These are chat archives for openworm/ChannelWorm

9th
Jul 2015
Travis Jacobs
@travs
Jul 09 2015 02:32
@VahidGh Excellent
Travis Jacobs
@travs
Jul 09 2015 02:42
@VahidGh @cheelee @stripathy Here is a link to download the screencast for the ChannelWorm workflow if you wanted to have a look. We can use this as the basis for our meeting tomorrow.
Travis Jacobs
@travs
Jul 09 2015 02:58
And this is a quick run-through of the steps I used in the video
Chee Wai Lee
@cheelee
Jul 09 2015 02:59
@VahidGh Cool, I should be there. Glad it got postponed, I kinda crashed early last night.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 08:49
@travs, The workflow screencast was great, sorry if some fields were not clear. We are separating different fields (optional and required) in the new UI.
@cheelee, great, see you then
@travs, it seems some fields do not display well in Opera browser. We've tested the app via Google Chrome, any feedback would be appreciated for other type of browsers.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 09:38
@travs, Also the screencast was limited by 15 mins. I don't think it was intentional, as it cut off suddenly and didn't include other steps!
Chee Wai Lee
@cheelee
Jul 09 2015 10:15
@VahidGh Hope you catch this on time. The 15 min restriction was due to Dropbox policy. They require you to actually download the file if you wanted to view past 15 min.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 10:21
@cheelee, gotcha, I watched it online. Does it mean the downloadable file, is the full version?
Chee Wai Lee
@cheelee
Jul 09 2015 10:45
@VahidGh yup, I downloaded it to my dropbox and watched it.
27:14 total length
Travis Jacobs
@travs
Jul 09 2015 14:43
Hey @VahidGh thanks for the compliment. Sorry yeah I should have mentioned you can only watch a preview by default.. I agree with the separating of required and optional fields. But this is awesome so far. I really like the digitization that you've embedded, and the DOI autofill feature is so cool
We'll talk more about the workflow in a few hours, but yeah, it seems like we can certainly start the curation process now :)
Vahid Ghayoomie
@VahidGh
Jul 09 2015 15:53
@travs, great, I also changed some units in accordance with papers
Chee Wai Lee
@cheelee
Jul 09 2015 16:29
@travs The workflow is great. I have some concerns over papers that have scanned images but I'm not sure what can be done about those older papers.
Travis Jacobs
@travs
Jul 09 2015 16:31
@cheelee Ah yes, that will not always be easy
I think when building up the list of papers we should take this into account
i.e. try to find an online supplemental copy of the figures if the PDF is of poor quality
Chee Wai Lee
@cheelee
Jul 09 2015 16:33
@travs Perhaps a tag for highly approximate original images?
So we know what to look out for
Travis Jacobs
@travs
Jul 09 2015 16:33
Yes, that would make sense
You mean a tag for the poorer quality ones, or the higher quality ones?
Chee Wai Lee
@cheelee
Jul 09 2015 16:34
Low quality ones
Travis Jacobs
@travs
Jul 09 2015 16:34
Right, that makes sense
Chee Wai Lee
@cheelee
Jul 09 2015 16:34
So we have some warning that the data we get may not be as accurate as we want them to be.
and if there are problems, we can either discard their use in experiments, or seek more accurate data.
Travis Jacobs
@travs
Jul 09 2015 16:35
I think we need to develop a more explicit protocol in general for gathering the papers
Yes I totally agree
Chee Wai Lee
@cheelee
Jul 09 2015 16:35
Seems pretty good so far. The spreadsheet does its job I think.
Travis Jacobs
@travs
Jul 09 2015 16:35
We can chat about this more when the rest of the guys join us in a little while; I'd be interested to get their opinions
Chee Wai Lee
@cheelee
Jul 09 2015 16:35
Yah :)
Travis Jacobs
@travs
Jul 09 2015 16:36
Yeah, I was imagining maybe a markdown gist or something with our explicit "best practices" on it for gathering papers, or something like that
Chee Wai Lee
@cheelee
Jul 09 2015 16:37
Right
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:07
@travs do we have a workflow meeting now?
Travis Jacobs
@travs
Jul 09 2015 17:08
@stripathy Yeah! Sorry, @cheelee were just finishing our chat
Ok
Chee Wai Lee
@cheelee
Jul 09 2015 17:08
@stripathy hey hey we just got done. Sorry about that!
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:08
Hi everyone
Travis Jacobs
@travs
Jul 09 2015 17:08
@VahidGh you around as well?
Alright, so did you guys get a chance to view that screencast?
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:09
just watching the screencast now
Chee Wai Lee
@cheelee
Jul 09 2015 17:09
I watched it.
Travis Jacobs
@travs
Jul 09 2015 17:09
Ok, and there is also a gist to accompany to give a very general overview of the workflow
I'll grab it one sec
Woah, so gitter embeds gists? Cool
Chee Wai Lee
@cheelee
Jul 09 2015 17:10
My main interest in this whole exercise is to figure out what you guys have to do, and then consider the final product from this process and how it integrates with the rest of the project.
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:10
that's very cool!
Chee Wai Lee
@cheelee
Jul 09 2015 17:10
haha nice!
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:11
@cheelee that's great - there were some questions about what kinds of most data would be most useful to the modelling team
Chee Wai Lee
@cheelee
Jul 09 2015 17:12
@stripathy yah, I'm trying to wrap my head around how the pieces will fit together. So far the only data I've had the chance to run code on are the LEMS_xxxx.xml files in the NeuroML2 folder for muscle_model.
I have NO clue what those mean.
Other than pretty graphs being generated.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:14
@cheelee, did you have a chance to look at this publication?
Travis Jacobs
@travs
Jul 09 2015 17:14
Right, so that markdown and video should serve as a starting point for how we enter the data. @cheelee and I were discussing earlier that, along with enumerating the actual steps to enter data, we should explicitly list the types of decisions we should make when confronted with choices
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:14
regarding the muscle model
Travis Jacobs
@travs
Jul 09 2015 17:14
In other words, in a markdown file or similar, say exactly the types of graphs we will accept at this stage
and what kinds of information to be looking out for other than figures
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:15
right - @travs I like the idea of specifying things for curation as much as possible
Travis Jacobs
@travs
Jul 09 2015 17:15
Thanks @stripathy I agree
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:15
the video is great btw
Travis Jacobs
@travs
Jul 09 2015 17:15
Haha thanks, it's my first screencast! :)
So yeah, that gist is probably not editable by you guys right now, but I can get that done
Unless @VahidGh is there a better place for this in the channelworm docs? Perhaps making a separate page?
The gist is temporary for sure
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:16
keep it simple for now? a google doc or something we can all edit? then you'll formalize?
Chee Wai Lee
@cheelee
Jul 09 2015 17:17
@VahidGh I've not read that paper yet. I'll spend some time on it and see if I can get the gist without requiring too much understanding for biology.
Travis Jacobs
@travs
Jul 09 2015 17:17
@stripathy Yup, google doc makes sense
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:17
@travs, yeah, we can complete the RTDs, as we are going to have some links to the docs in the web app.
Chee Wai Lee
@cheelee
Jul 09 2015 17:17
@stripathy yah a google docs would be a good starting point
Travis Jacobs
@travs
Jul 09 2015 17:17
I'll create one now and let's all jump in. We can make an issue on CW to formalize the google doc into CW documentation when we have this totally nailed down
Chee Wai Lee
@cheelee
Jul 09 2015 17:18
@travs sounds good. Standing by.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:18
@travs, sounds good
Chee Wai Lee
@cheelee
Jul 09 2015 17:19
@VahidGh That's the neuron system for all 302 neurons in the C. Elegans worm, correct?
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:19
For the big picture
Travis Jacobs
@travs
Jul 09 2015 17:19
Chee Wai Lee
@cheelee
Jul 09 2015 17:20
@travs thanks!
Travis Jacobs
@travs
Jul 09 2015 17:20
Can you guys edit or just view?
May have to log in
Chee Wai Lee
@cheelee
Jul 09 2015 17:20
@travs looks like view only
@travs Am logged in, but still view only. No biggie for now though.
Travis Jacobs
@travs
Jul 09 2015 17:22
@cheelee Try again
Chee Wai Lee
@cheelee
Jul 09 2015 17:23
@travs cool works now. Had to refresh screen.
Travis Jacobs
@travs
Jul 09 2015 17:23
Ok excellent
To the ibex making the decision points, good call
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:25
@travs, there was no need for duration, etc calculation :D
I corrected those fields
Travis Jacobs
@travs
Jul 09 2015 17:25
Ah! Ok, they are gone now?
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:25
The patch clam duration was 200 ms in the paper
Travis Jacobs
@travs
Jul 09 2015 17:26
I believe it said 1200 ms, was that total?
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:26
and as it was no explicit start and end time, so they could be 0 and 200
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:26
I think @travs is right - it seemed like 1200ms to me
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:26
really? I thought it was 200 ms
Ok, 1200 no difference
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:27
and if you look at the x axis scale bar in A, seems more like 1200ms
Travis Jacobs
@travs
Jul 09 2015 17:27
Ok, just making sure
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:27
I just guessed from what I was watching in screencast
Chee Wai Lee
@cheelee
Jul 09 2015 17:28
I couldn't quite tell if 1200ms as described in the figure caption referred to each step or the whole experiment.
Travis Jacobs
@travs
Jul 09 2015 17:28
@cheelee Good question, if you go to the methods section in the paper it clarifies I believe
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:28
My point was that if we don't have any explicit time start/end, this is as same as the whole duration
Travis Jacobs
@travs
Jul 09 2015 17:28
@VahidGh Ok right
So the fields are still present?
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:29
hmm... maybe we can be clearer with the interface about what fields are more essential than others?
Chee Wai Lee
@cheelee
Jul 09 2015 17:29
Ok, at 6:00 of the video, I just noticed why @VahidGh thinks it is 200ms.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:29
In some cases we have a start time other than 0, e.g. at 200 ms starts and at 1000 ms ends, but the duration could be 1200 ms
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:29
stimulation duration seems more important than time-interval deltat
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:30
@stripathy, yeah, in new UI we have a separate form for simulation purposes
Chee Wai Lee
@cheelee
Jul 09 2015 17:30
"Each data point represents the mean current amplitude during the last 200ms of the voltage step."
Travis Jacobs
@travs
Jul 09 2015 17:30
@stripathy I agree
@VahidGh I believe @stripathy said "stimulation" instead of "simulation" :)
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:31
oh crap, ok so it's more complicated than a simple paradigm uniformly applied
do you guys agree?
=\
Travis Jacobs
@travs
Jul 09 2015 17:31
@cheelee that's for inward currents
this is an outward one, jsut before that
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:32
ok, good
Travis Jacobs
@travs
Jul 09 2015 17:32
@stripathy yes, maybe if these fields had help text it could help a great deal?
Chee Wai Lee
@cheelee
Jul 09 2015 17:32
@travs gotcha
@travs If there were some mouse-over help text that'd definitely be good for new users.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:34
Ok, I corrected the duration and end time
Travis Jacobs
@travs
Jul 09 2015 17:34
@cheelee Totally. It's just because I'm not overly familiar with the language used here that this gave me a little confusion
@VahidGh What do you think of help text?
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:35
@travs, @cheelee, yeah this is possible, but I didn't spend more time, as the UI is going to be changed
Travis Jacobs
@travs
Jul 09 2015 17:35
Ok makes sense
And how about the versioning freeze we talked about last week
Can we start implementing that now?
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:36
@travs agree - i think we'll learn a lot from trying to curate a few manuscripts which will inform subsequent UI
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:37
Let's have it after these new changes @miladjafary is working on
Ok, another problem was with molar concentrations I guess
Travis Jacobs
@travs
Jul 09 2015 17:38
@stripathy You're right. It's nice being able to help build the tool one uses! :)
@VahidGh Yes, I just assumed they were meant to be in mol
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:39
I put those fields there for papers we have explicit concentration for Ca an Cl again
Travis Jacobs
@travs
Jul 09 2015 17:40
Ok, I just kind of hacked my way through by using the solution concentration, but I was thinking that was overly complicated
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:41
my sense is most papers will report concentrations in mM
most = >90%
i have some code for parsing solution concentrations from text: https://github.com/neuroelectro/neuroelectro_org/blob/master/article_text_mining/assign_metadata.py starting at line 513
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:47
@stripathy, the paper for EGL-19 was considering 6 uM for [Ca2+] in solution, so I decided to choose micro!
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:48
good point - [Ca2+] will usually be um
the rest are almost always mM
Travis Jacobs
@travs
Jul 09 2015 17:48
@stripathy Ok that's awesome! @VahidGh and @miladjafary could make use of this in the forms
@stripathy To go back to your point about usage changing the UI, I think there are a few things in this google doc that can be made into github issues
I'll start raising them now as you guys keep enumerating them
This is awesome
Chee Wai Lee
@cheelee
Jul 09 2015 17:51
:)
I'm just going through the video again and put myself into your shoes and pretending to be a brand-new user.
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:51
to me, it seems like digitizing the figure is kind of distinct from specifying the metadata about the experiment
(but obviously related)
Chee Wai Lee
@cheelee
Jul 09 2015 17:52
@stripathy right. In which case, clicking on the point makes as much of a value-judgement as deciding that the points really are 0.
Makes sense. We're dealing with inexact values that we can tweak later.
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:54
proposal: all numeric fields should be annotate-able with units which are automatically parsed and validated
e.g.: "10 mV"
Vahid Ghayoomie
@VahidGh
Jul 09 2015 17:55
@stripathy, yeah, good point
Travis Jacobs
@travs
Jul 09 2015 17:55
@stripathy I can see your point. I should have highlighted that separation in the video. The only reference I made to this is in the gist, which implies that some of the metadata may already be in the database
Chee Wai Lee
@cheelee
Jul 09 2015 17:55
So the field will flexibly parse and handle the fields accordingly?
Shreejoy Tripathy
@stripathy
Jul 09 2015 17:55
e.g.: units_re = re.compile(ur'm[sS]|mV|Hz|hz|hertz|min|pA|MΩ|mΩ|Ω|ohm|°C|(MΩ)|(mV)|(ms)|m[lL]', re.UNICODE)
line 75 here: https://github.com/neuroelectro/neuroelectro_org/blob/master/article_text_mining/assign_metadata.py
Chee Wai Lee
@cheelee
Jul 09 2015 17:56
nice
Travis Jacobs
@travs
Jul 09 2015 17:57
@stripathy That's awesome. Raising an issue for this
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:00
Another problem was with mutants and blockers
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:01
@VahidGh right - how would the modeling team use mutant info? would they infer the function of the ion channel by subtracting it from non-mutant?
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:01
If the experiment is based on xenopus oocyte then usually we don't need mutants
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:01
@VahidGh precisely
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:02
but for a experiment like the one Travis was going through, we need to know which mutants have used
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:03
the interactive plot digiitazation stuff is SUPER slick
kudos!
This is the main work for the digitizer, we grabbed some useful parts, and trying to customize others
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:05
how often is it that a single graph will contain multiple useful data traces?
like multiple mutants, etc?
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:06
Very common :D
Travis Jacobs
@travs
Jul 09 2015 18:06
@stripathy It seems quite often in the set of papers I've looked at, but that is a small set
Ok
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:06
agreed, my sense is that it'll be a common thing and should inform the UI, so as to avoid lots of duplication
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:07
Also @travs it would be nice if we include a voltage-clamp figure in the workflow
@stripathy, it is possible somehow, we can have different datasets for one figure
Travis Jacobs
@travs
Jul 09 2015 18:08
@VahidGh good point. I get the inkling that once we do this a few times we will have a good sense of when the UI is established, so I can create another screencast then maybe :)
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:08
yah - ideally there'd be some like semantic link or something between digitized traces and experimental metadata
Chee Wai Lee
@cheelee
Jul 09 2015 18:09
@stripathy @VahidGh @travs Perhaps some way of cloning the instance to accomodate multiple data points?
All the metadata associated with the same image would remain unchanged.
*data points = data series.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:09
@stripathy, there is a fk for every digitized data that relates to the experiment
Also it is the same for patch clamps
Chee Wai Lee
@cheelee
Jul 09 2015 18:10
@VahidGh I don't have permission to look at that document.
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:10
@VahidGh just got a 403 forbidden access for that link
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:10
BTW, It's some sketch from new UI that integrate everything in one page
Chee Wai Lee
@cheelee
Jul 09 2015 18:10
ah
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:11
ok - let's keep it simple for now
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:11
unnamed.png
Travis Jacobs
@travs
Jul 09 2015 18:12
@VahidGh Small point: the default value for time interval is 0.01 ms now. Just to note
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:12
@VahidGh what's the timeline on the new UI?
Travis Jacobs
@travs
Jul 09 2015 18:12
Balsamiq mockups! :D
Love that program
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:13
@stripathy, I hope in a week!
Chee Wai Lee
@cheelee
Jul 09 2015 18:13
Learned something new ... bookmarking Balsamiq
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:13
@travs, yeah, @miladjafary is working on it
Travis Jacobs
@travs
Jul 09 2015 18:14
@VahidGh Ok, just making sure it was known!
Chee Wai Lee
@cheelee
Jul 09 2015 18:14
@VahidGh - on that image - Experiment = data series. And you can associate that with an existing paper image, correct?
*image = figure.
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:15
@cheelee, actually we have it right now, but they are not in one page
If you create a new graph, you have to specify the experiment and patch clamp this figure is related to
Chee Wai Lee
@cheelee
Jul 09 2015 18:16
ah ok
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:16
you can have 1-n graph/patch clamp for each experiment
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:19
"If you create a new graph, you have to specify the experiment and patch clamp this figure is related to" - ideally there'd be a feature to "duplicate experiment/patch clamp like previous"
in @travs example, all of those would be the same, except the ion channel would be different (I think)
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:20
@stripathy, yeah, good point
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:20
@travs - I need to leave soon, can we wrap up?
Travis Jacobs
@travs
Jul 09 2015 18:21
@stripathy Yeah! I have to take off soon as well
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:21
@stripathy, thanks for participating.
Thanks everyone
Travis Jacobs
@travs
Jul 09 2015 18:22
So just to be clear on what some of the next steps that came out of this are, in terms of UI, I've raised #124 #125 and #126 because of your points
So those things will be taken care of, and there are some other questions we've raised and answered. And still more points in the google doc
Chee Wai Lee
@cheelee
Jul 09 2015 18:22
Thanks guys, this has been instructive.
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:22
can we make a decision on whether to start curating using the current UI now? or wait for new UI?
Travis Jacobs
@travs
Jul 09 2015 18:22
So how about we meet again when the new UI is through?
Ok good point
I'm thinking we can go ahead since the changes are mostly convenience/clarification. What do you think @VahidGh
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:23
we have a hackathon on Sun, i can try curating a couple things then using the current UI
Travis Jacobs
@travs
Jul 09 2015 18:23
@stripathy Yeah good idea!
Chee Wai Lee
@cheelee
Jul 09 2015 18:24
From what I can tell, all the pieces for curating appears to be in place.
Travis Jacobs
@travs
Jul 09 2015 18:24
@cheelee Agreed
Chee Wai Lee
@cheelee
Jul 09 2015 18:24
One last question.
Travis Jacobs
@travs
Jul 09 2015 18:24
Yup!
Chee Wai Lee
@cheelee
Jul 09 2015 18:24
How will the modeling team make use of the data after they have been curated?
I've tagged that part of the document as "output"
I'm guessing that's still undecided?
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:25
@cheelee great question - I think that's really going to inform what I/V plots are really useful to them
Travis Jacobs
@travs
Jul 09 2015 18:25
Right. That is kind of my end as well, and I am planning to do some more work integrating PyOpenWorm to be able to receive data from CW
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:25
and what kinds of data to focus on extracting (from xenopus oocytes, mutants, etc)
Travis Jacobs
@travs
Jul 09 2015 18:25
@stripathy Exactly
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:25
I think we have everything we need. I'll look at some easily implementable issues discussed today
Chee Wai Lee
@cheelee
Jul 09 2015 18:25
ah cool!
Travis Jacobs
@travs
Jul 09 2015 18:26
@VahidGh Ok great!
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:26
ok cool
Travis Jacobs
@travs
Jul 09 2015 18:26
Well guys, this has been fun :) See you in the hackathon sunday (if not before then)!
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:26
sure thing !
Chee Wai Lee
@cheelee
Jul 09 2015 18:26
well we have lots of work to do on this front :). And integration from that point on seems straightforward enough without worrying about implementation details
See you guys at the hackathon!
Shreejoy Tripathy
@stripathy
Jul 09 2015 18:26
see you /All then!
Travis Jacobs
@travs
Jul 09 2015 18:26
Thanks again to everyone :)
Chee Wai Lee
@cheelee
Jul 09 2015 18:26
thanks!
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:27
See you guys, thank you again.
The main intention of this project is to provide data for ion channel models
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:34
Every neuron/muscle consists of some ion channel that the overall current depicting how these flows shape action potentials and make a behavior such as movement
Chee Wai Lee
@cheelee
Jul 09 2015 18:34
@VahidGh awesome, thanks!
Vahid Ghayoomie
@VahidGh
Jul 09 2015 18:36
The first paper (Boyle and Cohen model) will give you some view about how a typical model of Neuron+Muscle and participating ion channels can reveal such a behavior