D-VASim

The motivation of developing D-VASim can be watched in the video shown below.

Note: To watch the video in HD mode, click settings and select Quality (1080p60)

A practical demo of D-VASim can be seen at User Manuals page. 

D-VASim (Dynamic Virtual Analyzer and simulator) is a tool to analyze and simulate the genetic logic circuit models developed in the Systems Biology Mark-up Language (SBML).

These models are usually tested in wet-lab which is a very time consuming and error prone process. Due to the mishandling of the apparatus, experiments are often required to be repeated. In order to avoid this time-consuming in-vitro experiments, these models can be tested through in-silico analysis first. To the best of our knowledge, there exist no in-silico tool which give users an intuitive feeling of performing laboratory experiments virtually.

D-VASim give the users an insight of performing laboratory experiments right in the in-silico environment. Similar to the way a user increases an input concentration from the test-tubes into the flask containing bio-model in the laboratory, a user can vary the concentration of input proteins with the help of control knobs and observe its effects on the output concentration graphically in runtime, using D-VASim. D-VASim is the first simulation tool which allow users to interact with the model during runtime.

In D-VASim, users can analyze the components of SBML models in a user-friendly manner. A separate virtual instrument can be generated for each SBML model, which serves as a standalone virtual instrument.

Technical Information of D-VASim.

Features of D-VASim v1.0.

  • User-friendly analysis of SBML components
  • Runtime interactive stochastic simulation
  • Deterministic simulation with ten different types of continuous solvers
  • Reflect the effects of changing parameters during runtime
  • Support changing the attributes of SBML events during runtime
  • Boolean logic analysis for up to two input complex genetic logic circuits
  • Threshold value and propagation delay analysis of genetic logic circuits
  • Allow modifier degradation
  • Store simulation traces for reproducing the model’s behavior
  • Generate separate virtual instrument for each SBML model
  • Simulation speed can be controlled

The latest version of D-VASim can be downloaded here.