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https://github.com/alleninstitute/ateam-tools

Shared model-based simulation and analysis tools (ranging from single-neuron to networks) as well as more general model/experiment analysis software (ephys, morphology, transcriptomics) of the Anastassiou team at the Allen Institute for Brain Science.

https://github.com/alleninstitute/ateam-tools

Science Score: 13.0%

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Shared model-based simulation and analysis tools (ranging from single-neuron to networks) as well as more general model/experiment analysis software (ephys, morphology, transcriptomics) of the Anastassiou team at the Allen Institute for Brain Science.

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 11.4 MB
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  • Watchers: 3
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Created over 7 years ago · Last pushed over 4 years ago
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README.md

ateam-tools

Shared modeling and analysis tools for internal use by the Anastassiou research team

For active development, install via pip install -e <path> or setup.py develop.

For much of the functionality to work, you will need the ateam branch of BMTK, at https://github.com/tmchartrand/bmtk.git.

Package organization and directory structure

ateam-tools ├── ateam: base directory for python code files, organized by function | ├── analysis | ├── sim | ├── ...etc ├── examples: scripts or notebooks that demonstrate use of our tools, organized by application | ├── subfolders organized by project or topic ├── scripts: tools for running analyses from the command line Some organizing principles: - Don't duplicate or copy and paste code! (Make a function instead.) - Code that has distinct functions (sim vs analysis) or distinct sets of dependencies (BMTK vs aiephys analysis) should be grouped in separate folders. (These distinctions tend to go together.) - Try to minimize new folders (packages), but generally keep your code in your own modules (.py files) - Try to minimize new dependencies if possible. If you must use a new package, try to separate code that needs it from code that doesn't into different modules.

Shared Conda environment for BMTK and NEURON

In order to have a stable, reproducible platform for testing and running simulations, we have created a standalone installation of the ateam-tools, BMTK, and NEURON software stack. The installation is packaged as a conda environment, and automatically configures the necessary paths for running NEURON when activated.

Setup of bmtk_ateam Conda environment

Simply run the shell script /allen/aibs/mat/ateam_shared/software/add_shared_conda.sh to add this shared conda environment to your local install of conda/miniconda.

Using the bmtk_ateam Conda environment

Following setup, simply call conda activate bmtk_ateam or source activate bmtk_ateam to activate the environment and use.

The environment also contains a full jupyter notebook server, so the jupyter notebook command will start a server running the shared environment. Alternatively, you may want to use a jupyter plugin to allow jupyter to access and switch between multiple conda environments:

nbcondakernels (https://docs.anaconda.com/anaconda/user-guide/tasks/use-jupyter-notebook-extensions/)

or jupyterenvironmentkernels (https://github.com/Cadair/jupyterenvironmentkernels)

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

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