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cooperative_channels_in_biological_neurons_via_dynamic_clamp
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Clusters of cooperative ion channels enable a membrane potential-based mechanism for short-term memory

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Paul Pfeiffer eb7eafe50f reformat README 5 tahun lalu
metadata c1aef4e38b filtering with extended comments 5 tahun lalu
out 9b0886f9cd gin commit from paulpfeiffer 5 tahun lalu
recordings 5f9a500b14 gin commit from paulpfeiffer 5 tahun lalu
scripts 4197d0d449 automatic generation of a report 5 tahun lalu
.gitignore 9b0886f9cd gin commit from paulpfeiffer 5 tahun lalu
LICENSE f4dc51e93f Initial commit 5 tahun lalu
README.md eb7eafe50f reformat README 5 tahun lalu
datacite.yml 73ad7c893c provide datacite file to request a doi 5 tahun lalu
environment.yml 3991b7b369 added README 5 tahun lalu
makefile 3991b7b369 added README 5 tahun lalu

README.md

Clusters of cooperative ion channels enable a membrane potential-based mechanism for short-term memory

This data repository holds the dynamic clamp recordings and analysis scripts to test whether cooperative ion channels could produce persistent activity in perirhinal cortex neurons.

Overview

Recordings

Cells were recorded intracellularly and the dynamic clamp was used to emulate the presence of multiple clusters of cooperative ion channels in the membrane. Succesive current pulses were used to test for persistent activity and graded persistent activity.

Analysis

The stimulation protocols were categorized according to the number of pulses and whether the pulses were de- or hyperpolarizing. Then the firing rate between pulses was estimated to test whether the cells were persistenly active and whether the persistent firing increased (respectively decreased) with the number of applied pulses.

Structure of the repository

The repository is structured as follows

  • recordings: each folder in here corresponds to a recording session from the recording software RELACS
  • metadata: contains a mapping of cells to the above recording sessions and a manually created blacklist of protocols that are excluded from the analysis
  • scripts: python scripts to read in the recordings, analyse the firing rates and generate a report
  • out: contains the automatically generated pdf report with an overview of all cells and plots of each stimulation

How to rerun the analysis

Tested in Linux

  1. Install python dependencies e.g. via conda

    conda env create -f environment.yml

  2. Run analysis and generate the report

    make all
datacite.yml
Title Clusters of cooperative ion channels enable a membrane potential-based mechanism for short-term memory
Authors Pfeiffer,Paul;Bernstein Center for Computational Neuroscience, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 4, 10115 Berlin, Germany;ORCID:0000-0001-5324-5886
Egorov,Alexei V.;Institute of Physiology and Pathophysiology, Heidelberg University, 69120 Heidelberg, Germany
Lorenz,Franziska;Institute of Physiology and Pathophysiology, Heidelberg University, 69120 Heidelberg, Germany
Schleimer,Jan-Hendrik;Bernstein Center for Computational Neuroscience, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 4, 10115 Berlin, Germany
Draguhn,Andreas;Institute of Physiology and Pathophysiology, Heidelberg University, 69120 Heidelberg, Germany
Schreiber,Susanne;Bernstein Center for Computational Neuroscience, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 6, 10115 Berlin, Germany and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Philippstr. 13, Haus 4, 10115 Berlin, Germany
Description This data repository holds the dynamic clamp recordings and analysis scripts to test whether cooperative ion channels could produce persistent activity in perirhinal cortex neurons.
License Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References
Funding BMBF, 01GQ0901
BMBF, 01GQ1403
DFG, GRK 1589/2
SFB, SFB1134, AO1
Volkswagen Foundation, SmartStart
Keywords Neuroscience
Electrophysiology
Ion channels
Dynamic clamp
Resource Type Dataset