BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.

Logging and Recovery in a Highly Concurrent Database

This report addresses the problem of fault tolerance to system failures for database systems that are to run on highly concurrent computers. It assumes that, in general, an application may have a wide distribution in the lifetimes of its transactions. Logging remains the method of choice for ensuring fault tolerance. Generational garbage collection techniques manage the limited disk space reserved for log information; this technique does not require periodic checkpoints and is well suited for applications with a broad range of transaction lifetimes. An arbitrarily large collection of parallel log streams provide the necessary disk bandwidth.