The aim was to build a worm emulation, simulate poking it on the head, and have it back away from the poke. This was achieved, but not in a biologically realistic way. They simulated the nematode neurons, but the connection weights were unknown. Instead of getting this information experimentally, a machine learning algorithm was used to generate weights. Papers:
- A Dynamic Body Model of C. elegans with Neural Oscillators
- A Model of Motor Control of C. elegans with Neuronal Circuits
2009 Jordan Boyle, Netta Cohen at University of Leeds, UK C. elegans locomotion: an integrated approach
2010 Mailler at Tulsa, USA A Biologically Accurate 3D Model of the Locomotion of Caenorhabditis Elegans.
September 2011 - October 2013 Project Nemaload (David Dalrymple). The aim was to use optogenetics to record the firing dynamics of the C. elegans neurons and then replicate it in a simulation. He delivered a lecture on the project in November 2011. As of June 2014 he works for Twitter so the project may now be defunct.
Credit to James Pearn of Artificial Brains for the information on projects similar to OpenWorm.
Credit to Eugenio Battaglia for the story on his blog of the early OpenWorm history