Getting Started

Overview

Infobiotics Workbench (IBW) is a user-friendly, integrated and scalable computational environment for the computer-aided design of synthetic biological systems. It supports an iterative workflow that begins with specification of the desired synthetic system, followed by simulation and verification of the system in high-performance environments and ending with the eventual compilation of the system specification into a genetic construct. This synergy is being achieved by integrating several state of the art features, such as:

  • The Infobiotics Language (IBL) - an expressive modelling language for synthetic biology, that embeds the iterative design-test-build development life-cycle of a synthetic biological entity into one unifying framework;
  • A stochastic simulator that implements all the variants of Gillespie’s stochastic simulation algorithms (SSA);
  • A parallel stochastic simulator, based on a GPU implementation of the Gillespie SSA, able to execute computationally-demanding simulations in a high-performance computing environment;
  • A verification engine, embedding various model checking tools, facilitating the verification of properties and design requirements by using natural language queries;
  • A biocompilation module, facilitating an automated compilation of a specified synthetic circuit into eventual genetic sequence information;
  • Import/export mechanisms to community-approved data exchange formats, i.e. SBOL and SBML.

Download

The Infobiotics Workbench binaries are distributed by taking advantage of Vagrant for provisioning a fully configured virtual environment based on Ubuntu 18.04 LTS, embedding all the required dependencies and configurations, thus providng a seamless experience on setting up and running IBW.

Please follow the steps below, in order to set up and run Inforbiotics Workbench:

  1. Download and install Virtual Box;

  2. Download and install Vagrant;

  3. Download the IBW Vagrant Configuration, in the form of ZIP archive;

  4. Unzip the IBW Vagrant Configuration achive in a suitable directory;

  5. Open un a terminal and change the current directory to the path of the IBW Vagrant Configuration files (where the Vagrantfile resides);

  6. Run the following command, in order to automatically create the Infobiotics Workbench virual environment, based on the above configuration files;

    1
       vagrant up

  7. After the provisioning of Infobiotics Wockbench virtual machine successfully completed, use the following credentials to log into the Ubuntu 18.04 OS: Username: vagrant, Password: vagrant;

  8. Open up IBW by using the desktop icon. Click “Trust and Launch” when the application launcher dialog is being displayed (only at the first access).

Contribute

Infobiotics Workbench is built on top of the Eclipse Platform, taking advantage of its robustness, extensibility and community support.

By inheriting the core design concepts from Eclipse, the IBW implementation is structured around the concept of plug-ins. The various features of IBW, such as IBL modelling, simulation, verification, biocompilation etc., are implemented in the form of plug-ins, as structured bundles of code and data that contribute functionality to the system in the form of code libraries or platform extensions, adding visual and computational features to IBW.

The Infobiotics Workbench source code in available on Github at https://github.com/Infobiotics/ibw, under the MIT license. If you are interested in contributing to the development of Infobiotics Workbench, please contact the autors.