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How to Use FlyBrainLab Full Installation

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Yiyin Zhou edited this page Feb 21, 2021 · 2 revisions

The instructions on this page apply to FlyBrainLab Full Installation (using default configuration) as well as the Docker Image.

Content

The full installation contains the following two folders:

  • ffbo: main application folder that contains the executable scripts and repositories.
  • orientdb: OrientDB folder where the databases are stored.

It also creates the following two conda environments:

  • ffbo: main environment with Python 3.7 for running FlyBrainLab application.
  • ffbo_legacy: environment with Python 2.7 for running NLP server.

Configuration folder:

  • ~/.ffbo

Executable Scripts

We provide a set of scripts in ~/ffbo/bin to help launching FlyBrainLab.

  • start.sh: start FlyBrainLab, including starting all backend servers, each in a tmux session.
  • shutdown.sh: stop FlyBrainLab and all backend servers, the tmux sessions will be killed.
  • update.sh: update all packages to the latest version (except for NeuroMynerva).
  • update_NeuroMynerva.sh: update NeuroMynerva.

Scripts for running individual server components:

  • run_processor.sh: start crossbar and FFBO processor.
  • run_nlp.sh: start NeuroNLP server.
  • run_database.sh: start OrientDB database.
  • run_neuroarch.sh: start NeuroArch server.
  • run_neurokernel.sh: start Neurokernel server.
  • run_fbl.sh: start FlyBrainLab.
  • download_datasets.sh: download some or all datasets.

Starting the FlyBrainLab

To start FlyBrainLab, run

ffbo/bin/start.sh

This will start the JupyterLab and in the background the following tmux sessions:

  • db: Runs the OrientDB Database,
  • processor: Runs the Processor (ffbo/bin/run_processor.sh)
  • nlp_hemibrain: Runs the NLP server for the Hemibrain dataset (ffbo/bin/run_nlp.sh hemibrain)
  • nlp_flycircuit: Runs the NLP server for the FlyCircuit dataset (ffbo/bin/run_nlp.sh flycircuit)
  • nlp_l1em: Runs the NLP server for the L1EM dataset (ffbo/bin/run_nlp.sh l1em)
  • na_hemibrain: Runs the NeuroArch server for the Hemibrain dataset (ffbo/bin/run_neuroarch.sh hemibrain)
  • na_flycircuit: Runs the NeuroArch server for the FlyCircuit dataset (ffbo/bin/run_neuroarch.sh flycircuit)
  • na_l1em: Runs the NeuroArch server for the L1EM dataset (ffbo/bin/run_neuroarch.sh l1em)

If any of the tmux session is missing, the program may have crashed. Please start a new tmux session and run the script associated with each session above.

To fully shutdown the FlyBrainLab application, after quitting JupyterLab, run

ffbo/bin/shutdown.sh
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