Procedures as a Representation for Data in a Computer Program for Understanding Natural Language

This paper describes a system for the computer understanding of English. The system answers questions, executes commands, and accepts information in normal English dialog. It uses semantic information and context to understand discourse and to disambiguate sentences. It combines a complete syntactic analysis of each sentence with a "heuristic understander" which uses different kinds of information about a sentence, other parts of the discourse, and general information about the world in deciding what the sentence means. It is based on the belief that a computer cannot deal reasonably with language unless it can "understand" the subject it is discussing. The program is given a detailed model of the knowledge needed by a simple robot having only a hand and an eye. We can give it instructions to manipulate toy objects, interrogate it about the scene, and give it information it will use in deduction. In addition to knowing the properties of toy objects, the program has a simple model of its own mentality. It can remember and discuss its plans and actions as well as carry them out. It enters into a dialog with a person, responding to English sentences with actions and English replies, and asking for clarification when its heuristic programs cannot understand a sentence through use of context and physical knowledge.

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.