Biological Nanoscale Simulator (BiNS2)

Download the latest release of the BiNS2 simulator

 

BiNS2_v.14.3 (executable) (last update: March 2014)
BiNS2_v.15.4 beta version (source files)  (last update: April 2015)
BiNS2_v.15.7 Continuous Emission (source files)  (last update: July 2016)
BiNS2_v.15.7 Continuous Emission (executable)  (last update: July 2015)
BiNS2_v.17.6 MolComML integration (source files)  (last update: June 2017)
BiNS2_v.19.6 parallel execution on GPU (source files)  (last update: June 2019)
BiNS2_v.20 (executable)  (last update: August 2020)

 

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

  1. Import the BiNS-NanoLibrary and BiNS-Simulator into your IDE

  2. 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

  3. Configure your MySQL Database and import the required tables (import DB_nanonetworks.sql  ) 

  4. Copy the /texture folder into your /home/user

 

Configuration

  1. 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...

  2. It is a best practice to set an higher heap memory size in the Java Virtual Machine configuration, e.g.:  -Xmx5000M -Xms5000M

  3. 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.

 

 

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