@gidili Should be reasonable to submit a "I don't use Facebook" image :). I've got a couple of "trust me" evidence in there myself. Kinda glad it got me to sign on to Twitter though ... I had resisted that for a good number of years and I'll admit, I kinda like it now that I'm on.
@VahidGh Sounds good. In terms of the cells we would be working with, I believe that there is data available for the adult cells. In C. elegans, there are developmental cells (e.g. with a nomenclature that generates names such as ABalaar) that divide until becoming fully-differentiated adult cells that do not divide. The WormAtlas database provides annotations for the adult cells. One thing we would need to do is make sure that the data we do extract are consistent with the adult nomenclature, and then annotate each cell with a separate database (I have access to a much larger set of adult cell names).
If you would like to take a first pass at this, let's talk about it at the next DevoWorm meeting. We meet on Mondays at 4pm CDT (-5 UTC). The meeting takes place in Google Hangouts: https://hangouts.google.com/call/xbp72yxc3zrptg6hhqecboaavqa If you cannot make that time, we can meet one-on-one sometime next week. In the meantime, see if you can take one of the files from the Gene Expression Omnibus database and see if you can extract the raw data. This might be a bit tricky and will involve some research, but if you are successful we can really do a lot in terms of data analysis. Thanks, and talk to you later.
I'm implementing the steering neurons in "An Integrated Neuromechanical Model of Steering in C . elegans" by Izquierdo and Beer and there this equation with an I component that isn't identified (unless its the last mention: Interneurons and motorneurons were modeled as passive, isopotential nodes,
(seems gitter pasted the equation in the separate previous comment)
where y represents the membrane potential (or neuron acti- vation) relative to the resting potential (thus y can assume positive and negative values); τ is the time-constant; θ is a bias term that shifts the range of sensitivity of the out- put function; wji represents the strength of the chemical synapse; gki represents the gap junction conductance be- tween cell k and i (gki > 0). Chemical synapses were modeled as a sigmoidal function of presynaptic voltage, σ(x) = 1/(1 + e−x). Neck motor neurons included self- connections representing the voltage dependence of inward currents.
(seems gitter pasted the equation in the separate previous comment)
where y represents the membrane potential (or neuron acti- vation) relative to the resting potential (thus y can assume positive and negative values); τ is the time-constant; θ is a bias term that shifts the range of sensitivity of the out- put function; wji represents the strength of the chemical synapse; gki represents the gap junction conductance be- tween cell k and i (gki > 0). Chemical synapses were modeled as a sigmoidal function of presynaptic voltage, σ(x) = 1/(1 + e−x). Neck motor neurons included self- connections representing the voltage dependence of inward currents.
@balicea, Thanks for your explanation. I was playing with C. elegans datasets from GEO today. The problem I'm still not sure about is how we are going to relate data from those files (e.g. Affymetrix) to specific cells you are talking about! Would be great to have a talk about this later.
@VahidGh Sounds like you are on the right track. Getting the GEO dataset defined and in numeric form is the first step. The next steps will involve building a relational database (or figuring out which cells the measurements are being taken from). Sometimes it is defined in the metadata (on the downloads page for the dataset). This is something we can talk about when we meet. See you then.
/all I put up a "preview" (meaning using free license/ads) android app called WormWorx in the Google Play store: https://play.google.com/store/apps/details?id=org.openworm.wormworx If you so desire check it out and review it with suggestions. It is based on a couple of papers from Izquierdo, Beer, Cohen, etc. See the references in wormworx.portegys.com. You can also get a WormWorx badge if you tune the worm's synapses to allow it to steer toward salt (food) properly.
I am using a Samsung Galaxy S6
@diegoflassa
There are a few different parts to OpenWorm, so it helps sometimes to have some aspect to focus on.
Most communications amongst the team have shifted over there. although I know Bradly Alicea uses the devoworm channel pretty regularly
Hi Diego, if you have not yet tried this link to sign on to Slack and get an automatic invite to the organization there, please give it a try! https://slackpass.io/openworm
And welcome! @diegoflassa Just let us know what your interests are, and we can try pointing you to some of the interesting projects that are active right now!
Hello! I'm not sure if this is the correct venue to ask this kind of quations, but as a curious outsider / spectator: what is the current status of the OpenWorm project / C. Elegans simulation model? https://github.com/openworm/OpenWorm/milestones is a bit difficult to parse...
Great question @aa-m-sa -- there's more conversation going on over in our other chat system you'll get an invite to if you fill out the following: http://bit.ly/OpenWormVolunteer
okay, thanks ... though I'm wary of signing up as an volunteer because I probably can't do much volunteering (too much of a time commitment) ... some background why I'm asking this: I've thought that C.Elegans model is still heavily Work-In-Progress, but today I was linked to this article https://www.smithsonianmag.com/smart-news/weve-put-worms-mind-lego-robot-body-180953399/ by a friend who exclaimed that "see, C. Elegans works in Lego!"
@aa-m-sa Yeah careful with that. There is a fair bit of sloppy reporting that has been going on about the project for some time. There is a very loose usage of "works" or "thinks" or "behaves like C. elegans" that some articles are using. For the record, OpenWorm's peer-reviewed publications are posted here: http://openworm.org/publications.html and anybody who contacts info@openworm.org for fact checking can get a clarification on how far along the project is (definitely Work in progress). We are having an extensive presentation about recent progress in a few weeks in London if anyone is interested in joining: http://blog.openworm.org/post/168271424220/royal-society-meeting-open-house-pub-night-in . For absolute latest, you can see what we have deployed recently at http://github.com/openworm/openworm
ah okay found it: "Meeting papers will be published in a future issue of Philosophical Transactions B.", https://royalsociety.org/science-events-and-lectures/2018/01/mind-of-a-worm/
Hi, @asmitks ! We have mostly moved onto Slack for communications in the project. You should be able to get an invite by this link: https://slackpass.io/openworm
Hi, Matt! That's a pretty big question. I don't think there's even a widely agreed upon definition for the physical correlates of consciousness, so talking about sharing consciousness seems rather premature. That said, we're not working on it, and, in my case, a suggestion on what you could do on that question would mostly be conjecture.
@EldritchEmber_gitlab , if you would like to learn more about the project, you can meet us on Slack (see the link above).
Hi Matt. There are social insects that are connected very through olfactory, tactile, etc. means, even if they don't share a nervous system. It would seem that if something like consciousness might emerge it might be there. Here is a great article on termites: https://www.theguardian.com/news/2018/sep/18/a-giant-crawling-brain-the-jaw-dropping-world-of-termites
@portegys thank you, though I admit, my interest is strictly in neural mass bonding, that was insightful all the same
Hi, @Kr3m. Thanks! There's been some steady progress on the software side and in the science -- our members have published well-received papers in Philosophical Transactions of the Royal Society (issue: https://royalsocietypublishing.org/toc/rstb/373/1758) and we've been pushing more on integration of key parts of the OpenWorm toolbox
Hi, Ilya. The project is still going on. To be fair, our social media presence is somewhat diminished. Most of our communications have moved to Slack (https://slackpass.io/openworm).
At this point I would say DevoWorm is the most active - DevoWorm intersects with OpenWorm but also there's work that isn't necessarily "OpenWorm". Dr. Bradly Alicea heads that effort and there are scheduled meetings on a monthly basis.