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.

Site Controller: A System for Computer-Aided Civil Engineering and Construction

A revolution\0\0\0 in earthmoving, a $100 billion industry, can be achieved with three components: the GPS location system, sensors and computers in bulldozers, and SITE CONTROLLER, a central computer system that maintains design data and directs operations. The first two components are widely available; I built SITE CONTROLLER to complete the triangle and describe it here. SITE CONTROLLER assists civil engineers in the design, estimation, and construction of earthworks, including hazardous waste site remediation. The core of SITE CONTROLLER is a site modelling system that represents existing and prospective terrain shapes, roads, hydrology, etc. Around this core are analysis, simulation, and vehicle control tools. Integrating these modules into one program enables civil engineers and contractors to use a single interface and database throughout the life of a project.

Structure and Interpretation of Computer Programs

"The Structure and Interpretation of Computer Programs" is the entry-level subject in Computer Science at the Massachusetts Institute of Technology. It is required of all students at MIT who major in Electrical Engineering or in Computer Science, as one fourth of the "common core curriculum," which also includes two subjects on circuits and linear systems and a subject on the design of digital systems. We have been involved in the development of this subject since 1978, and we have taught this material in its present form since the fall of 1980 to approximately 600 students each year. Most of these students have had little or no prior formal training in computation, although most have played with computers a bit and a few have had extensive programming or hardware design experience. Our design of this introductory Computer Science subject reflects two major concerns. First we want to establish the idea that a computer language is not just a way of getting a computer to perform operations, but rather that it is a novel formal medium for expressing ideas about methodology. Thus, programs must be written for people to read, and only incidentally for machines to execute. Secondly, we believe that the essential material to be addressed by a subject at this level, is not the syntax of particular programming language constructs, nor clever algorithms for computing particular functions of efficiently, not even the mathematical analysis of algorithms and the foundations of computing, but rather the techniques used to control the intellectual complexity of large software systems.