BμG@Sbase—a microbial gene expression and comparative genomic database

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future

Enhancing Clinical Learning Through an Innovative Instructor Application for ECMO Patient Simulators

© 2018 The Authors. Reprinted by permission of SAGE PublicationsBackground. Simulation-based learning (SBL) employs the synergy between technology and people to immerse learners in highly-realistic situations in order to achieve quality clinical education. Due to the ever-increasing popularity of extracorporeal membrane oxygenation (ECMO) SBL, there is a pressing need for a proper technological infrastructure that enables high-fidelity simulation to better train ECMO specialists to deal with related emergencies. In this article, we tackle the control aspect of the infrastructure by presenting and evaluating an innovative cloud-based instructor, simulator controller, and simulation operations specialist application that enables real-time remote control of fullscale immersive ECMO simulation experiences for ECMO specialists as well as creating custom simulation scenarios for standardized training of individual healthcare professionals or clinical teams. Aim. This article evaluates the intuitiveness, responsiveness, and convenience of the ECMO instructor application as a viable ECMO simulator control interface. Method. A questionnaire-based usability study was conducted following institutional ethical approval. Nineteen ECMO practitioners were given a live demonstration of the instructor application in the context of an ECMO simulator demonstration during which they also had the opportunity to interact with it. Participants then filled in a questionnaire to evaluate the ECMO instructor application as per intuitiveness, responsiveness, and convenience. Results. The collected feedback data confirmed that the presented application has an intuitive, responsive, and convenient ECMO simulator control interface. Conclusion. The present study provided evidence signifying that the ECMO instructor application is a viable ECMO simulator control interface. Next steps will comprise a pilot study evaluating the educational efficacy of the instructor application in the clinical context with further technical enhancements as per participants’ feedback.Peer reviewedFinal Accepted Versio

TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure

Personal Food Computer: A new device for controlled-environment agriculture

Due to their interdisciplinary nature, devices for controlled-environment agriculture have the possibility to turn into ideal tools not only to conduct research on plant phenology but also to create curricula in a wide range of disciplines. Controlled-environment devices are increasing their functionalities as well as improving their accessibility. Traditionally, building one of these devices from scratch implies knowledge in fields such as mechanical engineering, digital electronics, programming, and energy management. However, the requirements of an effective controlled environment device for personal use brings new constraints and challenges. This paper presents the OpenAg Personal Food Computer (PFC); a low cost desktop size platform, which not only targets plant phenology researchers but also hobbyists, makers, and teachers from elementary to high-school levels (K-12). The PFC is completely open-source and it is intended to become a tool that can be used for collective data sharing and plant growth analysis. Thanks to its modular design, the PFC can be used in a large spectrum of activities.Comment: 9 pages, 11 figures, Accepted at the 2017 Future Technologies Conference (FTC