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.

A HOLISTIC APPROACH TO MANUFACTURING SYSTEM DESIGN IN THE DEFENSE AEROSPACE INDUSTRY

Manufacturing has evolved to become a critical element of the competitive skill set of defense aerospace firms. Given the changes in the acquisition environment and culture; traditional “thrown over the wall” means of developing and manufacturing products are insufficient. Also, manufacturing systems are complex systems that need to be carefully designed in a holistic manner and there are shortcomings with available tools and methods to assist in the design of these systems. This paper outlines the generation and validation of a framework to guide this manufacturing system design process.

Inverse Metabolic Engineering of Synechocystis PCC 6803 for Improved Growth Rate and Poly-3-hydroxybutyrate Production

Synechocystis PCC 6803 is a photosynthetic bacterium that has the potential to make bioproducts from carbon dioxide and light. Biochemical production from photosynthetic organisms is attractive because it replaces the typical bioprocessing steps of crop growth, milling, and fermentation, with a one-step photosynthetic process. However, low yields and slow growth rates limit the economic potential of such endeavors. Rational metabolic engineering methods are hindered by limited cellular knowledge and inadequate models of Synechocystis. Instead, inverse metabolic engineering, a scheme based on combinatorial gene searches which does not require detailed cellular models, but can exploit sequence data and existing molecular biological techniques, was used to find genes that (1) improve the production of the biopolymer poly-3-hydroxybutyrate (PHB) and (2) increase the growth rate. A fluorescence activated cell sorting assay was developed to screen for high PHB producing clones. Separately, serial sub-culturing was used to select clones that improve growth rate. Novel gene knock-outs were identified that increase PHB production and others that increase the specific growth rate. These improvements make this system more attractive for industrial use and demonstrate the power of inverse metabolic engineering to identify novel phenotype-associated genes in poorly understood systems.

A Holistic Approach to Manufacturing System Design in the Defense Aerospace Industry

Manufacturing has evolved to become a critical element of the competitive skill set of defense aerospace firms. Given the changes in the acquisition environment and culture; traditional “thrown over the wall” means of developing and manufacturing products are insufficient. Also, manufacturing systems are complex systems that need to be carefully designed in a holistic manner and there are shortcomings with available tools and methods to assist in the design of these systems. This paper outlines the generation and validation of a framework to guide this manufacturing system design process.

Experience in introduction of English terminology in engineering lessons: methodology and evaluation

This communication explains a experience for the introduction of English terminology in a technical degree of higher education. We present the methodology and assessment procedures used to evaluate the way the students perceived the introduction of terminology in English in two different subjects from 3rd and 5th year courses of a Computer Science degree in which English was not the vehicular language. We propose a strategy based on two main pillars, namely: 1) The design of materials, explanations, and exams, paying particular attention to the way in which the specific terminology was exposed to the students, and 2) The assessment of the impact in the students by means of the analysis of the feedback trough a set of enquiries. Our experience showed that the students responded very positively to the introduction of English terminology, and presented an affirmative feedback about the impact that an improvement of their linguistic abilities would have in their future work. Further, we present statistics regarding the use of English as the vehicular language for technical reports, which is envisaged as very useful by the students. Finally, we propose a set of questions for further debate which are centered in the role that English terminology should pay in technical degrees, and about the way in which universities should deploy resources in English languages within the different Syllabus

Engineering Foundation Year Sustaining Success Lecture 4

slides to take students through part of task of preparing portfolio - also addresses skills development (embedded in tasks)this week - self knowledge and using feedback

Knowledge Technologies

An overview of COMP3028 Knowledge Technologies

Programming Principles: Software Design

In this session we look at some of the basics of good code design, including avoiding duplication and designing for loose coupling and high cohesion.

COMP1004 Programming Principles

These are the resources used for the Computer Science course Programming Principles, designed to teach students the fundamentals of computer programming and object orientation via learning the Java language. We also touch on some software engineering basics, such as patterns, software design and testing. The course assumes no previous knowledge of programming, but there is a fairly steep learning curve, and students are encouraged to practice, practice, practice!

System Design: Using UML Use Cases

In this lecture we cover how UML Use Cases can be used for requirements capture. We look at the anatomy of a Use Case Description, and the way in which use cases can be brought together in a use case diagram. We also look at the way that use cases can be derived from problems using noun verb analysis.

System Design: UML Activity and Sequence Diagrams

In this session we look at how to model flow of control and interactions between components using UML Activity and Sequence Diagrams. This is an introductory session and so for Activity Diagrams we only cover branching, forks and joins and swim lanes, and for Sequence we cover lifelines, messages and returns, and alt, par and opt frames.

System Design: UML Class Diagrams

In this session we look at UML Class Diagrams and how they fit into both the family of UML models, and also the software engineering process. We look at some basic features of class diagrams including properties, operations, associations, generalisation, aggregation and composition.