Differential motif enrichment analysis of paired ChIP-seq experiments
- Lesluyes, Tom, Johnson, James, Machanick, Philip, Bailey, Timothy L
- Authors: Lesluyes, Tom , Johnson, James , Machanick, Philip , Bailey, Timothy L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439250 , vital:73559 , https://doi.org/10.1186/1471-2164-15-752
- Description: Motif enrichment analysis of transcription factor ChIP-seq data can help identify transcription factors that cooperate or compete. Previously, little attention has been given to comparative motif enrichment analysis of pairs of ChIP-seq experiments, where the binding of the same transcription factor is assayed under different conditions. Such comparative analysis could potentially identify the distinct regulatory partners/competitors of the assayed transcription factor under different conditions or at different stages of development.
- Full Text:
- Authors: Lesluyes, Tom , Johnson, James , Machanick, Philip , Bailey, Timothy L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439250 , vital:73559 , https://doi.org/10.1186/1471-2164-15-752
- Description: Motif enrichment analysis of transcription factor ChIP-seq data can help identify transcription factors that cooperate or compete. Previously, little attention has been given to comparative motif enrichment analysis of pairs of ChIP-seq experiments, where the binding of the same transcription factor is assayed under different conditions. Such comparative analysis could potentially identify the distinct regulatory partners/competitors of the assayed transcription factor under different conditions or at different stages of development.
- Full Text:
How to establish a bioinformatics postgraduate degree programme—a case study from South Africa
- Machanick, Philip, Tastan Bishop, Özlem
- Authors: Machanick, Philip , Tastan Bishop, Özlem
- Date: 2014
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124641 , vital:35641 , https://doi.10.1093/bib/bbu014
- Description: The Research Unit in Bioinformatics at Rhodes University (RUBi), South Africa, offers a Masters of Science in Bioinformatics.Growing demand for bioinformatics qualifications results in applications from across Africa.Courses aim to bridge gaps in the diverse backgrounds of students who range from biologists with no prior computing exposure to computer scientists with no biology background. The programme is evenly split between coursework and research, with diverse modules from a range of departments coveringmathematics, statistics, computer science and biology, with emphasis on application to bioinformatics research. The early focus on research helps bring students up to speed with working as a researcher. We measure success of the programme by the high rate of subsequent entry to PhD study: 10 of 14 students who completed in the years 2011-2013.
- Full Text:
- Authors: Machanick, Philip , Tastan Bishop, Özlem
- Date: 2014
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124641 , vital:35641 , https://doi.10.1093/bib/bbu014
- Description: The Research Unit in Bioinformatics at Rhodes University (RUBi), South Africa, offers a Masters of Science in Bioinformatics.Growing demand for bioinformatics qualifications results in applications from across Africa.Courses aim to bridge gaps in the diverse backgrounds of students who range from biologists with no prior computing exposure to computer scientists with no biology background. The programme is evenly split between coursework and research, with diverse modules from a range of departments coveringmathematics, statistics, computer science and biology, with emphasis on application to bioinformatics research. The early focus on research helps bring students up to speed with working as a researcher. We measure success of the programme by the high rate of subsequent entry to PhD study: 10 of 14 students who completed in the years 2011-2013.
- Full Text:
Preliminary thoughts on services without servers
- Machanick, Philip, Hunt, Kieran
- Authors: Machanick, Philip , Hunt, Kieran
- Date: 2014
- Language: English
- Type: Conference paper
- Identifier: vital:6612 , http://hdl.handle.net/10962/d1014082
- Description: Warehouse-scale computing supports cloud-based services such as shared disk space, computation services and social networks. Although warehouse-scale computing is inexpensive per user, the cost to entry is high, and the pressures to generate revenues to cover costs leads service providers to pursue monetizing services aggressively. In this paper, we explore some ideas for removing the need for central servers by exploiting peer-to-peer technologies.
- Full Text:
- Authors: Machanick, Philip , Hunt, Kieran
- Date: 2014
- Language: English
- Type: Conference paper
- Identifier: vital:6612 , http://hdl.handle.net/10962/d1014082
- Description: Warehouse-scale computing supports cloud-based services such as shared disk space, computation services and social networks. Although warehouse-scale computing is inexpensive per user, the cost to entry is high, and the pressures to generate revenues to cover costs leads service providers to pursue monetizing services aggressively. In this paper, we explore some ideas for removing the need for central servers by exploiting peer-to-peer technologies.
- Full Text:
Teaching Without Technology
- Authors: Machanick, Philip
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439238 , vital:73558 , https://homes.cs.ru.ac.za/philip/Publications/_SACLA/teachWOtech-2014.pdf
- Description: Technology is touted as a solution to problems in education. But is it? I report here on experiences with dropping use of slides in lectures and returning to working on the board. The apparent result is more interactive, engaged classes. Unfortunately there are too many other variables to make the experiences here definitive. The purpose of this paper is to provoke discussion on whether technology is overused in teaching when the goals of improving student engagement and general effectiveness of learning can be met many ways. Technology is not necessarily bad, but making it the starting point risks locking out nontechnological options.
- Full Text:
- Authors: Machanick, Philip
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439238 , vital:73558 , https://homes.cs.ru.ac.za/philip/Publications/_SACLA/teachWOtech-2014.pdf
- Description: Technology is touted as a solution to problems in education. But is it? I report here on experiences with dropping use of slides in lectures and returning to working on the board. The apparent result is more interactive, engaged classes. Unfortunately there are too many other variables to make the experiences here definitive. The purpose of this paper is to provoke discussion on whether technology is overused in teaching when the goals of improving student engagement and general effectiveness of learning can be met many ways. Technology is not necessarily bad, but making it the starting point risks locking out nontechnological options.
- Full Text:
- «
- ‹
- 1
- ›
- »