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Attenuation of Post-Synaptic Potentials in a Passive Dendrite

In this repository we collect code which allows to define a passive chain of compartments for experiments on BrainScaleS-2 as well as simulations in Arbor. It furthermore provides code to classify the attenuation of excitatory post-synaptic potentials along the chain of compartments and visualize these results.

How to build

Build- and runtime dependencies

All build- and runtime dependencies are encapsulated in a Singularity Container. If you want to build this project outside the Electronic Vision(s) cluster, please start by downloading the most recent version from here.

For all following steps, we assume that the most recent Singularity container is located at /containers/stable/latest – you are free to choose any other path.

Github-based build

To build this project from public resources, adhere to the following guide:

# 1) Most of the following steps will be executed within a singularity container
#    To keep the steps clutter-free, we start by defining an alias
shopt -s expand_aliases
alias c="singularity exec --app dls /containers/stable/latest"

# 2) Add the cross-compiler and toolchain for the embedded processor to your environment
#    If you don't have access to the module, you may build it as noted here:
#    https://github.com/electronicvisions/oppulance
module load ppu-toolchain

# 2) Prepare a fresh workspace and change directory into it
mkdir workspace && cd workspace

# 3) Fetch a current copy of the symwaf2ic build tool
git clone https://github.com/electronicvisions/waf -b symwaf2ic symwaf2ic

# 4) Build symwaf2ic
c make -C symwaf2ic
ln -s symwaf2ic/waf

# 5) Setup your workspace and clone all dependencies (--clone-depth=1 to skip history)
c ./waf setup --repo-db-url=https://github.com/electronicvisions/projects --project=model-hw-mc-attenuation

# 6) Build the project
#    Adjust -j1 to your own needs, beware that high parallelism will increase memory consumption!
c ./waf configure
c ./waf build -j1

# 7) Install the project to ./bin and ./lib
c ./waf install

# 8) If you run programs outside waf, you'll need to add ./lib and ./bin to your path specifications
export SINGULARITYENV_PREPEND_PATH=`pwd`/bin:$SINGULARITYENV_PREPEND_PATH
export SINGULARITYENV_LD_LIBRARY_PATH=`pwd`/lib:$SINGULARITYENV_LD_LIBRARY_PATH
export LD_LIBRARY_PATH=`pwd`/lib:$LD_LIBRARY_PATH
export PYTHONPATH=`pwd`/lib:$PYTHONPATH
export PATH=`pwd`/bin:$PATH

On the Electronic Vision(s) Cluster

  • Work on the frontend machine, helvetica. You should have received instructions how to connect to it.
  • Follow aforementioned instructions with the following simplifications
    • Replace steps 3) and 4) by module load waf
    • Make sure to run step 6) within a respective slurm allocation: Prefix srun -p compile -c8; depending on your shell, you might need to roll out the c-alias.
    • Replace step 8) by module load localdir.

Build from internal sources

If you have access to the internal Gerrit server, you may drop the --repo-db-url-specification in step 5) of aforementioned instructions.

Acknowledgment

The software in this repository has been developed by staff and students of Heidelberg University as part of the research carried out by the Electronic Vision(s) group at the Kirchhoff-Institute for Physics. The research is funded by Heidelberg University, the State of Baden-Württemberg, the European Union Sixth Framework Programme no. 15879 (FACETS), the Seventh Framework Programme under grant agreements no 604102 (HBP), 269921 (BrainScaleS), 243914 (Brain-i-Nets), the Horizon 2020 Framework Programme under grant agreement 720270, 785907, 945539 (HBP) as well as from the Manfred Stärk Foundation.

License

PSP attenuation along passive dendrite ('model_hw_mc_attenuation')
Copyright (C) 2023–2023 Electronic Vision(s) Group
                        Kirchhoff-Institute for Physics
                        Ruprecht-Karls-Universität Heidelberg
                        69120 Heidelberg
                        Germany

This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
USA