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Bioinformatics Service Platform

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Background

The Department of Science and Technology has contracted with the Council for Scientific and Industrial Research for CHPC to establish and host the Bioinformatics Support Platform (BSP). This contract of the BSP was based on a proposal submitted and approved by DST to expand from the pilot project (which was funded in 2013/14 financial year) into a national platform, with the possibility of extending it into a national institute of applied bioinformatics/computational biology. The BSP is overseen by a steering committee as well as two subcommittees for Services and Training respectively.

Key objectives

The following are the main objectives for the BSP in the 2014/15 financial year:

  • establish and implement a governance framework
  • define business model, service level agreements, and operational procedures
  • assemble a BSP team
  • provide bioinformatics services to academic and industrial researchers
  • provide support to bioinformaticians in lab-based research groups (embedded bioinformaticians);
  • install and maintain relevant software tools and data resources
  • improve the usability and accessibility of CHPC facilities
  • interact with the wider biological science communities and foster formalised collaboration
  • provide a coordinated platform of relevant bioinformatics services
  • facilitate specialised short-term courses and postgraduate training
  • foster collaboration with the private sector
  • engage in international activities to improve capabilities and attract projects and funding

 

Technical and Research Support

The application scientist (Dane Kennedy) interacts with the commercial/academic researchers, providing programming, application and experiment analysis support, conducts training to improve the affectivity of HPC users, and assists in the setup, running and development of HPC software and job scripts, while the systems engineer (Inus Scheepers) sets up and ensures the availability of computing, storage and network resources for computational biology work, and explores hardware and software options to support and amplify the research efforts. These job functions overlap to some extent. BSP makes use of a dedicated cluster node and virtual machines to stage and manage cluster jobs, deploy various software systems, and host training-related material.

 

The BSP web site http://bio.chpc.ac.za has been set up and populated, linking to the various resources available. The reference databases are regularly and automatically mirrored, and a mailing list, CHPC-Bio, was created on the CHPC list server for community announcements and discussions.

 

Human Capital Development

The BSP’s training activities will be coordinated by an Education Committee in conjunction with relevant stakeholders, including the South African Bioinformatics Society. They will determine the training needs and develop criteria for hosting or participating in a course and they will also develop appropriate evaluation procedures to ensure a high quality, integrated training programme. 

Last Updated on Tuesday, 25 November 2014 12:42

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Vacancies and Tenders

No vacancies at the moment.

Last Updated on Thursday, 20 November 2014 12:32

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Last Updated on Thursday, 19 June 2014 13:09

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Cliffton M Masedi

Cliffton M Masedi: Computational Modelling of Materials Researcher

Cliffton holds a BSc degree in Physics and Chemistry and a BSc Hons (Physics). His MSc was upgraded in the year 2013 at University of Limpopo (Turfloop Campus), and he is currently studying towards a PhD. During his post-graduate studies, he served as a Research Assistant at the Materials Modelling Centre, a dedicated research centre in University of Limpopo. His thesis entails the computational modelling of advanced materials which are applied in energy storage technologies. Part of his research focus is on the discharge products of rechargeable lithium batteries, which could play a key role in the advancement of next-generation batteries.

In July 2011, he joined the Centre for High Performance Computing (CHPC) as a part of his MSc studentship. He has successfully coordinated some outreach and public awareness programmes through the CHPC. In March 2014 he was the first person to represent Limpopo and the CHPC at the International FameLab South Africa competition; his presentation was about the benefit of using High Performance Computing in the development of energy storage technologies. Cliffton has presented his research findings at local, national and international conferences. The excellence of his academic efforts has rewarded him with awards; this includes a best MSc research paper award in 2011 and a best MSc research paper award in 2013 both from the Faculty of Science and Agriculture Research Day at University of Limpopo.

Last Updated on Tuesday, 08 April 2014 09:38

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