c302 | generating network models in NeuroML

 by   openworm Python Version: 0.7.8 License: No License

X-RayKey FeaturesCode Snippets(2)Community Discussions(7)VulnerabilitiesInstallSupport

kandi X-RAY | c302 Summary

kandi X-RAY | c302 Summary

c302 is a Python library typically used in Utilities, Framework applications. c302 has no bugs, it has no vulnerabilities, it has build file available and it has low support. You can install using 'pip install c302' or download it from GitHub, PyPI.

c302 is a framework for generating network models in NeuroML 2 based on C. elegans connectivity data. It is primarily intended as a way to generate neuronal networks at multiple levels of detail for the OpenWorm project. To see how c302 relates to other OpenWorm subprojects click on the image below:. It uses information on the synaptic connectivity of the network (from here) and uses libNeuroML to generate a network in valid NeuroML, which can be run in jNeuroML or pyNeuroML. c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans Padraig Gleeson, David Lung, Radu Grosu, Ramin Hasani, Stephen D. Larson, Phil. Trans. R. Soc. B 2018 373 20170379; DOI: 10.1098/rstb.2017.0379.
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              c302 has a low active ecosystem.
              It has 63 star(s) with 16 fork(s). There are 18 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 13 open issues and 11 have been closed. On average issues are closed in 74 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of c302 is 0.7.8

            kandi-Quality Quality

              c302 has no bugs reported.

            kandi-Security Security

              c302 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              c302 does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              c302 releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed c302 and discovered the below as its top functions. This is intended to give you an instant insight into c302 implemented functionality, and help decide if they suit your requirements.
            • Generate a network
            • Get information about the cell
            • Add a cell to the network
            • Add a new connection to the network
            • Setup a parameterised model
            • Set the default parameters
            • Add a bioparameter object
            • Plot C302 results
            • Generate matplotlib plots
            • Generate the traces plot
            • Generates the matrix representation of the connection matrix
            • Generate c302 information for c302
            • Process command line arguments
            • Determine the case sensitivity of a neuron
            • Generate C302 plot
            • Calculate the ec syncs for a given cell
            • Reads the csv file
            • Gets the inh_syn_syn_synchronous_syn
            • Reads neuron data from csv file
            • Write a graph to a file
            • Comparitor for two files
            • Add a new sinusoidal input
            • Returns a list of elecents for the elec
            • Get the 3D positions of a 3D cell
            • Get a list of chemical projections
            • Parse a command line argument
            Get all kandi verified functions for this library.

            c302 Key Features

            No Key Features are available at this moment for c302.

            c302 Examples and Code Snippets

            The c302 modelling framework for ,Usage Examples
            Pythondot img1Lines of Code : 54dot img1no licencesLicense : No License
            copy iconCopy
               # generate 2 neurons & 1 muscle with current inputs using parameter set A
   pynml examples/LEMS_c302_A_IClamp.xml      

   # generate full scale network using parameter set C
   pynml examples/LEMS_c302_C_Full.xml    

   # generate pharynge
            The c302 modelling framework for ,To install & test
            Pythondot img2Lines of Code : 5dot img2no licencesLicense : No License
            copy iconCopy
            git clone https://github.com/openworm/c302.git
cd c302
pip install .
owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'

 ./test.sh  # or ./test3.sh if you use Python 3

            Community Discussions

            Trending Discussions on c302

            Writing binary file using in Extendscript. Incorrect file size
            What does Aggregation mean for SAT problems in SCIP?
            How to change the value of cells in a pandas?
            SVG Background image not stretching horizontally cross-browsers
            How to make a centered SVG image and text responsive?
            How do I make a certain section be completely align with each other using CSS?
            Get all record of Level 1 which has only specified number of values in Level 2

            QUESTION

            Writing binary file using in Extendscript. Incorrect file size
            Asked 2020-Aug-05 at 01:07

            Further to my question here I'm writing a list of hex colours to a binary file from within Photoshop using Extendscript. So far so good.

            Only the binary file written with the code below is 119 bytes. When cut and pasted and saved using Sublime Text 3 it's only 48 bytes, which then causes complications later on.

            This is my first time in binary land, so I may be a little lost. I suspect it's an either an encoding issue (which could explain the 2.5 file size), or doing something very wrong trying to recreate the file in a literal, character for character sense. *

            ...

            ANSWER

            Answered 2020-Aug-05 at 01:07

            I'm rubbish at JavaScript but I have hacked something together that will show you how to write 3 bytes of hex to a file in binary. I hope it is enough for you to work out how to do the rest!

            I saved this file as /Users/mark/StackOverflow/AdobeJavascript.jsx

            Source https://stackoverflow.com/questions/63173144

            QUESTION

            What does Aggregation mean for SAT problems in SCIP?
            Asked 2020-Mar-25 at 11:28

            In the SCIP Optimization Suite 6.0 paper, there is a section on Aggregation Presolver. The example given is a linear constraint with 2 variables a1x1+a2x2=b where either x1 or x2 is made the subject, then substituting it to the other constraints. I understand the logic when this is a linear program.

            However, for SAT problems, my problem file and transproblem files show the following:

            ...

            ANSWER

            Answered 2020-Mar-25 at 11:28

            (Lots of guessing as i don't know much about scip internals)

            The example

            Source https://stackoverflow.com/questions/60846555

            QUESTION

            How to change the value of cells in a pandas?
            Asked 2019-Aug-29 at 02:51

            I have a CSV that I want to edit in Pandas. He has such columns:

            ...

            ANSWER

            Answered 2019-Aug-29 at 02:51
            import pandas as pd
from io import StringIO

# sample data
df = pd.read_csv(StringIO("""
P-N,U-N,I,R,C,I-L,L-D,RS,em,D,l_1,l_2,l_3,l_4,l_5,l_6,l_7,l_8,l_9,l_10,l_11,l_12,l_13,l_14,l_15,l_16,l_17,l_18
TEXT,TEXT,https://is5-ssl.mzstatic.com/image/thumb/Podcasts123/v4/11/46/8b/11468ba5-05a1-6b61-56e8-9389416c3fed/mza_8280916651621281968.jpg/268x0w.jpg,6,TEXT,https://podcasts.apple.com/us/podcast/alav-el-pinche-podcast/id1459010039,Aug 1 2019,https://feed.podbean.com/alav/feed.xml,quinonescristian@yahoo.com,TEXT,,,,,,,,,,,,,,,,,,
TEXT,TEXT,https://is2-ssl.mzstatic.com/image/thumb/Podcasts123/v4/9c/3c/5d/9c3c5dd7-049c-0a36-51a5-146a6b67c032/mza_2227232542399366991.png/268x0w.jpg,22,TEXT,https://podcasts.apple.com/us/podcast/couple-goals-with-s-m/id1354222194,18 Aug 2019,https://couplegoals.podbean.com/feed.xml,No email,TEXT,,,,,,,,,,,,,,,,,,
TEXT,TEXT,https://is4-ssl.mzstatic.com/image/thumb/Podcasts123/v4/19/99/2a/19992a8a-c302-6416-27d2-78d4a751ff2d/mza_8707044730009010204.jpg/268x0w.jpg,1053,TEXT,https://podcasts.apple.com/us/podcast/all-crime-no-cattle/id1327729036,Jul 26 2019,https://www.spreaker.com/show/3202978/episodes/feed,allcrimenocattle@gmail.com,TEXT",https://podcasts.apple.com/us/podcast/id1207505792,https://podcasts.apple.com/us/podcast/id1298179135,https://podcasts.apple.com/us/podcast/id1255329049,https://podcasts.apple.com/us/podcast/id1256792057,https://podcasts.apple.com/us/podcast/id1250294822,https://podcasts.apple.com/us/podcast/id1317929691,https://podcasts.apple.com/us/podcast/id1328036628,https://podcasts.apple.com/us/podcast/id1244309070,https://podcasts.apple.com/us/podcast/id1377988275,https://podcasts.apple.com/us/podcast/id1214679007,https://podcasts.apple.com/us/podcast/id1166399817,https://podcasts.apple.com/us/podcast/id1242028887,https://podcasts.apple.com/us/podcast/id1184429621,https://podcasts.apple.com/us/podcast/id1289005078,https://podcasts.apple.com/us/podcast/id1396717244,https://podcasts.apple.com/us/podcast/id1259478351,https://podcasts.apple.com/us/podcast/id1295887970,https://podcasts.apple.com/us/podcast/id1278924392
TEXT,TEXT,https://is2-ssl.mzstatic.com/image/thumb/Podcasts123/v4/30/b6/46/30b6469c-0e15-e3d3-4063-6207d8020824/mza_1356338398462313394.jpg/268x0w.jpg,1186,TEXT,https://podcasts.apple.com/us/podcast/extraterrestrial/id1449220604,Aug 13 2019,https://feeds.megaphone.fm/extraterrestrial,support@parcast.com,TEXT,https://podcasts.apple.com/us/podcast/id1156724104,https://podcasts.apple.com/us/podcast/id1441968144,https://podcasts.apple.com/us/podcast/id1441824608,https://podcasts.apple.com/us/podcast/id1449997236,https://podcasts.apple.com/us/podcast/id1440306805,https://podcasts.apple.com/us/podcast/id1434465245,https://podcasts.apple.com/us/podcast/id1437682381,https://podcasts.applcom/us/podcast/id1441348407,https://podcasts.apple.com/us/podcast/id1449762156,https://podcasts.apple.com/us/podcast/id1438804143,https://podcasts.apple.com/us/podcast/id1440107092,https://podcasts.apple.com/us/podcast/id1454411295,https://podcasts.apple.com/us/podcast/id1449191242,https://podcasts.apple.com/us/podcast/id1094490100,https://podcasts.apple.com/us/podcast/id1450027383,https://podcasts.apple.com/us/podcast/id1294529191,https://podcasts.apple.com/us/podcast/id1197087242,https://podcasts.apple.com/us/podcast/id1468956772
TEXT,TEXT,https://is3-ssl.mzstatic.com/image/thumb/Podcasts123/v4/06/9e/c7/069ec760-12cb-fdef-4b28-ac96cc649f3f/mza_1930766855883297019.jpg/268x0w.jpg,No rating,TEXT,https://podcasts.apple.com/us/podcast/another-dead-man-walking/id1449476437,Nov 7 2018,https://www.spreaker.com/show/3287452/episodes/feed,radio@sky.uk,TEXT,https://podcasts.apple.com/us/podcast/id1448403218,https://podcasts.apple.com/us/podcast/id1453587264,https://podcasts.apple.com/us/podcast/id1453829416,https://podcasts.apple.com/us/podcast/id1435009373,https://podcasts.apple.com/us/podcast/id1462249765,https://podcasts.apple.com/us/podcast/id1448205703,https://podcasts.apple.com/us/podcast/id1458485904,https://podcasts.apple.com/us/podcast/id1451783176,https://podcasts.apple.com/us/podcast/id1436485458,https://podcasts.apple.com/us/podcast/id1462332471,https://podcasts.apple.com/us/podcast/id1447656582,https://podcasts.apple.com/us/podcast/id1447037392,https://podcasts.apple.com/us/podcast/id1459952501,https://podcasts.apple.com/us/podcast/id1458931325,https://podcasts.apple.com/us/podcast/id1448556563,https://podcasts.apple.com/us/podcast/id1409087641,https://podcasts.apple.com/us/podcast/id1400426755,https://podcasts.apple.com/us/podcast/id1462323616
"""))

# A function for splitting at last "/'
# with safety for null (NaN) values
def splitter(s):
    if isinstance(s, str):
        return s.split("/")[-1]
    else:
        return s

# apply the splitter to each column
cols = ["I-L"] + [f"l_{ln}" for ln in range(1, 19)]
for col in cols:
    df[col] = df[col].apply(splitter)

# print a few
print(df[["I-L", "l_1", "l_2", "l_18"]])

#             I-L           l_1           l_2          l_18
# 0  id1459010039           NaN           NaN           NaN
# 1  id1354222194           NaN           NaN           NaN
# 2  id1327729036  id1207505792  id1298179135  id1278924392
# 3  id1449220604  id1156724104  id1441968144  id1468956772
# 4  id1449476437  id1448403218  id1453587264  id1462323616

            Source https://stackoverflow.com/questions/57699291

            QUESTION

            SVG Background image not stretching horizontally cross-browsers
            Asked 2019-Jul-14 at 09:40

            I've been trying to place an SVG image as the background on a button to stretch horizontally whilst ignoring its aspect ratio.

            Changes made to the SVG (pasted below) itself:

            1. Doesn't have a height/width specified
            2. Has a viewbox specified
            3. Has preserveAspectRatio set to none

            On the button CSS, I have set the background-size to contain as cover cuts off the image really badly. (Tried all variants, cover/contain/100%, etc.)

            The issue I'm having is in chrome/internet explorer it works, the top/bottom of the SVG don't get clipped and the image will stretch the entire button width not preserving the aspect ratio however in Firefox it's behaving differently. With contain it will not cut the image off but it won't stretch horizontally (left to right).

            I've even tried to modify the viewport attribute of the image to trick it into thinking that the SVG starts in a negative x-axis and ends on a few pixels after however the cutting off is so bad that it doesn't really help.

            ...

            ANSWER

            Answered 2019-Jul-12 at 16:50

            In my FF browser, it works if you change background-size: 100% to background-size: 100% 100%. This property takes two arguments, width and height, and sets height to auto if not provided. I guess that, depending on the version, you may need to set -moz-background-size.

            Source https://stackoverflow.com/questions/56970084

            QUESTION

            How to make a centered SVG image and text responsive?
            Asked 2019-Jul-04 at 22:08

            I'm looking for a way to make responsive a SVG image and a text above it, that are centered in the page. The solution posted here doesn't work in my case.

            Here is my code:

            ...

            ANSWER

            Answered 2019-Jul-04 at 15:05

            Consider using viewport-related sizing units, in this case vw:

            Source https://stackoverflow.com/questions/56890448

            QUESTION

            How do I make a certain section be completely align with each other using CSS?
            Asked 2018-Sep-19 at 21:15

            I am trying to recreate this graphic by scratch using css, html and javascript thinking in terms of mobile first. This is the original :

            This is my version

            The part where I am stuck is aligning the key specs perfectly in both mobile and 1024px size. But I'm not having any luck. I am using flexbox, and I was thinking of using the direction as a way but I don't know where I should you a container div or what. I don't want to use a framework like Bootstrap. I need to do this by scratch. Can you please me ? Thank you so much

            ...

            ANSWER

            Answered 2018-Sep-19 at 21:15

            There are a few ways to achieve this.

            Static

            The easiest, but most fragile way would be to wrap the top section in a

            determine the height of the tallest box, and set that as the min-height in CSS. But this runs into maintainability issues if the text is too long, or the boxes adjust width on different screen sizes.

            HTML

            Source https://stackoverflow.com/questions/52412032

            QUESTION

            Get all record of Level 1 which has only specified number of values in Level 2
            Asked 2017-Jun-23 at 05:47
             level1 | level2  |level3 
--------|---------|--------
 A100   | NULL    | NULL
 A101   | B200    | C300
 A101   | B200    | C301
 A101   | B200    | C302
 A101   | B201    | C310
 A102   | B209    | NULL
 A103   | B211    | NULL
 A103   | B213    | NULL
 A103   | B214    | NULL
 A104   | B240    | NULL
            ...

            ANSWER

            Answered 2017-Jun-22 at 21:46

            Join the table with a subquery that counts the number of rows for the parent, and only select the ones with the count you want.

            Source https://stackoverflow.com/questions/44709222

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install c302

            The full set of dependencies for c302 can be installed with the following (see also the Travis-CI script):. This will install c302 as well as all dependencies, including pyNeuroML and owmeta.
            Regenerate the NeuroML & LEMS files for one instance of the model: python c302/c302_Pharyngeal.py B # generate pharyngeal network (see fig. above) using parameter set B
            Run a simulation with pyNeuroML: pynml examples/LEMS_c302_B_Pharyngeal.xml

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
            Find more information at:

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            Install
          • PyPI

            pip install c302

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            https://github.com/openworm/c302.git

          • CLI

            gh repo clone openworm/c302

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            git@github.com:openworm/c302.git

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