Conceptual framework for a Malaria VRE in South Africa


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Presentation about the proposed South African Malaria Virtual Research Environment (VRE) at the Research Information Centre (RIC) Stakeholder Event 23 March 2009

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  • Conceptual framework for a Malaria VRE in South Africa

    1. 1. Conceptual framework for a Malaria VRE in South Africa Dr Heila Pienaar (UP) & Dr Martie van Deventer (CSIR) The Research Information Centre Stakeholder Event London, 23 March 2009
    2. 2. Timeline of investigation <ul><li>South African Research Information Services (SARIS) project – 2004 </li></ul><ul><ul><li>Identified virtual research environments (VRE’s) as an important component of current global research – no national initiative was forthcoming </li></ul></ul><ul><li>Utilising the SERA relationship between CSIR & UP </li></ul><ul><ul><li>SERA – Southern Education Research Alliance </li></ul></ul><ul><ul><li>Our aim was to establish a conceptual framework for a VRE </li></ul></ul><ul><ul><li>Needed research area with much data generation </li></ul></ul><ul><ul><li>African Centre for Gene Technologies’ South African Malaria Initiative (ACGT SAMI) was identified by Executives </li></ul></ul><ul><li>Malaria VRE investigation – 2006 / 2007 </li></ul><ul><ul><li>ACGT management agreed to participate </li></ul></ul><ul><ul><li>Completed ‘a day in the life’ & research tools via semi-structured interviews with 20 malaria researchers in the SAMI network to establish their readiness to move to an integrated VRE </li></ul></ul><ul><li>Building of a Malaria VRE demonstrator (not a prototype) – 2007 </li></ul><ul><li>Final Report – July 2008 (including feedback to researchers). This investigation identified the following as priorities for our future work: </li></ul><ul><ul><li>The activities carried out to perform scientific experiments i.e. the experimental workflow needs more investigation. </li></ul></ul><ul><ul><li>The wider context in which the research is conducted needs to be taken into consideration. </li></ul></ul><ul><ul><li>The current tools used by the SAMI researchers have to be embedded for all before they are expanded and enhanced by new tools. </li></ul></ul><ul><ul><li>The collaboration needs of this specific group needs to drive the priorities for their VRE’s development </li></ul></ul><ul><li>The next step should be to build a prototype Malaria or generic VRE that can function on top of the South African NREN with the support of key South African stakeholders and by using software elements of other international VRE-type developments e.g. the British Library’s RIC, University of Purdue’s HUBzero, JISC’s myExperiment and Australia’s ARCHER e-Research toolkit </li></ul>
    3. 3. A day in the life <ul><li>Researchers </li></ul><ul><ul><li>Start the day with e-mail </li></ul></ul><ul><ul><li>Largest chunk of day spent in wet lab </li></ul></ul><ul><ul><li>Articles are written by teams </li></ul></ul><ul><ul><li>Management of research data: majority of files only traceable via the paper lab book </li></ul></ul><ul><ul><li>The value of electronic lab books and managing their data and information properly is understood by all … but is not currently done in any coherent fashion </li></ul></ul><ul><ul><li>Much time spent on report writing …. </li></ul></ul><ul><ul><li>Whatever ‘assistance’ is added should not contribute to their administrative burden </li></ul></ul><ul><li>Managers </li></ul><ul><ul><li>Days are planned around scheduled meetings </li></ul></ul><ul><ul><li>Face-to-face their preferred mode of communication </li></ul></ul><ul><ul><li>Spend “alone time” looking at research agendas, trends and opportunities </li></ul></ul><ul><ul><li>Understand that the ‘big problems’ associated with malaria could only be resolved by multi-disciplinary teams …. </li></ul></ul>Conclusion: the researchers and their managers are ready for a changed work environment!
    4. 4. Consolidated SAMI VRE components Red: none Orange: some Yellow: all Scientific workflow (Collaborative) Electronic Lab book Sophisticated instruments that generate digital information and data Servers with data files (Free) Data analysis software Integrated data management system Access to research networks & super computers; access to labs with in silico screening + Mathematical modelling tools; numerical algorithm tools; simulation software; in silico experiments Conclusion: the infrastructure needs much work to be converted to an integrated VRE Project management Project management system Proposal writing Document management system Generic software e.g. MS / Open Office Real time communication Skype, smart board, video conferences Training / mentoring etc E-learning system for researchers Identification of funding sources Identification of research area Literature review & indexing Identification of collaborators Internal shared database of indexed articles Dissemination & artifacts Web/wiki/blog : search engines, databases; researchers & topics; funders, portals, communication, projects Repositories : research results; experiments; literature & documents
    5. 5. Demonstrator Interface Access and authentication Alerts and RSS feeds – may help with info overload Library resources Internet resources
    6. 6. BL / MS RIC: Manage-ment of published info ResearchGate: research collaboration OPENWETWARE: Lab Notebook on Blog myexperiment: scientific workflows archer e-Research toolkit: data management nanoHUB: subject gateway built on HUBzero platform HUBzero: access to interactive simulation tools