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added README

Paul Pfeiffer 1 year ago
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commit
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  1. 34 0
      README.md
  2. 82 0
      environment.yml
  3. 1 1
      makefile

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README.md

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+# 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 patchclamped 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 recordings with increasing (respectively decreasing) levels of persistent activity were labelled as successful trials. 
+
+### 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](http://relacs.sourceforge.net/index.html)
+- `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
+   
+   ```bash
+   conda env create -f environment.yml 
+   ```
+2. Run analysis and generate the report
+
+   ```bash
+   make all 
+   ```

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environment.yml

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+name: cooperative_channels_analysis
+channels:
+  - defaults
+  - conda-forge
+  - ostrokach-forge
+  - pkgw-forge
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - backports=1.0=py_2
+  - backports.functools_lru_cache=1.5=py_2
+  - backports_abc=0.5=py_0
+  - blas=1.0=mkl
+  - ca-certificates=2019.5.15=0
+  - certifi=2019.6.16=py27_0
+  - cycler=0.10.0=py27_0
+  - dbus=1.13.6=h746ee38_0
+  - expat=2.2.6=he6710b0_0
+  - fontconfig=2.13.0=h9420a91_0
+  - freetype=2.9.1=h8a8886c_1
+  - functools32=3.2.3.2=py27_1
+  - futures=3.3.0=py27_0
+  - glib=2.56.2=hd408876_0
+  - gst-plugins-base=1.14.0=hbbd80ab_1
+  - gstreamer=1.14.0=hb453b48_1
+  - icu=58.2=h9c2bf20_1
+  - intel-openmp=2019.4=243
+  - jinja2=2.10.1=py27_0
+  - jpeg=9b=h024ee3a_2
+  - kiwisolver=1.1.0=py27he6710b0_0
+  - libedit=3.1.20181209=hc058e9b_0
+  - libffi=3.2.1=hd88cf55_4
+  - libgcc-ng=9.1.0=hdf63c60_0
+  - libgfortran-ng=7.3.0=hdf63c60_0
+  - libpng=1.6.37=hbc83047_0
+  - libstdcxx-ng=9.1.0=hdf63c60_0
+  - libuuid=1.0.3=h1bed415_2
+  - libxcb=1.13=h1bed415_1
+  - libxml2=2.9.9=hea5a465_1
+  - markupsafe=1.1.1=py27h7b6447c_0
+  - matplotlib=2.2.3=py27hb69df0a_0
+  - mkl=2019.4=243
+  - mkl_fft=1.0.12=py27ha843d7b_0
+  - mkl_random=1.0.2=py27hd81dba3_0
+  - ncurses=6.1=he6710b0_1
+  - numpy=1.16.4=py27h7e9f1db_0
+  - numpy-base=1.16.4=py27hde5b4d6_0
+  - openssl=1.1.1c=h7b6447c_1
+  - pandas=0.24.2=py27he6710b0_0
+  - pcre=8.43=he6710b0_0
+  - pip=19.1.1=py27_0
+  - pyparsing=2.4.0=py_0
+  - pyqt=5.9.2=py27h05f1152_2
+  - python=2.7.16=h9bab390_0
+  - python-dateutil=2.8.0=py27_0
+  - pytz=2019.1=py_0
+  - qt=5.9.7=h5867ecd_1
+  - readline=7.0=h7b6447c_5
+  - scipy=1.2.1=py27h7c811a0_0
+  - setuptools=41.0.1=py27_0
+  - singledispatch=3.4.0.3=py27h9bcb476_0
+  - sip=4.19.8=py27hf484d3e_0
+  - six=1.12.0=py27_0
+  - sqlite=3.29.0=h7b6447c_0
+  - subprocess32=3.5.4=py27h7b6447c_0
+  - tk=8.6.8=hbc83047_0
+  - tornado=5.1.1=py27h7b6447c_0
+  - wheel=0.33.4=py27_0
+  - xz=5.2.4=h14c3975_4
+  - zlib=1.2.11=h7b6447c_3
+  - pip:
+    - cairocffi==0.9.0
+    - cairosvg==1.0.22
+    - cffi==1.12.3
+    - cssselect2==0.2.1
+    - html5lib==1.0.1
+    - pdfrw==0.4
+    - pycparser==2.19
+    - pyphen==0.9.5
+    - tinycss2==0.6.1
+    - weasyprint==0.42.3
+    - webencodings==0.5.1
+

+ 1 - 1
makefile

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-all: prepare_folder_structure extract_stimulations assign_protocols filter analyse_firing_rates analyse_persistent_activity plot_traces report
+all: clean prepare_folder_structure extract_stimulations assign_protocols filter analyse_firing_rates analyse_persistent_activity plot_traces plot_firing_rates report
 
 prepare_folder_structure:
 	python scripts/check_folder_structure.py