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.

FastAero – A Precorrected FFT – Fast Multipole Tree Steady and Unsteady Potential Flow Solver

In this paper a precorrected FFT-Fast Multipole Tree (pFFT-FMT) method for solving the potential flow around arbitrary three dimensional bodies is presented. The method takes advantage of the efficiency of the pFFT and FMT algorithms to facilitate more demanding computations such as automatic wake generation and hands-off steady and unsteady aerodynamic simulations. The velocity potential on the body surfaces and in the domain is determined using a pFFT Boundary Element Method (BEM) approach based on the Green’s Theorem Boundary Integral Equation. The vorticity trailing all lifting surfaces in the domain is represented using a Fast Multipole Tree, time advected, vortex participle method. Some simple steady state flow solutions are performed to demonstrate the basic capabilities of the solver. Although this paper focuses primarily on steady state solutions, it should be noted that this approach is designed to be a robust and efficient unsteady potential flow simulation tool, useful for rapid computational prototyping.

SketchIT: A Sketch Interpretation Tool for Conceptual Mechanical Design

We describe a program called SketchIT capable of producing multiple families of designs from a single sketch. The program is given a rough sketch (drawn using line segments for part faces and icons for springs and kinematic joints) and a description of the desired behavior. The sketch is "rough" in the sense that taken literally, it may not work. From this single, perhaps flawed sketch and the behavior description, the program produces an entire family of working designs. The program also produces design variants, each of which is itself a family of designs. SketchIT represents each family of designs with a "behavior ensuring parametric model" (BEP-Model), a parametric model augmented with a set of constraints that ensure the geometry provides the desired behavior. The construction of the BEP-Model from the sketch and behavior description is the primary task and source of difficulty in this undertaking. SketchIT begins by abstracting the sketch to produce a qualitative configuration space (qc-space) which it then uses as its primary representation of behavior. SketchIT modifies this initial qc-space until qualitative simulation verifies that it produces the desired behavior. SketchIT's task is then to find geometries that implement this qc-space. It does this using a library of qc-space fragments. Each fragment is a piece of parametric geometry with a set of constraints that ensure the geometry implements a specific kind of boundary (qcs-curve) in qc-space. SketchIT assembles the fragments to produce the BEP-Model. SketchIT produces design variants by mapping the qc-space to multiple implementations, and by transforming rotating parts to translating parts and vice versa.