Back to good health
- Authors: Machanick, Philip
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61144 , vital:27984 , http://dx.doi.org/10.18489/sacj.v29i3.565
- Description: 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.
- Full Text:
- Authors: Machanick, Philip
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61144 , vital:27984 , http://dx.doi.org/10.18489/sacj.v29i3.565
- Description: 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.
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Challenges with modelling transcription factor binding
- Machanick, Philip, Kibet, Caleb K
- Authors: Machanick, Philip , Kibet, Caleb K
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439158 , vital:73551 , 10.1109/NEXTCOMP.2017.8016178
- Description: Modelling transcription factor binding presents a number of challenges. In its simplest form, binding can be modelled by a consensus sequence but a number of factors including degeneracy of binding sites, alternative modes of binding and differences between artificially-constructed and in vivo DNA make modelling binding complex. In this paper we outline difficulties and report on progress with improving modelling of binding. We focus on improving measurement of binding models, a necessary prerequisite for finding better models.
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- Authors: Machanick, Philip , Kibet, Caleb K
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439158 , vital:73551 , 10.1109/NEXTCOMP.2017.8016178
- Description: Modelling transcription factor binding presents a number of challenges. In its simplest form, binding can be modelled by a consensus sequence but a number of factors including degeneracy of binding sites, alternative modes of binding and differences between artificially-constructed and in vivo DNA make modelling binding complex. In this paper we outline difficulties and report on progress with improving modelling of binding. We focus on improving measurement of binding models, a necessary prerequisite for finding better models.
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Data structures and algorithms for bioinformatics
- Authors: Machanick, Philip
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439172 , vital:73552 , https://homes.cs.ru.ac.za/philip/Courses/BioinfMScAlgorithms/BioinfAlgorithms.pdf
- Description: 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 once
- Full Text:
- Authors: Machanick, Philip
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439172 , vital:73552 , https://homes.cs.ru.ac.za/philip/Courses/BioinfMScAlgorithms/BioinfAlgorithms.pdf
- Description: 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 once
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The FOXP2 forkhead domain binds to a variety of DNA sequences with different rates and affinities
- Webb, Helen, Steeb, Olga, Blane, Ashleigh, Rotherham, Lia, Aron, Shaun, Machanick, Philip, Dirr, Heinrich W, Fanucchi, Sylvia
- Authors: Webb, Helen , Steeb, Olga , Blane, Ashleigh , Rotherham, Lia , Aron, Shaun , Machanick, Philip , Dirr, Heinrich W , Fanucchi, Sylvia
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439326 , vital:73567 , https://doi.org/10.1093/jb/mvx003
- Description: FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA-binding domain of which is the winged helix forkhead domain (FHD). In this work we show that the FOXP2 FHD is able to bind to various DNA sequences, including a novel sequence identified in this work, with different affinities and rates as detected using surface plasmon resonance. Combining the experimental work with molecular docking, we show that high-affinity sequences remain bound to the protein for longer, form a greater number of interactions with the protein and induce a greater structural change in the protein than low-affinity sequences. We propose a binding model for the FOXP2 FHD that involves three types of binding sequence: low affinity sites which allow for rapid scanning of the genome by the protein in a partially unstructured state; moderate affinity sites which serve to locate the protein near target sites and high-affinity sites which secure the protein to the DNA and induce a conformational change necessary for functional binding and the possible initiation of downstream transcriptional events.
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- Authors: Webb, Helen , Steeb, Olga , Blane, Ashleigh , Rotherham, Lia , Aron, Shaun , Machanick, Philip , Dirr, Heinrich W , Fanucchi, Sylvia
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439326 , vital:73567 , https://doi.org/10.1093/jb/mvx003
- Description: FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA-binding domain of which is the winged helix forkhead domain (FHD). In this work we show that the FOXP2 FHD is able to bind to various DNA sequences, including a novel sequence identified in this work, with different affinities and rates as detected using surface plasmon resonance. Combining the experimental work with molecular docking, we show that high-affinity sequences remain bound to the protein for longer, form a greater number of interactions with the protein and induce a greater structural change in the protein than low-affinity sequences. We propose a binding model for the FOXP2 FHD that involves three types of binding sequence: low affinity sites which allow for rapid scanning of the genome by the protein in a partially unstructured state; moderate affinity sites which serve to locate the protein near target sites and high-affinity sites which secure the protein to the DNA and induce a conformational change necessary for functional binding and the possible initiation of downstream transcriptional events.
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Video on demand in a high bandwidth world
- Authors: Machanick, Philip
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439121 , vital:73546 , https://doi.org/10.1145/3129416.3129424
- Description: Video on Demand (VoD) is a challenging area requiring complex server and distributed systems architectures. In this paper I describe an alternative implementation of VoD that exploits the growing affordability of fibre bandwidth to remove the latency problems of scaling up VoD. I call the general principle Information Mass Transit (IMT). By analogy with regular mass transit, making all traffic move in bulk without individual service variation makes for a much more efficient system. The core idea is to broadcast the same movie repeatedly at short intervals. To explicate the design, I set this interval at 1 minute, implying a latency of up to a minute to start a movie. However, this latency can be disguised if a user has a catalogue of movies that includes the first minute of each. Provided the number of users is much higher than the number of movies, this approach is affordable in terms of bandwidth and totally removes any need for servers or network infrastructure, beyond new connections for new users, to scale with the number of users. I call this approach Scalable Architecture for Video on Demand or SAVoD.
- Full Text:
- Authors: Machanick, Philip
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439121 , vital:73546 , https://doi.org/10.1145/3129416.3129424
- Description: Video on Demand (VoD) is a challenging area requiring complex server and distributed systems architectures. In this paper I describe an alternative implementation of VoD that exploits the growing affordability of fibre bandwidth to remove the latency problems of scaling up VoD. I call the general principle Information Mass Transit (IMT). By analogy with regular mass transit, making all traffic move in bulk without individual service variation makes for a much more efficient system. The core idea is to broadcast the same movie repeatedly at short intervals. To explicate the design, I set this interval at 1 minute, implying a latency of up to a minute to start a movie. However, this latency can be disguised if a user has a catalogue of movies that includes the first minute of each. Provided the number of users is much higher than the number of movies, this approach is affordable in terms of bandwidth and totally removes any need for servers or network infrastructure, beyond new connections for new users, to scale with the number of users. I call this approach Scalable Architecture for Video on Demand or SAVoD.
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