Bioinformatics tool and web server development focusing on structural bioinformatics applications
- Authors: Nabatanzi, Margaret
- Date: 2022-10-14
- Subjects: Structural bioinformatics , Proteins Structure , Protein structure prediction , Proteins Conformation , Protein complex
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365700 , vital:65777 , DOI https://doi.org/10.21504/10962/365700
- Description: This thesis is divided into two main sections: Part 1 describes the design, and evaluation of the accuracy of a new web server – PRotein Interactive MOdeling (PRIMO-Complexes) for modeling protein complexes and biological assemblies. The second part describes the development of bioinformatics tools to predict HIV-1 drug resistance and support bioinformatics research and education. Recent technological advances have resulted in a tremendous increase in the number of sequences and protein structures deposited in the Universal Protein Resource Knowledgebase (UniProtKB) and the Protein Data Bank (PDB). However, the number of sequences has increased at a higher rate compared with the experimentally solved multimeric protein structures. This is partly due to advances in high-throughput sequencing technology. To fill this protein sequence-structure gap, computational approaches have been developed to predict protein structures from available sequences. Computational approaches include template-based and ab initio modeling with the former being the most reliable. Template-based modeling process can be achieved using either standalone software or automated modeling web servers. However, using standalone software requires familiarity with command-line interfaces as well as utilising other intermediate programs which could be daunting to novice users. To alleviate some of these problems, the modeling process has been automated, however, it still has numerous challenges. To date, only a few web servers that support multimeric protein modeling have been developed and even these provide little, if any user involvement in the process. To address some of these issues, a new web server – PRIMO-Complexes – was developed to model protein complexes and biological assemblies. The existing PRIMO web server could only model monomeric proteins. Part 1 of this thesis provides a detailed account of the development and evaluation of PRIMO-Complexes. The rationale for developing this new web server was based on the understanding that most proteins function as protein multimers and often the ligand-binding sites, and enzyme active sites are located at the protein-protein interfaces. It, therefore, necessitated developing capabilities for modeling multimeric proteins. PRIMO-Complexes web server was developed using the Waterfall system development life cycle model, is based on the Django web framework and makes use of high-performance computing resources to execute jobs. The accuracy of the algorithms embedded in PRIMO- Complexes was evaluated and the results were promising. Additionally, PRIMO-Complexes performs comparatively well in relation to other web servers that offer multimeric protein modeling. Another unique feature of PRIMO-Complexes is its interactivity. The webserver was developed with capabilities for allowing users to model multimeric proteins with an appreciable degree of control over the process. In the second part of the thesis several other bioinformatics tools are described, for example, a webserver for predicting HIV-1 drug resistance, the RUBi protein model repository, and a bioinformatics web portal for education and research resources. RUBi protein model repository stores verified theoretical models built using various modeling approaches. This enables users to easily access models to reproduce and/or further the research. This is described in chapter 5. Chapter 6 describes the design and development of the Human Immunodeficiency type 1 Resistance Predictor (HIV-1 ResPredictor), a web application that employs artificial neural networks (ANN) to predict drug resistance in patients infected with HIV-1 subtype B. The ANNs and subtype classifiers performed well making this web application potentially useful to both clinicians and researchers in this era of personalised medicine. Finally, chapter 7 describes a bioinformatics education web portal that equips students with information on how to use bioinformatics online resources. Being aware of these resources is not enough without a deeper understanding and guidance on how to apply bioinformatics methods to solve practical problems. This web portal was aimed at familiarising students with the basic terminology and approaches in structural bioinformatics. Students will potentially gain skills to conduct real-life bioinformatics research to obtain biological insights. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Nabatanzi, Margaret
- Date: 2022-10-14
- Subjects: Structural bioinformatics , Proteins Structure , Protein structure prediction , Proteins Conformation , Protein complex
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365700 , vital:65777 , DOI https://doi.org/10.21504/10962/365700
- Description: This thesis is divided into two main sections: Part 1 describes the design, and evaluation of the accuracy of a new web server – PRotein Interactive MOdeling (PRIMO-Complexes) for modeling protein complexes and biological assemblies. The second part describes the development of bioinformatics tools to predict HIV-1 drug resistance and support bioinformatics research and education. Recent technological advances have resulted in a tremendous increase in the number of sequences and protein structures deposited in the Universal Protein Resource Knowledgebase (UniProtKB) and the Protein Data Bank (PDB). However, the number of sequences has increased at a higher rate compared with the experimentally solved multimeric protein structures. This is partly due to advances in high-throughput sequencing technology. To fill this protein sequence-structure gap, computational approaches have been developed to predict protein structures from available sequences. Computational approaches include template-based and ab initio modeling with the former being the most reliable. Template-based modeling process can be achieved using either standalone software or automated modeling web servers. However, using standalone software requires familiarity with command-line interfaces as well as utilising other intermediate programs which could be daunting to novice users. To alleviate some of these problems, the modeling process has been automated, however, it still has numerous challenges. To date, only a few web servers that support multimeric protein modeling have been developed and even these provide little, if any user involvement in the process. To address some of these issues, a new web server – PRIMO-Complexes – was developed to model protein complexes and biological assemblies. The existing PRIMO web server could only model monomeric proteins. Part 1 of this thesis provides a detailed account of the development and evaluation of PRIMO-Complexes. The rationale for developing this new web server was based on the understanding that most proteins function as protein multimers and often the ligand-binding sites, and enzyme active sites are located at the protein-protein interfaces. It, therefore, necessitated developing capabilities for modeling multimeric proteins. PRIMO-Complexes web server was developed using the Waterfall system development life cycle model, is based on the Django web framework and makes use of high-performance computing resources to execute jobs. The accuracy of the algorithms embedded in PRIMO- Complexes was evaluated and the results were promising. Additionally, PRIMO-Complexes performs comparatively well in relation to other web servers that offer multimeric protein modeling. Another unique feature of PRIMO-Complexes is its interactivity. The webserver was developed with capabilities for allowing users to model multimeric proteins with an appreciable degree of control over the process. In the second part of the thesis several other bioinformatics tools are described, for example, a webserver for predicting HIV-1 drug resistance, the RUBi protein model repository, and a bioinformatics web portal for education and research resources. RUBi protein model repository stores verified theoretical models built using various modeling approaches. This enables users to easily access models to reproduce and/or further the research. This is described in chapter 5. Chapter 6 describes the design and development of the Human Immunodeficiency type 1 Resistance Predictor (HIV-1 ResPredictor), a web application that employs artificial neural networks (ANN) to predict drug resistance in patients infected with HIV-1 subtype B. The ANNs and subtype classifiers performed well making this web application potentially useful to both clinicians and researchers in this era of personalised medicine. Finally, chapter 7 describes a bioinformatics education web portal that equips students with information on how to use bioinformatics online resources. Being aware of these resources is not enough without a deeper understanding and guidance on how to apply bioinformatics methods to solve practical problems. This web portal was aimed at familiarising students with the basic terminology and approaches in structural bioinformatics. Students will potentially gain skills to conduct real-life bioinformatics research to obtain biological insights. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
The effect of various substrate pretreatment methods on the enzymatic degradability of a Eucalyptus sp. – a potential feedstock for producing fermentable sugars
- Authors: Thoresen, Mariska
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/178580 , vital:42952
- Description: Access restricted until April 2022. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Thoresen, Mariska
- Date: 2021-04
- Subjects: To be added
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/178580 , vital:42952
- Description: Access restricted until April 2022. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2021
- Full Text:
- Date Issued: 2021-04
Perceptions of teachers on the implementation of positive learner discipline: A case study of three primary schools in the Amathole-West Education District
- Authors: Bantom, Laetitia Anneline
- Date: 2020-06
- Subjects: School discipline , Classroom management
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/19980 , vital:44915
- Description: The aim of this study was to gain an insight into perceptions of teachers on the implementation of positive learner discipline in three primary schools in the Amathole- West Education District. The study was in the interpretive paradigm and adopted a qualitative approach in the collection of data. A case study design through face-to-face interviews and document analysis related to positive discipline were used for data collection. Three schools were selected through purposive sampling. Four teachers per school participated in the study and these were purposively sampled. Data from the findings were thematically presented and analysed by scrutinizing it for commonalities. The study revealed that teachers had ample knowledge on positive learner discipline and therefore tried to implement it to the best of their abilities. The study also established that teachers perceived positive discipline as a good approach for disciplining learners. Participants were aware that positive learner discipline made learners feel and that it assisted them to improve and sustain good behaviour. Data revealed that schools used different strategies to implement positive learner discipline, such as, class rules, rewards and awards, personal relationship with learners, role model, communication with learners, point system, goal setting, hand-system and sign language, isolated area in front of the classroom, positive attention and guidelines on discipline. In contrast, the study also revealed that a minority of teachers still administered corporal punishment, which is unlawful and traditional. They also applied punitive disciplinary measures. The study concluded that the selected schools encountered various challenges on the implementation of positive learner discipline. These included undisciplined learners, limited involvement and minimal support from the Department of Education (DoE) and limited support from the School Management Team (SMT), uninformed, ignorant and rude parents, lack of parental involvement, parents using punitive measures, no proper training for teachers and parents, overcrowded classrooms and unhappy teachers. As for monitoring and support from the SMT and DoE, the study envisaged that most participants were supported by the SMT, other than the DoE. , Thesis (MEd) -- Faculty of Education, 2020
- Full Text:
- Date Issued: 2020-06
- Authors: Bantom, Laetitia Anneline
- Date: 2020-06
- Subjects: School discipline , Classroom management
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/19980 , vital:44915
- Description: The aim of this study was to gain an insight into perceptions of teachers on the implementation of positive learner discipline in three primary schools in the Amathole- West Education District. The study was in the interpretive paradigm and adopted a qualitative approach in the collection of data. A case study design through face-to-face interviews and document analysis related to positive discipline were used for data collection. Three schools were selected through purposive sampling. Four teachers per school participated in the study and these were purposively sampled. Data from the findings were thematically presented and analysed by scrutinizing it for commonalities. The study revealed that teachers had ample knowledge on positive learner discipline and therefore tried to implement it to the best of their abilities. The study also established that teachers perceived positive discipline as a good approach for disciplining learners. Participants were aware that positive learner discipline made learners feel and that it assisted them to improve and sustain good behaviour. Data revealed that schools used different strategies to implement positive learner discipline, such as, class rules, rewards and awards, personal relationship with learners, role model, communication with learners, point system, goal setting, hand-system and sign language, isolated area in front of the classroom, positive attention and guidelines on discipline. In contrast, the study also revealed that a minority of teachers still administered corporal punishment, which is unlawful and traditional. They also applied punitive disciplinary measures. The study concluded that the selected schools encountered various challenges on the implementation of positive learner discipline. These included undisciplined learners, limited involvement and minimal support from the Department of Education (DoE) and limited support from the School Management Team (SMT), uninformed, ignorant and rude parents, lack of parental involvement, parents using punitive measures, no proper training for teachers and parents, overcrowded classrooms and unhappy teachers. As for monitoring and support from the SMT and DoE, the study envisaged that most participants were supported by the SMT, other than the DoE. , Thesis (MEd) -- Faculty of Education, 2020
- Full Text:
- Date Issued: 2020-06
A study of four-dimensional oscillator groups and the associated left-invariant control affine systems
- Authors: Biggs, Rory
- Date: 2012
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164941 , vital:41186
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Department of Mathematics, 2012
- Full Text:
- Date Issued: 2012
- Authors: Biggs, Rory
- Date: 2012
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164941 , vital:41186
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Department of Mathematics, 2012
- Full Text:
- Date Issued: 2012
Ritualised discourse practices of feedback in a university foundation programme: a critical investigation
- Authors: Richardson, Amy
- Date: 2012
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MA
- Identifier: http://hdl.handle.net/10962/164955 , vital:41187
- Description: In order for students to become true members of academic communities of practice they need epistemological access, including guidance on central institutional knowledge-producing processes and mastery of key academic literacy practices. A powerful source of guidance is marker feedback. Drawing on key insights from the New Literacy Studies and taking up the mandate of Critical Ethnography to improve the status quo, this thesis reports on the feedback practices in a university foundation programme. The findings are based on three micro-case studies compiled and analysed by means of methods drawn from Ethnography, Sociolinguistics and Critical Analysis in conjunction with an expanded, multimodal, APPRAISAL analysis, including adjusted categories and the author’s own feedback typologies. Two major arguments emerge: the feedback provided amounts to a set of ritualised discourse practices and its effects can be likened to the product of the children’s game of Head-body-tail. Consequently, feedback conventions are opaque and, potentially, impede epistemological access. They further entrench five sets of ideologies: (1) Students must master basic English literacy before they are coached in more complex issues such as argumentation; an assumption which leads to differential socialisation. (2) There is a single set of literacy practices that is rewarded. (3) Students have different levels of authorial authority depending on their language abilities. (4) ‘Middle students’ may benefit the most from feedback. (5) Specific comments are preferred over general ones. Analysis of feedback, furthermore, shows that markers’ frames of reference shape their pedagogy and that draft and final versions of work may be framed differently by markers. These findings require a response and, in order to facilitate epistemological access, suggestions are made for improved marker training based on the problematisation of the ritual involved in marking students’ work in this university foundation programme. , Thesis (MA)--Rhodes University, Faculty of Humanities, Linguistics, 2012
- Full Text:
- Date Issued: 2012
- Authors: Richardson, Amy
- Date: 2012
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MA
- Identifier: http://hdl.handle.net/10962/164955 , vital:41187
- Description: In order for students to become true members of academic communities of practice they need epistemological access, including guidance on central institutional knowledge-producing processes and mastery of key academic literacy practices. A powerful source of guidance is marker feedback. Drawing on key insights from the New Literacy Studies and taking up the mandate of Critical Ethnography to improve the status quo, this thesis reports on the feedback practices in a university foundation programme. The findings are based on three micro-case studies compiled and analysed by means of methods drawn from Ethnography, Sociolinguistics and Critical Analysis in conjunction with an expanded, multimodal, APPRAISAL analysis, including adjusted categories and the author’s own feedback typologies. Two major arguments emerge: the feedback provided amounts to a set of ritualised discourse practices and its effects can be likened to the product of the children’s game of Head-body-tail. Consequently, feedback conventions are opaque and, potentially, impede epistemological access. They further entrench five sets of ideologies: (1) Students must master basic English literacy before they are coached in more complex issues such as argumentation; an assumption which leads to differential socialisation. (2) There is a single set of literacy practices that is rewarded. (3) Students have different levels of authorial authority depending on their language abilities. (4) ‘Middle students’ may benefit the most from feedback. (5) Specific comments are preferred over general ones. Analysis of feedback, furthermore, shows that markers’ frames of reference shape their pedagogy and that draft and final versions of work may be framed differently by markers. These findings require a response and, in order to facilitate epistemological access, suggestions are made for improved marker training based on the problematisation of the ritual involved in marking students’ work in this university foundation programme. , Thesis (MA)--Rhodes University, Faculty of Humanities, Linguistics, 2012
- Full Text:
- Date Issued: 2012
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