A Proposal for Dynamic Access Lists for TCP/IP Packet Filering

The use of IP filtering to improve system security is well established, and although limited in what it can achieve has proved to be efficient and effective. In the design of a security policy there is always a trade-off between usability and security. Restricting access means that legitimate use of the network is prevented; allowing access means illegitimate use may be allowed. Static access list make finding a balance particularly stark -- we pay the price of decreased security 100% of the time even if the benefit of increased usability is only gained 1% of the time. Dynamic access lists would allow the rules to change for short periods of time, and to allow local changes by non-experts. The network administrator can set basic security guide-lines which allow certain basic services only. All other services are restricted, but users are able to request temporary exceptions in order to allow additional access to the network. These exceptions are granted depending on the privileges of the user. This paper covers the following topics: (1) basic introduction to TCP/IP filtering; (2) semantics for dynamic access lists and; (3) a proposed protocol for allowing dynamic access; and (4) a method for representing access lists so that dynamic update and look-up can be done efficiently performed.Comment: 12 pages. Shortened version appeared in SAICSIT 200

An overview of the wcd EST clustering tool

Summary: The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d 2 distance function or edit distance, improving existing implementations of d 2. It supports merging, refinement and reclustering of clusters. It is ‘drop in’ compatible with the StackPack clustering package. wcd supports parallelization under both shared memory and cluster architectures. It is distributed with an EMBOSS wrapper allowing wcd to be installed as part of an EMBOSS installation (and so provided by a web server)

The Effects of the Makgadikgadi Wildlife Fence on Cattle Populations and Local Cattle Industry

This study was conducted to determine the effects of the erection of the Makgadikgadi wildlife fence along the western border of the Makgadikgadi Pans National Park on cattle populations and livestock owners to the west of the fence. Cattle foraging behavior and movement patterns were recorded using GPS and focal observation methods to determine resource use and pressures affecting the populations. Interviews were also conducted in the area of Meno-a-Kwena camp to examine the effects of the fence on the economics of the local cattle industry. Signs of resource stress were found in the continued selection of poor quality forage, land degradation around boreholes, and movement patterns that pushed the water bearing capacity of the animals as they searched for quality forage. Interviews contradicted these findings to a certain extent, while extolling the good effects of the fence on cattle predation by wildlife and premium prices offered by BMC as a result of the fence’s disease-controlling effects

Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

<p>Abstract</p> <p>Background</p> <p>Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution.</p> <p>Results</p> <p>A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (<b><it>F</it></b>unctional <b><it>I</it></b>nference using the <b><it>R</it></b>ates of <b><it>E</it></b>volution), which aligns sequences using the evolutionary rate at codon sites, as measured by the <it>dN</it>/<it>dS </it>ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions). Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data) may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the method of choice in these cases.</p> <p>Conclusions</p> <p>FIRE provides proof of concept that it is possible to align sequences and infer domain function by using evolutionary rates rather than residue similarity. This represents a new approach to sequence analysis with a wide range of potential applications in molecular biology.</p

Resource sharing across heterogenous networks

Sharing resources on a computer network, especially in heterogeneous environments, has m any benefits: new applications become possible, and use of technology cheaper. This dissertation investigates how resources— in particular printing resources—may b e shared. While still incomplete, an existing theoretical framework for data communication and resource sharing, the ISO-051 Reference Model, provides useful background information and tools for analysis. A discussion o f this framework complements a survey o f the principles and current state of file and printer servers, and distributed systems. An analysis of the design and implementation of a printer server acting as a b ridge between two networks illustrates problem s and results found in distributed system s generally. The dissertation concludes by analyzing the strengths and shortcomings of the Reference Model and distributed systems. This and developments in technology lead to a proposal of an extended model for printer services, and clarification of printer servers' needs and requirements

Fast packet filtering using N-ary decision diagrams

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PEACE: Parallel Environment for Assembly and Clustering of Gene Expression

We present PEACE, a stand-alone tool for high-throughput ab initio clustering of transcript fragment sequences produced by Next Generation or Sanger Sequencing technologies. It is freely available from www.peace-tools.org. Installed and managed through a downloadable user-friendly graphical user interface (GUI), PEACE can process large data sets of transcript fragments of length 50 bases or greater, grouping the fragments by gene associations with a sensitivity comparable to leading clustering tools. Once clustered, the user can employ the GUI's analysis functions, facilitating the easy collection of statistics and allowing them to single out specific clusters for more comprehensive study or assembly. Using a novel minimum spanning tree-based clustering method, PEACE is the equal of leading tools in the literature, with an interface making it accessible to any user. It produces results of quality virtually identical to those of the WCD tool when applied to Sanger sequences, significantly improved results over WCD and TGICL when applied to the products of Next Generation Sequencing Technology and significantly improved results over Cap3 in both cases. In short, PEACE provides an intuitive GUI and a feature-rich, parallel clustering engine that proves to be a valuable addition to the leading cDNA clustering tools

Establishing an academic biobank in a resource-challenged environment

Past practices of informal sample collections and spreadsheets for data and sample management fall short of best-practice models for biobanking, and are neither cost effective nor efficient to adequately serve the needs of large research studies. The biobank of the Sydney Brenner Institute for Molecular Bioscience serves as a bioresource for institutional, national and international research collaborations. It provides high-quality human biospecimens from African populations, secure data and sample curation and storage, as well as monitored sample handling and management processes, to promote both non-communicable and infectious-disease research. Best-practice guidelines have been adapted to align with a low-resource setting and have been instrumental in the development of a quality-management system, including standard operating procedures and a quality-control regimen. Here, we provide a summary of 10 important considerations for initiating and establishing an academic research biobank in a low-resource setting. These include addressing ethical, legal, technical, accreditation and/or certification concerns and financial sustainability