Comparison of Bacteriophage Annotation Methods

The rise of antibiotic-resistant bacteria has increased interest in bacteriophages (viruses that kill bacteria) in recent years. Due to the decreasing cost of genome sequencing, the number of sequenced phage genomes is growing at a geometric rate. Sequencing is followed by annotation, in which genes, start codons, and putative protein functions are identified. Most phage genomes are auto-annotated with programs designed for prokaryotes. Accuracy metrics for these programs with regard to phage genomes are not available. The genome of Escherichia coli phage Lambda was used to benchmark the accuracy of several genome annotation methods and programs. Discovered in 1951, Lambda is the most well studied phage, with nearly all gene functions and start sites demonstrated experimentally. Eight programs were used to annotate the Lambda genome: Glimmer, BASys, RAST, GeneMark, GeneMark.hmm, GeneMarkS, GeneMarkS2, and GeneMark with Heuristic models. Calls were compared to the reference genome from the literature in order to determine the accuracy of the eight selected programs in regard to bacteriophage genome annotation. Manual curation and compilation of auto-annotation results obtained from several programs is expected to yield more accurate gene feature and start codon prediction than auto-annotation alone

BASys: a web server for automated bacterial genome annotation

BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and hyperlinked image output. BASys uses >30 programs to determine ∼60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, secondary structure, 3D structure, reactions and pathways. The depth and detail of a BASys annotation matches or exceeds that found in a standard SwissProt entry. BASys also generates colorful, clickable and fully zoomable maps of each query chromosome to permit rapid navigation and detailed visual analysis of all resulting gene annotations. The textual annotations and images that are provided by BASys can be generated in ∼24 h for an average bacterial chromosome (5 Mb). BASys annotations may be viewed and downloaded anonymously or through a password protected access system. The BASys server and databases can also be downloaded and run locally. BASys is accessible at

Creation and detection of hardware trojans using non-invasive off-the-shelf technologies

As a result of the globalisation of the semiconductor design and fabrication processes, integrated circuits are becoming increasingly vulnerable to malicious attacks. The most concerning threats are hardware trojans. A hardware trojan is a malicious inclusion or alteration to the existing design of an integrated circuit, with the possible effects ranging from leakage of sensitive information to the complete destruction of the integrated circuit itself. While the majority of existing detection schemes focus on test-time, they all require expensive methodologies to detect hardware trojans. Off-the-shelf approaches have often been overlooked due to limited hardware resources and detection accuracy. With the advances in technologies and the democratisation of open-source hardware, however, these tools enable the detection of hardware trojans at reduced costs during or after production. In this manuscript, a hardware trojan is created and emulated on a consumer FPGA board. The experiments to detect the trojan in a dormant and active state are made using off-the-shelf technologies taking advantage of different techniques such as Power Analysis Reports, Side Channel Analysis and Thermal Measurements. Furthermore, multiple attempts to detect the trojan are demonstrated and benchmarked. Our simulations result in a state-of-the-art methodology to accurately detect the trojan in both dormant and active states using off-the-shelf hardware

"Regulating Healthcare Technologies and Medical Supplies: A Comparative Overview"

A complex relationship exists among EU regulations, current national practices and rules, institutional capacities to implement regulatory adjustments and the legacy of past health and regulatory policy and traditions. However, there is little empirical information on medical devices policy, the medical devices industry, and the assurance of medical device safety and usage. Drawing on a review of the secondary literature and on-going field work, the evidence suggests that the current mix of statecentric and self-regulatory traditions will be as important in determining the implementation and final outcomes of EU-rules as the new rules themselves. EU directives redesign rules, but they do not necessarily lead to institutional change, create institutional capacities, or alter old practices in the short term. Neither EU directives nor national regulatory adjustments determine the "man-machine/skill-experience" interface which is shaped and influenced by local medical traditions and the acceptance of these traditions by local publics

Conversion of Digital Circuits Labs

The engineering technology department at ETSU currently lacks a modern method to teach digital circuits. The aim of this thesis is to convert our current digital circuits labs to equivalent labs suited to run on the Basys 3. The Basys has several advantages over the aging NI Elvis boards (and now just breadboards) currently in use. The first advantage is that the Basys gives students a taste of FPGA programming without being overwhelmingly; like the systems currently in place for the digital signal processing class. The Basys is also a more modern system; our current integrated circuit and breadboard system is from the 70’s and has little to do with the modern world of electronics. There are several major difficulties with moving towards the Basys 3. It requires several tweaks to the current computer security setting of the lab computers. The other issue to be solved is that very few people in the department have even an inkling of how to program in VHDL and most of them are outgoing students. This lack of skills could be a threat to the class but I have included an appendix and a few recommendations for books on the subject to ensure that system development can continue. The other objective of this project was to see if there were ways to incorporate new educational techniques into the engineering technology curriculum. While there have been no actual tests on students, the groundwork has been laid to use some new ideas in the classroom. All of these new systems are designed to get students to think about how devices actually work and develop models to help them fully understand what is being taught