PRIMO: an interactive homology modeling pipeline
- Hatherley, Rowan, Brown, David K, Glenister, Michael, Tastan Bishop, Özlem
- Authors: Hatherley, Rowan , Brown, David K , Glenister, Michael , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148282 , vital:38726 , doi: 10.1371/journal.pone.0166698
- Description: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling.
- Full Text:
- Date Issued: 2017
- Authors: Hatherley, Rowan , Brown, David K , Glenister, Michael , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148282 , vital:38726 , doi: 10.1371/journal.pone.0166698
- Description: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling.
- Full Text:
- Date Issued: 2017
Intellectualisation of isiXhosa literature: the case of Jeff Opland
- Authors: Kaschula, Russell H
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67030 , vital:29022 , https://doi.org/10.17159/2309-9070/tvl.v.54i2.413
- Description: publisher version , The origins of the intellectualisation of written isiXhosa literature are often attributed to the missionaries John Ross and John Bennie. They set up a printing press in the Tyhume Valley which later became known as Lovedale Press. They introduced written isiXhosa in 1823 and for this they are acknowledged as the first to write and publish in isiXhosa. This article attempts to trace this intellectualisation process of isiXhosa literature, concentrating on a critique and assessment of the life-long work of Professor Jeff Opland, who has contributed enormously to the present understanding of both oral and written isiXhosa literature. It is argued in this article that his corpus of books and academic articles require some contextualisation within the broader debate of the continued intellectualisation of isiXhosa language and literature. Reference is also made to the Opland isiXhosa literature archive and its contribution to the further intellectualisation of isiXhosa literature. It is suggested in this article that Opland is one of the greatest contributors to academic debates concerning isiXhosa literature and history. Izibongo or oral poems written by, and about Jeff Opland are analysed to further enhance the context of his contribution.
- Full Text:
- Date Issued: 2017
- Authors: Kaschula, Russell H
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67030 , vital:29022 , https://doi.org/10.17159/2309-9070/tvl.v.54i2.413
- Description: publisher version , The origins of the intellectualisation of written isiXhosa literature are often attributed to the missionaries John Ross and John Bennie. They set up a printing press in the Tyhume Valley which later became known as Lovedale Press. They introduced written isiXhosa in 1823 and for this they are acknowledged as the first to write and publish in isiXhosa. This article attempts to trace this intellectualisation process of isiXhosa literature, concentrating on a critique and assessment of the life-long work of Professor Jeff Opland, who has contributed enormously to the present understanding of both oral and written isiXhosa literature. It is argued in this article that his corpus of books and academic articles require some contextualisation within the broader debate of the continued intellectualisation of isiXhosa language and literature. Reference is also made to the Opland isiXhosa literature archive and its contribution to the further intellectualisation of isiXhosa literature. It is suggested in this article that Opland is one of the greatest contributors to academic debates concerning isiXhosa literature and history. Izibongo or oral poems written by, and about Jeff Opland are analysed to further enhance the context of his contribution.
- Full Text:
- Date Issued: 2017
The thin edge of the wedge: ukuthwala, alienation and consent
- Mwambene, Lea, Kruuse, Helen
- Authors: Mwambene, Lea , Kruuse, Helen
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/129165 , vital:36226 , https://doi.org/10.1080/02587203.2017.1303902
- Description: Ukuthwala, a mock abduction of a girl for the purpose of a customary marriage, has been subject to debate at both local and national level. This debate culminated into a South African Law Reform Commission Report on the practice of ukuthwala. However, the case of Jezile v S brings theory into reality, putting in stark relief the issues that surround this custom in a constitutional democracy. The Jezile case highlights the disjuncture between communities’ lived realities and the constitutional imperatives of the right to practice one’s culture, as well as the rights to equality and dignity, specifically for women and the girl child in the context of ukuthwala. Based on field research conducted in September 2015 and April 2016 in Engcobo (where the ukuthwala was alleged to take place in Jezile), this article sets out the community’s views in the aftermath of the case. Highlighting the alienation of the community from the law, and the complexities in understanding consent, the article posits that much more needs to be done from the ‘bottom up’ to ensure gender equality and protection of the girl child from harm.
- Full Text:
- Date Issued: 2017
- Authors: Mwambene, Lea , Kruuse, Helen
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/129165 , vital:36226 , https://doi.org/10.1080/02587203.2017.1303902
- Description: Ukuthwala, a mock abduction of a girl for the purpose of a customary marriage, has been subject to debate at both local and national level. This debate culminated into a South African Law Reform Commission Report on the practice of ukuthwala. However, the case of Jezile v S brings theory into reality, putting in stark relief the issues that surround this custom in a constitutional democracy. The Jezile case highlights the disjuncture between communities’ lived realities and the constitutional imperatives of the right to practice one’s culture, as well as the rights to equality and dignity, specifically for women and the girl child in the context of ukuthwala. Based on field research conducted in September 2015 and April 2016 in Engcobo (where the ukuthwala was alleged to take place in Jezile), this article sets out the community’s views in the aftermath of the case. Highlighting the alienation of the community from the law, and the complexities in understanding consent, the article posits that much more needs to be done from the ‘bottom up’ to ensure gender equality and protection of the girl child from harm.
- Full Text:
- Date Issued: 2017
The Creolization of Political Theory and the dialectic of emancipatory thought: a plea for synthesis
- Authors: Neocosmos, M
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66076 , vital:28897 , https://doi.org/10.5195/jffp.2017.821
- Description: publisher version , The paper discusses Jane-Anna Gordon's important idea of the Creolization of Poitical Theory with reference to the work of Jean-Jacques Rousseau and Frantz Fanon. It makes an argument for synthesizing this initiative with dialectical thought in order to transcend the analytical vision which gave birth to the creolizing of theory. This synthesis is proposed in order to make sense of the real of any politics of universal emancipation and to incorporate the theoretical inventions of popular actions.
- Full Text:
- Date Issued: 2017
The Creolization of Political Theory and the dialectic of emancipatory thought: a plea for synthesis
- Authors: Neocosmos, M
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66076 , vital:28897 , https://doi.org/10.5195/jffp.2017.821
- Description: publisher version , The paper discusses Jane-Anna Gordon's important idea of the Creolization of Poitical Theory with reference to the work of Jean-Jacques Rousseau and Frantz Fanon. It makes an argument for synthesizing this initiative with dialectical thought in order to transcend the analytical vision which gave birth to the creolizing of theory. This synthesis is proposed in order to make sense of the real of any politics of universal emancipation and to incorporate the theoretical inventions of popular actions.
- Full Text:
- Date Issued: 2017
Deep wounds... left... in hearts and minds: South African public history
- Authors: Wells, Julia C
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69742 , vital:29574 , http://dx.doi.org/10.5130/phrj.v24i0.5781
- Description: Public history practise in South Africa holds out much promise of further things to come. It can close the gulf between history and heritage. This chapter argues that the role of the public historian should not be conflated with the dynamics of the heritage sector, but suggests how trained academics can indeed put their skills to work in a society that is passionately interested in understanding itself and how its pasts created the present. The student movement sharply raised the image of universities in crisis, requiring a whole new, relevant curriculum and rethinking the ways that universities relate to their publics. Public historians can work towards creating invented spaces for co-production of knowledge, moving beyond the traditional oral history interview. The divide between academia and communities is huge and needs to be constantly tackled, providing access to the secluded information of the professional world. I suggest that due to their privileged place in society, many historians have been unable or unwilling to engage with the recovery agenda – the massive need for affirmation of African identity, capacity and culture. A handful of dedicated public historians do not fit this mould and have been exemplary in rolling up their sleeves and boldly engaging with the messy complications of dealing with non-academic communities to produce new forms of historical knowledge, based on inclusiveness.
- Full Text:
- Date Issued: 2017
- Authors: Wells, Julia C
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69742 , vital:29574 , http://dx.doi.org/10.5130/phrj.v24i0.5781
- Description: Public history practise in South Africa holds out much promise of further things to come. It can close the gulf between history and heritage. This chapter argues that the role of the public historian should not be conflated with the dynamics of the heritage sector, but suggests how trained academics can indeed put their skills to work in a society that is passionately interested in understanding itself and how its pasts created the present. The student movement sharply raised the image of universities in crisis, requiring a whole new, relevant curriculum and rethinking the ways that universities relate to their publics. Public historians can work towards creating invented spaces for co-production of knowledge, moving beyond the traditional oral history interview. The divide between academia and communities is huge and needs to be constantly tackled, providing access to the secluded information of the professional world. I suggest that due to their privileged place in society, many historians have been unable or unwilling to engage with the recovery agenda – the massive need for affirmation of African identity, capacity and culture. A handful of dedicated public historians do not fit this mould and have been exemplary in rolling up their sleeves and boldly engaging with the messy complications of dealing with non-academic communities to produce new forms of historical knowledge, based on inclusiveness.
- Full Text:
- Date Issued: 2017
- «
- ‹
- 1
- ›
- »