Author Archives: Mikkel Lepperød

Mikkel Lepperød

About Mikkel Lepperød

I have a background in environmental physics and applied mathematics from the Norwegian University of Life Sciences (NMBU).

My research interests  are within computational and experimental neuroscience.

Add ssh key (Git)

Open a terminal

ssh-keygen

Press enter if you don’t want to change filename

Write a passphrase (optional)

cat ~/.ssh/id_rsa.pub

Copy output

Go to github.com account > settings
Select ssh keys on left side, select add ssh key
Write name of key and paste key from terminal

Select ssh when you want to copy the “clone adress”.
Enter previously passphrase and select “remember”.

To change an existing https key do:

git remote set-url origin SSH_ADDRESS

Install neo++ in a virtual environment

sudo apt-get install virtualenvwrapper python-pyqt4
mkvirtualenv NEO --system-site-packages
workon NEO

Then copy the following into a bashfile and run it – bash bashfile

#!/bin/bash
# Install script
set -x  # make sure each command is printed in the terminal

function pip_install {
  pip install --upgrade "$@"
  if [ $? -ne 0 ]; then
    echo "could not install $p - abort"
    exit 1
  fi
}

pip_install cython
pip_install h5py==2.5.0
pip_install tables
pip_install sqlalchemy
pip_install sqlalchemy-migrate
pip_install scikit-learn
pip_install pywavelets

git clone https://github.com/NeuralEnsemble/elephant.git
git clone https://github.com/OpenElectrophy/OpenElectrophy.git
git clone https://github.com/rproepp/spykeviewer.git
git clone https://github.com/rproepp/spykeutils.git
git clone https://github.com/jzaremba/guidata.git
git clone https://github.com/PierreRaybaut/guiqwt.git

cd guidata && python setup.py install
cd ..
cd guiqwt && python setup.py build install
cd ..
cd python-neo && python setup.py develop
cd ..
cd spykeutils && python setup.py develop
cd ..
cd spykeviewer && python setup.py develop
cd ..
cd OpenElectrophy && python setup.py develop
cd ..
cd elephant && python setup.py develop

Install klustakwik and klustaviewa on ubuntu

Note that this project is being replaced by phy

First of all you need the right dependencies, its easiest to do with anaconda – make a virtual environment!

cd into your preferred directory e.g. $HOME/apps/ in this example, clone the necessary repos, make symlink and install.

git clone https://github.com/klusta-team/klustaviewa.git
git clone https://github.com/rossant/qtools
git clone https://github.com/rossant/galry
git clone https://github.com/klusta-team/spikedetekt
git clone https://github.com/klusta-team/kwiklib
git clone https://github.com/klusta-team/klustakwik.git 

cd klustaviewa

ln -s ../qtools/qtools qtools
ln -s ../galry/galry galry
ln -s ../spikedetekt2/spikedetekt2 spikedetekt2
ln -s ../kwiklib/kwiklib kwiklib

python setup.py develop

make klustakwik and rename the executable

cd $HOME/apps/klustakwik
make 
mv KlustaKwik klustakwik

export path in your ~/.bashrc file

export PATH=$HOME/apps/klustakwik/:$PATH

Download test data (.zip) and change params.prm to this file cd to example dir and enter

klusta params.par