Virtual research environments: learning gained from a situation and needs analysis for malaria researchers

Transcription

1 Virtual research environments: learning gained from a situation and needs analysis for malaria researchers Martie van Deventer (CSIR), Heila Pienaar (UP), Jane Morris (ACGT) and Zoleka Ngcete (SAMI) African Digital Scholarship and Curation Conference, Pretoria: 12 May 2009

2 Roadmap Context/ Timeline Results: A day in my life Conceptual model The demonstrator Way forward & conclusions

3 Definition - VRE The VRE concept helps to broaden the popular definition of e-science from grid-based distributed computing for scientists with huge amounts of data to the development of online tools, content, and middleware within a coherent framework for all disciplines and all types of research (Fraser, 2005). The specific aim of a VRE is to help researchers manage the increasingly complex range of tasks involved in carrying out research. Therefore a VRE provides a framework of resources to support the underlying processes of research on both small and large scales, particularly for those disciplines which are not well catered for by current infrastructure (JISC, 2006).

4 Context/Timeline of investigation South African Research Information Services (SARIS) project 2004 Identified virtual research environments (VRE s) as an important component of current global research SERA partnership SERA Southern Education Research Alliance Our aim was to establish a conceptual framework for a VRE Needed research area with much data generation African Centre for Gene Technologies South African Malaria Initiative (ACGT SAMI) was identified by Executives Malaria VRE investigation 2006 / 2007 ACGT management agreed to participate Completed a day in the life & research tools via semistructured interviews with 20 malaria researchers in the SAMI network to establish their readiness to move to an integrated VRE Built VRE demonstrator (not a prototype) 2007 Final Report July 2008 Current: building a prototype

5 Demographics: A day in my life Age group Institution # Interviewed Male Female Management Research < >40 CSIR UP Other SAMI Total

6 Areas of specialization Bio-Chemist Biochemistry and Pharmacology Bio-Chemistry/ Molecular Chemistry/ Proteins/ Bio-Informatics Bio-Informaticist Bio-Inorganic Chemistry Bio-Organic Chemistry Cell biology (Malaria) Functional Genomics (Malaria) Infectious Diseases Malaria / GMOs Molecular Biology (2) Molecular Biotechnology Peptide structure chemistry Pharmacology Research Management (4) Synthetic Medicinal Chemistry

7 Researchers All work >40 hrs per week Start the day with Largest chunk of day spend in wet lab Articles are written by teams Management of research data: majority of files only traceable via the lab book Electronic lab books? Much time spending on report writing.

8 Researchers (2) All work in collaborative teams no individual authors Often - complex contractual/ agreement structure that needs to be understood Very little awareness of open access movement Credibility: as good as the last paper you wrote Very little awareness of curation needs for electronic artefacts Information overload is a common concern & a variety of strategies to cope have been developed

9 Researchers (3) Need for Information Scientists/ Librarians Only if faster at or more specialized at retrieval Only if they are connected to the research network Only if the knew/ could contribute to scientific discussions Only if they had informaticist skills could they help with research data Conclusion: undergraduate subject training

10 Managers Days are planned around scheduled meetings Face-to-face their preferred mode of communication Spend alone time looking at research agendas, trends and opportunities Problems with malaria could only be resolved by multi-disciplinary teams.

11 The preferred research process for SA Malaria researchers research area Literature review & indexing Sometimes go directly to Scientific workflow (little sub-routine) to test an idea or build a track record before going to further Dissemination & artefacts collaborators Real time communication Training / mentoring etc Scientific workflow Project management Proposal writing funding sources IP Management was not identified but needs to be taken into consideration

12 High impact traditional & open journals data sets required by some journals; conferences ; face-toface; phone; webex; wiki; web site; meetings Face-to-face; hands on; UP: e-learning for students Personal networks; faceto-face; literature; government documents research area Dissemination & artifacts Real time communication Training / mentoring etc Scientific workflow Sophisticated instruments with own software write data to servers; Free analysis software; Paper lab book; Referencing system between lab book and instruments; Ad hoc management of data (curation) Preferred databases: PubMed, Science Direct, Scopus; Retrieval: Google Scholar, Browser favourites; Filing: manual; database Literature review & indexing collaborators Proposal writing funding sources Project management CSIR: formal pm with tools & staff; UP: informal Personal networks; EU portal; literature; search engines; ACGT expert list MS Word / Open Office; templates; generic proposal Personal networks; funding agencies; institutional resources e.g. SAMI Current practices & tools

13 Research output repository Skype; collaborative e- Lab books; Smart board; video conf; project portal e-learning system for researchers Grouping of info in one place research area Dissemination & artifacts Real time communication Training / mentoring etc Scientific workflow Even more sophisticated instruments; Electronic lab book; Systems biology software; Experiment repository; Labs with in silico screening+; Bio-information specialist List of search engines; Internal shared database of indexed articles; Person to assist in retrieval of relevant literature Literature review & indexing collaborators Proposal writing funding sources Project management Proper pm system; MS Project SAMI wish list List of researchers & topics Document management system List of funders easily accessible e.g. web site

14 None of these researchers had access to/ used: A web / wiki / blog to use for lists of search engines, databases, researchers, funders, portals, projects, software, instruments Repositories for research results (articles, data etc), experiments and documents An integrated data management / curation system Collaborative electronic lab book system An e-learning system for researchers, e.g. to transfer knowledge about new methodologies Only some of the researchers were making use of: An internally shared database of indexed articles. Individual databases (paper / electronic) are quite popular. A document management system (CSIR) A project management system (CSIR) Acess to research networks, super computers and labs with insilico screening+ In silico experiment software Electronic communication tools (Skype, Smart board, Video conferencing etc) All of the researchers were making use of: Sophisticated instruments that generate digital information and data Servers with data files Mathematical modeling tools Numerical algorithm tools Simulation software Data analysis software (mostly freeware) Generic software e.g. MS and Open Office

15 Repositories: research results; experiments; literature & documents Web/wiki/blog: search engines, databases; researchers & topics; funders, portals, communication, projects research area Consolidated SAMI VRE components Literature review & indexing Red: none Orange: some Yellow: all Internal shared database of indexed articles Skype, smart board, video conferences Dissemination & artifacts Real time communication collaborators Proposal writing Document management system E-learning system for researchers Training / mentoring etc Scientific workflow funding sources Project management Generic software e.g. MS / Open Office (Collaborative) Electronic Lab book Integrated data management system Servers with data files Sophisticated instruments that generate digital information and data Mathematical modelling tools; numerical algorithm tools; simulation software; in silico experiments Access to research networks & super computers; access to labs with in silico screening + Project management system (Free) Data analysis software

16 Building the VRE demonstrator This was seen as an example not a pilot nor the start of a working VRE Utilised Web 2.0 tools Made use of third year UP Information Science students (practical work) and CSIR Interns (were already populating our institutional repository using DSpace) Development happened over a two week period

17 Web 2.0 tools used Training / mentoring etc Real time communication collaborators/ shared resources/ Experts Media Wiki MSM/ Google IM/ GMail Literature review & indexing RSS & Alerts Commercial Resources via Library funding sources research area Google Documents Management Proposal writing Dissemination & artifacts Combination of Blogger & DSpace Scientific workflow WebCoLab Project management IP Management was not identified but needs to be taken into consideration Portal interface Xoops

18 Interface Access and authentication Library resources Internet resources Alerts and RSS feeds may help with info overload

19 Personal space Blogger Authorisation through application Wiki Commercial Resources via Library Shared space DSpace WebCoLab MSM/Google Groups

20 Way forward The specific collaboration needs of this group have to remain the primary focus. The VRE would therefore need to grow and expand as the trust and the collaboration behaviour amongst group members grow. The current tools used by the SAMI researchers will have to be embedded for all first before the toolset could be expanded and perhaps be enhanced by new tools. The activities carried out to perform scientific experiments i.e. the experimental workflow needs much more investigation. The wider developing country/region cyber infrastructure will at all times need to be taken into consideration.

21 Conclusion Developing country context certainly holds constraints that need to be considered VRE would have to be designed for home access low bandwidth & limited computing power Researchers are rarely able to focus on one area of research (ie malaria) exclusively VRE should therefore also cater for other fields of research interest The collaboration between researcher, information specialist/librarian & information technologist needs facilitation its not a natural partnership!

22 Questions?