BioLogix Home

BioLogix

Welcome to our wiki page, this wiki contains links to all our documents that can be downloaded directly also there is a link to our SVN repository in order to be able to checkout a read-only version of our project code.

Introduction

Our system, named BioLogix, aids synthetic biologists in the task of constructing biological circuits which when done in vivo, is a costly and time consuming process. This application enables biologists to build complex biological systems and observe the behaviour when components are added, removed or edited. Nevertheless simulation does not eliminate the need for wet lab experiments involving DNA synthesis and manipulation. The BioLogix program provides an intuitive interactive environment for biological circuit design and simulation. A user can either use the predefined logic gates (AND and NOT) or define complex gates, that can be programmed together to make a biological rendition of a logic circuit. These biological circuits can be simulated to predict the interaction of the genes within various biological components resulting in a lab like experience.


The jar file with dependencies can be downloaded from :

Project Progress

Our project is now in it's final release phase. We currently have a complete working product. Our program can add components to a circuit, connect them, specify genes on connections and finally simulate the circuit and output a graph. We can also save and load projects thus adding an element of persistence to our product. Our product now features also the capability to export valid SBML, which can be imported into CellDesigner. Also the graph can be exported as a png or jpeg image, and the run data (simulated values) can be exported to a csv(comma separated values) file. Finally in order to have input values for simulation a csv file can be imported.

Screenshots

Building a circuit

Validation of a circuit

Simulation of a circuit

Saving of a circuit

Complex circuit construction

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Documentation

Documents for a further explanation on the requirements that played a role in the designing of this program, a full architectural design and finally a test and implementation plan can be found in the [Documents] wiki.

Contact Us

You can contact us at biologixxx@gmail.com