TEMPEST: A Template Editor for Structured Text

TEMPEST is a full-screen text editor that incorporates a structural paradigm in addition to the more traditional textual paradigm provided by most editors. While the textual paradigm treats the text as a sequence of characters, the structural paradigm treats it as a collection of named blocks which the user can define, group, and manipulate. Blocks can be defined to correspond to the structural features of he text, thereby providing more meaningful objects to operate on than characters of lines. The structural representation of the text is kept in the background, giving TEMPEST the appearance of a typical text editor. The structural and textual interfaces coexist equally, however, so one can always operate on the text from wither point of view. TEMPEST's representation scheme provides no semantic understanding of structure. This approach sacrifices depth, but affords a broad range of applicability and requires very little computational overhead. A prototype has been implemented to illustrate the feasibility and potential areas of application of the central ideas. It was developed and runs on an IBM Personal Computer.

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.