Download the latest release of the BiNS2 simulator
System requirements
Before starting the installation, make sure your system has the Sun/Oracle JSE Development Kit 11 or the OpenJDK 11 installed and a reachable MySQL database.
Installation
- Import the BiNS-NanoLibrary and BiNS-Simulator into your IDE
- Configure your build path, importing the BiNS-NanoLibrary package and the following jar files:
- jpct.jar
- flanagan_v6.jar
- mysql-connector-java-5.1.22-bin.jar
- Configure your MySQL Database and import the required tables (import DB_nanonetworks.sql )
- Copy the /texture folder into your /home/user
Configuration
- Edit the file config.xml into the BiNS-Simulator folder and define all simulation parameters, such as the database connection configuration, the nano objects parameters, the 3D navigation window and so on...
- It is a best practice to set an higher heap memory size in the Java Virtual Machine configuration, e.g.: -Xmx5000M -Xms5000M
- Some of the simulation parameters have to be defined in the command line and depend on the type of simulation chosen, e.g.: -simBlood or -simTCPLike.
- for the Blood Vessel simulations: -simBlood -l0 -domainStrategy1 -vmean0.00085 -ECReceptor2000
- for the TCP Like simulations: -simTCPLike -d5000 -xd78125 -yd78125 -zd78125 -burst1500 -rttth5 -alfa2 -beta0.95 -scheduled10000 -estimatorQ -sd10
- for the Continuous Emission simulations: -simTCPLike -receptorStats -paramRTT0.5 -d20000 -xd878125 -yd878125 -zd878125 -burst0 -txth100000000 -rttth5 -alfa2 -beta0 -scheduled10000 -estimatorQ -c4eRESTART -t4eNOCHANGE -enableHALVE0 -enableSTOP0 -absorbentRX0 -rejectingRX0 -RXIdle1 -receptorRandomTime
- for the MolComML configuration file: -simMolComML
(Please note that the actual version of the MolComML importer is compatible only with the Diffusion Based scenario, described by the configuration file "punctiformEmitter_xml_revised_2.3.xml" provided in the above package "BiNS2_v.17.6 MolComML integration") - for the Blood Vessel CTC simulations: -simCTCBlood -domainStrategy1 -vmean0.005 -vesselRadius30E3 -vesselLength6E6 -concRBC5000000 -concWBC7500 -concPLA250000 -timeCTC0.1 -typePLA113 -typeRBC114 -typeWBC115 -typeCTC116 -typeRXCTC117 -cellFreeLayer5800 -levelCTC1 -levelRXCTC1 -angleCTC0.5 -angleRXCTC0.5 -distanceRXCTC2E6
You may want to change these values according to your simulation needs. For a detailed explanation of these parameters, refer to our publications. A more detailed guide will be soon published here.
Run
To execute the simulation launch java -jar bins2_v.14.3.jar followed by the simulation parameters defined at points 2 and 3 on the configuration section.