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Giovanni Idili
@gidili
I dont have a personal facebook page because I am too cool for it, can I still earn the badge?
Bradly Alicea
@balicea
@gidili Thanks!
Stephen Larson
@slarson
Ah.. hmm so you have no facebook account? Yeah you could still earn it @gidili
Giovanni Idili
@gidili
Can I submit without the FB proof?
Stephen Larson
@slarson
Yeah; just try submitting an image that explains the problem :) @gidili
Chee Wai Lee
@cheelee
@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.
Bradly Alicea
@balicea

@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.

Tom Portegys
@portegys
blob
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.
Tom Portegys
@portegys
/all Should have put all on my above note I guess!
Stephen Larson
@slarson
Screen Shot 2016-10-27 at 4.36.20 PM.png
Stephen Larson
@slarson
@portegys They reference the model from their 2013 paper — and in there they say that “the third term represents external input to the neuron"
Tom Portegys
@portegys
@stephen I'm just not sure what to set that to or where it comes from. Might just fudge a value that works.
Vahid Ghayoomie
@VahidGh
@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.
Stephen Larson
@slarson
@portegys You can just set it to zero unles you specifically want to add stimulation to a given neuron, like from the outside
Bradly Alicea
@balicea
@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.
Matt Stephenson
@skyblader123
Hi, I am interested in iterating on your codes
Tom Portegys
@portegys
/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.
Michael Currie
@MichaelCurrie
The screenshots look great, @portegys. I get the message that "Yourdevice isn't compatible with this version" so I can't install, though.
I am using a Samsung Galaxy S6
diegoflassa
@diegoflassa
Hello!
Mark Watts
@mwatts15
Hi, @diegoflassa
diegoflassa
@diegoflassa
Hello, @mwatts15 . I'm new around here, and i'm trying familiarize with the project and the community.
Mark Watts
@mwatts15
Cool. What do you like to do?
@diegoflassa
There are a few different parts to OpenWorm, so it helps sometimes to have some aspect to focus on.
Mark Watts
@mwatts15
That said, I should also direct you to our slack group: https://openworm.slack.com/messages/general
Most communications amongst the team have shifted over there. although I know Bradly Alicea uses the devoworm channel pretty regularly
Chee Wai Lee
@cheelee
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!
Jarl Victor
@JarlV
Hi!
Chee Wai Lee
@cheelee
Welcome @JarlV !!!
Aaro Salosensaari
@aa-m-sa
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...
Stephen Larson
@slarson
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
Aaro Salosensaari
@aa-m-sa
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!"
Stephen Larson
@slarson
@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
Aaro Salosensaari
@aa-m-sa
thanks! not in UK though ... do you know if the presentation materials will be published on internet?
Aaro Salosensaari
@aa-m-sa
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/
ASMIT SINGH
@asmitks
Hello! This is Asmit Singh a CSE undergrad from IIITD , New Delhi. I find the work really interesting and I would love to contribute to the organization under GSOC 2019. I am a machine learning and AI enthusiast.Please help me get started
Mark Watts
@mwatts15
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
ASMIT SINGH
@asmitks
Thanks!!
Handsome Jack 🃏
@Jest_Of_Gotham_twitter
Hi everyone!
Matt
@EldritchEmber_gitlab
I had a question on the Openworm project: I am an undergraduate psychology major, whose research area is on how consciousness might be shared between connected neural masses. Could Openworm be used to connect multiple C. Elegans brains, or if not, what should I try
Mark Watts
@mwatts15
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).
Tom Portegys
@portegys
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
Matt
@EldritchEmber_gitlab
@mwatts15 fair enough. I was hoping to model connected nervous systems using openworm, but I didn't expect it to work
@portegys thank you, though I admit, my interest is strictly in neural mass bonding, that was insightful all the same
Kevin Remisoski
@Kr3m
ha cool. I've never used gitter before and while browsing another project stumbled in here. I haven't seen this project in quite some time, but it looks like some amazing progress has been made. :)
Mark Watts
@mwatts15
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