BVS-Bio: An ns-3 Extension of BloodVoyager Simulator For Exploring Intra-Body Nano-Communication in Human Cardiovascular System

Introduction

Existing codes: https://github.com/RegineWendt/blood-voyager-s Regine Wendt <wendt@itm.uni-luebeck.de> v1.1, 2019-04-24

BVS is a ns-3 module that simulates the global movement of nanobots in the human body. It features a simplified model of a human body’s cardiovascular system to simulate the nanobots’ mobility.

Laurenz Ebner <ebnerlaurenz@gmail.com> v2.1, 2024-02-12

BVS v2.1 introduces the possibility to model the communication channel, between the nanobots and the gateways, which would in real apllications be situated at the skin level and is in simulation a synthetic data generator for database usage. The mobility model is left unchanged, but we added multiple modules to measure, transmit and receive data.

To enhance the realism of existing BVS, BVS-Bio introduces multiple classes to integrate the source of infection, release biomarkers from the infection, and mobility of the biomarkers. The modules also enable communication between biomarkers and on-body gateways through a network device. It further facilitates interactions with nanobots.

LocateInfectionSource Method:

• Simulates the release of biomarkers from an infection source within a blood vessel

• Triggers initial biomarker release and schedules continuous releases at 1-second intervals during the simulation.

releaseBiomarkers Method:

• Handles the generation and distribution of biomarkers in the bloodstream

• Creates a BiomarkerChannel for communication between biomarkers and nanobots.

Biomarker Class:

• Models biomarker entities, managing their properties, behaviors, and interactions within the BVS.

• Manages the lifecycle, positioning, and network communication of biomarkers using BiomarkerNetDevice.

Bloodstream Class:

• Manages a collection of biomarkers within the bloodstream.

• Provides methods to add, remove, and count biomarkers.

BiomarkerChannel Class:

• Manages communication between biomarkers and nanobots within a blood vessel.

• Handles the transmission of data packets from biomarkers to nanobots using NanoNetDevice.

• Facilitates the detection of nanobots within range and ensures correct data exchange.

BiomarkerNetDevice Class:

• Implements a network device to enable communication between biomarkers and nanobots.

• Associates biomarkers with communication channels and manages data packet transmission.

• Verifies biomarker associations and manages network addresses and channels.

PrintBiomarkers Class:

• Logs biomarkers detected at the gateways positioned at various body locations (heart, left arm, right arm, left hip, right hip).

• Tracks biomarkers' positions and stream IDs over time, outputting data to CSV files for analysis.

Existing parameters

• tissue thickness

• Size of symbols of one transmitted package: TESTPACKETSIZE 200

• transmission frequency: FREQ_THZ 0.5*10^12

• initial distance between nanobot and gateway: DIST_INIT 850*10^-6

• initial thickness of skin: SKIN_THICKNESS 76*10^-6

• initial thickness of blood vessel: VESSEL_THICKNESS 200*10^-6

• initial transmit power: POWER 4*10^3

• structure of output packet: — struct MAC_PHY_DATA

  int nanobot_ID; // ID of nanobot

  int tissue_ID; // ID of body part where to measure

  vector<int> PDU_TX; // Bit stream of measurement data at nanobot

  vector<double> SEQ_TX; // Amplitude stream of measurement data send at nanobot

  vector<double> SEQ_RX; // Amplitude stream of measurement data received at gateway

  vector<int> PDU_RX; // decoded bit stream of measurement data at gateway

• Number of nanobots m_numberOfNanobots

• Injection vessel m_injectionVessel [1-94]

• Simulation duration in seconds m_simulationDuration

• Duration between each simulation step m_deltaT

• Velocities: m_arteryVelocity = 10 cm/s, m_veinVelocity = 3,7 cm/s, m_organVelocity = 1cm/s

• Number of streams m_numberOfStreams [1-5]

Class overview

Figure 1. Process diagram of test-blood-voyager-s

Tutorial/Get started

Advised setup working with this code:

Windows: Visual Studio Code and WSL
Mac: Visual Studio Code
Linux: Visual Studio Code

Detailed setup description:

install visual studio code
install Ubuntu 22.04.3 LTS
(optional) open Turn Windows features on or off, checkmark windows subsystems for linux, restart the PC
(optional) update the kernel component at https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi
(optional) open Turn Windows features on or off, and activate Virtual Machine Platform Windows

Open Ubuntu 22.04.3 LTS and create and UNIX user in the prompt
in the WSL terminal run the code

install ns-3 with the commands following: (https://www.nsnam.com/2022/06/ns3-installation-in-ubuntu-2204.html, 4.3. Downloading ns-3 using Git in https://www.nsnam.org/docs/tutorial/html/getting-started.html#downloading-ns-3-using-git)

sudo apt update

sudo apt upgrade

sudo apt install g++ python3 python3-dev pkg-config sqlite3 cmake python3-setuptools git qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools gir1.2-goocanvas-2.0 python3-gi python3-gi-cairo python3-pygraphviz gir1.2-gtk-3.0 ipython3 openmpi-bin openmpi-common openmpi-doc libopenmpi-dev autoconf cvs bzr unrar gsl-bin libgsl-dev libgslcblas0 wireshark tcpdump sqlite sqlite3 libsqlite3-dev  libxml2 libxml2-dev libc6-dev libc6-dev-i386 libclang-dev llvm-dev automake python3-pip libxml2 libxml2-dev libboost-all-dev

wget https://www.nsnam.org/releases/ns-allinone-3.36.1.tar.bz2

tar jxvf ns-allinone-3.36.1.tar.bz2

cd ns-allinone-3.36.1/

./build.py --enable-examples --enable-tests

cd ns-3.36.1/

./ns3 run hello-simulator

Copy the BVS+Comm project and extract in \wsl.localhost\Ubuntu-22.04\home\jorge\ns-allinone-3.36.1\ns-3.36.1\src

Rename the folder with blood-voyager-s

Copy the "vasculature.csv" to \wsl.localhost\Ubuntu-22.04\home\jorge\ns-allinone-3.36.1\ns-3.36.1
The csv file is accesible in https://github.com/RegineWendt/blood-voyager-s/tree/master

for linking to Visual Studio run the command (code .) in the WSL terminal

When Visual Studio Opens, just install the add-on (WSL) that appears in the bottom corner window
In Visual Studio go to extentions (icon in the bar at left bar) and install C/C++

WSL installed a Linux partition in the PC

Open the terminal in Visual Studio in the tab View/Terminal
In the Visual studio terminal run the code

./ns3 clean
./ns3 configure --enable-examples --enable-tests
./ns3 configure start-bvs --enable-examples --enable-tests
./ns3 build start-bvs

whenever you update the code you run the code
./ns3 build start-bvs

For running BVS
./ns3 run start-bvs

The code can be accessed in explorer button and navigate to the main file in /home/jorge/ns-allinone-3.36.1/ns-3.36.1/src/blood-voyager-s/examples/start-blood-voyager-s.cc

Always Open Visual studio from the WSL terminal with the running (code .)

You’ve already installed ns-3.40

Take the blood-voyager-s version for ns-3.40 and copy the bvs folder in the !!!source location /src!!! of your ns3 version.

You’re new to ns-3

You need to download the complete ns-3.40(or newer) and follow the instructions in this ns-3 tutorial. Then you download the blood-voyager-s folder from here and put it in the src folder. In addition, you need to put the vasculature.csv in your ns-3.x folder. For further instructions see "Run BVS".

Run BVS Version ns-3.40 or newer

   SIMDURATION=   # simulation duration in seconds (default 500)
   NUMOFNANOBOTS= # number of nanobots (default 100)
   INJECTVESSEL=  # injection vessel [1-94] (default 29)
TYPEOFSIMULATION= # 0 is single run and 1 is sweep over vesselthickness (default 0)
GATEWAYPOSITION= # gateway position [1-94] (default 1)
TISSUE_ID = # tissue position, where to measure data [1-94] (default 94)

./ns3 run "start-bvs --simulationDuration=SIMDURATION, --numOfNanobots=NUMOFNANOBOTS, --injectionVessel=INJECTVESSEL, --typeofsimulation=TYPEOFSIMULATION, --gatewayposition=GATEWAYPOSITION, --tissue_ID=TISSUE_ID"
   or with default values
   ./ns3 run start-bvs

The simulation returns: - a csv-file (/ns-3.40/csvNano.csv) with the position data of the simulated nanobots in every timestep. - a csv-file (/ns-3.40/gateway.csv) with the transmitted data of the simulated nanobots. - a csv-file (/ns-3.40/gateway_ber.csv) with the calcualted ber and per of the simulated nanobots.

Appendix: Model