How Multithreading Addresses the Memory Wall

The memory wall is the predicted situation where improvements to processor speed will be masked by the much slower improvement in dynamic random access (DRAM) memory speed. Since the prediction was made in 1995, considerable progress has been made in addressing the memory wall. There have been advances in DRAM organization, improved approaches to memory hierarchy have been proposed, integrating DRAM onto the processor chip has been investigated and alternative approaches to organizing the instruction stream have been researched. All of these approaches contribute to reducing the predicted memory wall effect; some can potentially be combined. This paper reviews several approaches with a view to assessing the most promising option. Given the growing CPU-DRAM speed gap, any strategy which finds alternative work while waiting for DRAM is likely to be a win

MEME-LaB : motif analysis in clusters

Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. While there are tools for ab initio discovery of transcription factor binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web-tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding, and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets

The Management of a Child with a Learning Disability

Diagnostic facilities for children with learning disabilities are essential and can be made available, even in smaller centres. Parents must be made aware of the child's needs, and details of treatment such as medication should be carefully explained to them. The remedial programme must be selected according to the severity of the child's difficulties. Assistant tutors are required to alleviate the personnel shortage. An investigation into the views of 43 children and their parents led to the conclusion that there is a definite place for clinics offering full-time remedial education.S. Afr. Med. J., 48, 753 (1974)

Epstein-Barr virus transcription factor Zta acts through distal regulatory elements to directly control cellular gene expression

Lytic replication of the human gamma herpes virus Epstein-Barr virus (EBV) is an essential prerequisite for the spread of the virus. Differential regulation of a limited number of cellular genes has been reported in B-cells during the viral lytic replication cycle. We asked whether a viral bZIP transcription factor, Zta (BZLF1, ZEBRA, EB1), drives some of these changes. Using genome-wide chromatin immunoprecipitation coupled to next-generation DNA sequencing (ChIP-seq) we established a map of Zta interactions across the human genome. Using sensitive transcriptome analyses we identified 2263 cellular genes whose expression is significantly changed during the EBV lytic replication cycle. Zta binds 278 of the regulated genes and the distribution of binding sites shows that Zta binds mostly to sites that are distal to transcription start sites. This differs from the prevailing view that Zta activates viral genes by binding exclusively at promoter elements. We show that a synthetic Zta binding element confers Zta regulation at a distance and that distal Zta binding sites from cellular genes can confer Zta-mediated regulation on a heterologous promoter. This leads us to propose that Zta directly reprograms the expression of cellular genes through distal elements

Data structures and algorithms for bioinformatics

WHY THIS MATERIAL? Bioinformatics is a difficult subject because it integrates so much from multiple disciplines. The emphasis here is on algorithmic thinking–working from a problem to an implementation while thinking analytically about efficiency concerns. The picture illustrates a general plan for algorithmic thinking. Anything that can be classed as an algorithm can be analysed and your design choices are not always to find the most efficient algorithm possible. The aim is to solve a problem as efficiently as possible; if it is something you do only once, that results in a rather different set of choices than if you are going to do it many times. And–of course–size counts. That is what this course is am I doing this onc

How general-purpose can a GPU be?

The use of graphics processing units (GPUs) in general-purpose computation (GPGPU) is a growing field. GPU instruction sets, while implementing a graphics pipeline, draw from a range of single instruction multiple datastream (SIMD) architectures characteristic of the heyday of supercomputers. Yet only one of these SIMD instruction sets has been of application on a wide enough range of problems to survive the era when the full range of supercomputer design variants was being explored: vector instructions. Supercomputers covered a range of exotic designs such as hypercubes and the Connection Machine (Fox, 1989). The latter is likely the source of the snide comment by Cray: it had thousands of relatively low-speed CPUs (Tucker & Robertson, 1988). Since Cray won, why are we not basing our ideas on his designs (Cray Inc., 2004), rather than those of the losers? The Top 500 supercomputer list is dominated by general-purpose CPUs, and nothing like the Connection Machine that headed the list in 1993 still exists

Back to good health

From introduction: We have a bumper issue, with eleven research papers and one letter to the editor. 2016 was a difficult year for academia in South Africa with highly disruptive protests. 2017 was mostly better from that point of view, though the protest movement has not completely gone away. This issue contains some papers that were submissions to special issues that were not ready in time and hence to some extent is a catch-up issue. In previous issues this year, 29(1), published in July, contained nine research papers, of which five were extended papers from the 2016 SAICSIT annual conference. There was also a special issue on ICT in Education published in October, 29(2), which had five research papers. Two papers from the ICT in Education special issue spilled over to this issue. Overall, we have published 25 research papers this year, compared with four in 2016, fourteen in 2015 and nineteen in 2014. Numbers are therefore looking healthy again; I hope the underlying causes of protest are addressed so we do not have to endure another year like 2016. In the remainder of this editorial, I give an update on the effects of indexing in Scopus, list papers in this issue and end with changes in the editorial team

Mips2C: programming from the machine up

WHY THIS BOOK? Some years ago I took part in a panel discussion titled “Programming Early Considered Harmful” at the SIGCSE 2001 conference [Hitchner et al. 2001]. Once of those present was Yale Patt, whom I had met briefly on a sabbatical at University of Michigan, where he was at the time a professor working in computer architecture. His role on the panel was to proselytise his book, Introduction to Computing Systems: From bits and gates to C and beyond [Patt and Patel 2013], which introduced programming from the low level up. I found the idea intriguing particularly as I also was concerned with the problem that students tend to stick with the first thing they learn. If my concern was correct, it should be better to start with the programming model you want them to internalize, rather than start with machine level programming. Nonenetheless, I am always open to new ideas, and when the opportunity presented itself to run a computer organization course followed by a C course, I decided to try the idea for myself

Software design to meet third world requirements: an experimental software engineering approach

Appropriate technology refers to technology appropriate for use in less developed parts of the world, especially the Third World; this paper raises some problems in adapting a definition of appropriate technology to computer software. A partial solution, a strategy called experimental software engineering, is introduced. The potential of this solution is demonstrated by a case study, in which software for medical education is developed. The result is a clearer understanding of both appropriate technology and design of software for usability.School of Computin