Automating functional enzyme screening & characterization

This work has been presented in the 10th IWBDA workshop.Microfluidics continue to gain traction as an inexpensive alternative to standard multi-well plate-based, and flow cytometry- based, assay platforms. These devices are especially useful for the types of ultra-high throughput screens needed for enzyme discovery applications where large numbers (>106) of unique samples must be screened rapidly1. Coupled with cell-free protein synthesis2, microfluidics are being used to identify novel enzymes useful for a variety of applications with unprecedented speed. However, these devices are typically produced using PDMS, and require considerable infrastructure and artisanal skill to fabricate, limiting their accessibility. Likewise, enzyme hits obtained from a screen are often validated manually and would benefit from automation of downstream validation processes. To address these limitations, we propose a workflow which leverages software tools to automate the rapid design and fabrication of low-cost polycarbonate microfluidic devices for use as high-throughput screening platforms for enzyme discovery, as well as an automated DNA assembly tool to streamline validation of screening candidates. Using this workflow, we aim to identify novel oxidoreductase enzymes from environmental metagenomic DNA libraries, for use in electrochemical biosensors

Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Automated illustration of multimedia stories

Submitted in part fulfillment of the requirements for the degree of Master in Computer ScienceWe all had the problem of forgetting about what we just read a few sentences before. This comes from the problem of attention and is more common with children and the elderly. People feel either bored or distracted by something more interesting. The challenge is how can multimedia systems assist users in reading and remembering stories? One solution is to use pictures to illustrate stories as a mean to captivate ones interest as it either tells a story or makes the viewer imagine one. This thesis researches the problem of automated story illustration as a method to increase the readers’ interest and attention. We formulate the hypothesis that an automated multimedia system can help users in reading a story by stimulating their reading memory with adequate visual illustrations. We propose a framework that tells a story and attempts to capture the readers’ attention by providing illustrations that spark the readers’ imagination. The framework automatically creates a multimedia presentation of the news story by (1) rendering news text in a sentence by-sentence fashion, (2) providing mechanisms to select the best illustration for each sentence and (3) select the set of illustrations that guarantees the best sequence. These mechanisms are rooted in image and text retrieval techniques. To further improve users’ attention, users may also activate a text-to-speech functionality according to their preference or reading difficulties. First experiments show how Flickr images can illustrate BBC news articles and provide a better experience to news readers. On top of the illustration methods, a user feedback feature was implemented to perfect the illustrations selection. With this feature users can aid the framework in selecting more accurate results. Finally, empirical evaluations were performed in order to test the user interface,image/sentence association algorithms and users’ feedback functionalities. The respective results are discussed

Teaching with infographics: practising new digital competencies and visual literacies

This position paper examines the use of infographics as a teaching assignment in the online college classroom. It argues for the benefits of adopting this type of creative assignment for teaching and learning, and considers the pedagogic and technical challenges that may arise in doing so. Data and insights are drawn from two case studies, both from the communications field, one online class and a blended one, taught at two different institutions. The paper demonstrates how incorporating a research-based graphic design assignment into coursework challenges and encourages students' visual digital literacies. The paper includes practical insights and identifies best practices emerging from the authors' classroom experience with the infographic assignment, and from student feedback. The paper suggests that this kind of creative assignment requires students to practice exactly those digital competencies required to participate in an increasingly visual digital culture

Evaluating the Benefits of Computer Aided-Design (CAD) in Fashion Education, the Case of Accra Polytechnic

The main purpose of this research was to evaluate the introduction and use of Computer-Aided Designing (CAD) in Fashion Education in Accra Polytechnic over a three - year period (2009-2012). It was revealed that some level of CAD has been inculcated into Fashion Education in the institution in the three specializations (Fashion production, Textiles and Fashion design) as they use the softwares available to draw garments, developing motifs for textiles prints and also to draw human figures. However, there were some challenges confronting the department and the students as well, some of which include insufficient computers and the requisite software equipment. It was recommended, that a CAD Resource Centre for Fashion Education should be set up in Accra with a state-of-the-art hard and software which will provide a suitable environment for teaching and learning for the training of Fashion Design and Textiles students. Also, CAD should be introduced early so that it will motivate students to search for and learn the commands that allow for actions and operations in CAD to enhance creativity and innovation. Keywords: Computer Aided Design (CAD), Skills, Nuffi