The CybertoryTM Virtual Molecular Biology Laboratory project aims to develop an on-line virtual environment for conducting simulated experiments in molecular genetics. It is funded by an SBIR grant from the National Institutes of Health to Attotron Biosensor Corporation.
This site supports collaborative aspects of the project. These include both open-source software modules being developed to model various molecular biology reactions, and teaching exercises that use these modules.
The commercial platform (still in development) will integrate these modules through a common graphical user interface. It uses a database back end to support communication among the modules and allow long-term storage of data from simulated experiments.
Major Modules
The sequence trace generator creates reverse-engineered chromatograms in SCF format. The user selects a template sequence, a primer sequence, and reaction conditions, and the simulator finds the place or places in the template where it estimates that the primer would bind. The resulting SCF file contains a superimposed result from all priming sites, each weighted for how well they prime. This means the student has to design an appropriate primer and select adequately stringent reaction conditions to achieve good experimental results. The SCF files can be viewed, assembled, and managed in the Staden package, or other sequence data management software that uses the standard Sequence Chromatogram Format. We have submitted a paper describing a shotgun sequencing exercise based on this module, and will make an announcement here when that is published.
The microarray image generator lets you create simplified reverse-engineered two-color spotted microarray images for teaching data analysis concepts. You can download the zip file containing the program and documentation.
Open source philosophy
There are two reasons we have made the reaction simulation modules open-source:
First, they can serve as vehicles for collaboration with academic scientists. If you are a researcher or bioinformatician with an interest in modeling molecular biology reactions, you may find these modules to be useful starting points. You are free to modify, redistribute, and use them in accordance with their open source licenses, which means that the result of your work will also be open source.
Second, these modules have been released to encourage scientists and teachers to create educational resources based upon the simulations. An exercise consists of appropriate starting data (DNA sequences, expression profiles, etc) for specification of "virtual reagents", together with a protocol for an experiment to perform using these "reagents". Third-party exercise developers are not expected to have extensive programming experience. Releasing the open source modules assures prospective exercise developers that the platform for their exercise will always be available for their own use and for distribution to others at no charge.
The commercial platform will be designed so that exercises developed for the open source modules will be easily used there as well. In addition, the commercial platform will include support for more extensive experiments, such as those involving multiple modules working together, or those requiring user data to be stored on the server for multiple sessions.