Bioemus - IBEA

Bioemus version compatible with Indicator-Based Evolutionary Algorithm (IBEA) to be installed on FPGA.

WARNING: this code is different from the original one published Nature Communication, which is instead available on this github url. It contains major changes in the configuration files (the "rat brain" model) and the possibility to stimulate from an output pin of the board (several changes in the code regarding bioemus-genoa). This repository can be cloned inside a new board and used to run locally the IBEA algorithm, directly on the Ubuntu onboard Processing System.

Installation

1. Setup ubuntu 22.04 operating system for Kria

Follow the instructions at this link to install Ubuntu on the board (by flashing it in the microSD).

2. Connect via SSH

• Connect USB serial (1) to PC (USB micro B).
• Communicate with the board using Putty (Windows) or Minicom (macOS/Linux).
• After inserting the password, check the IP address with the ifconfig command (it should be under eth0 or eth1, next the inet: word).
• Close the terminal and disconnect the USB cable.
• Connection via SSH ssh ubuntu@[IPaddress]

3. Setup the system to work with Bioemus

• Update system

sudo apt-get update && sudo apt upgrade
sudo reboot now

On Kria™ KR260 the boot time can be quite long (~180 seconds) from the TPM self test message.

• Install Xilinx Development Tools package

# Ubuntu 22.04
sudo snap install xlnx-config --classic --channel=2.x
# Initialize xilinx config package
xlnx-config.sysinit
# Bootgen
sudo apt install bootgen-xlnx

• Install BioemuS dependencies

# ZeroMQ
sudo apt install libzmq3-dev
# Python
sudo apt install python3-pip python3-pyqt5

• (optional, install Ubuntu Software)

sudo snap install snap-store

• (optional, utilities)

sudo apt install net-tools
sudo apt install devmem2

4. Clone this repository

Clone this repository on the board at ~/. The folder should be renamed "bioemus".

git clone https://github.com/barbaLab/bioemus-ibea.git bioemus

Build the drivers to work properly

cd bioemus
source ./build.sh

Usage

Creating and launching a simulation

1. Configure the network using the mainIBEA.ipynb notebook. By running, it should generate a .json and a .txt files in the config/ folder.
2. Call the bash script to begin the simulation:

source init.sh
source ./launch_app ./config/[json_file.json]

This runs the simulation and produce a .bin file within the folder data, containing the raster plot of the simulation.

Running IBEA algorithm

1. To run the IBEA algorithm directly within the ubuntu onboard system you have first to setup the python venv IBEAvenv by running on bash:

source setup_IBEA_venv.sh
source IBEAvenv/bin/activate

2. Configure and run the IBEA algorithm from the mainIBEA script. I suggest to open the folder with the Remote-SSH extension in vscode for better usability (from the host PC this extension will automatically install vscode on the board). Use the python kernel IBEAvenv to run the notebook.