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To VRE Or Not to VRE?: Do South African Malaria Researchers Need a Virtual Research Environment?

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Heila Pienaar and Martie van Deventer identify the requirements of a Virtual Research Environment (VRE) for malaria researchers in South Africa.

Worldwide, the research paradigm is in the process of expanding into eResearch and open scholarship. This implies new ways of collaboration, dissemination and reuse of research results, specifically via the Web. Developing countries are also able to exploit the opportunity to make their knowledge output more widely known and accessible and to co-operate in research partnerships. Although there are exisiting examples of eResearch activities, the implementation of eResearch is not yet being fully supported in any co-ordinated way within the South African context. The South African Research Information Services (SARIS) Project was started inter alia because of the extremely high costs to South African research institutes and university libraries to access the global research literature. From the research it was very soon clear though that a new research paradigm was emerging and that this paradigm presented 'a broader range of information support service challenges' [1]. The project team established that 'activities making up the family of eResearch were to be found in various stages of development in the research life of South Africa in 2004 but, typically, a "Team South Africa" approach was not evident'. It was therefore recommended that a framework for eResearch services to the entire South African research community be created - as depicted in Figure 1.

The intention was that the 'eResearch development and innovation services' would be jointly funded as projects (conducted by competent agents in the system). Those projects that proved to be essential would then be transferred to the 'service delivery' arm (see Figure 1), where sustainable funding would be generated by those who made use of the service. The whole system was to be co-ordinated at country level. However, it soon became evident that there would be no national co-ordination of these efforts in the near future, and that individual institutions would have to start their own initiatives.

diagram (61KB) : Figure 1 : 2004 version of a proposed structure for eResearch support service for South Africa - a governance and management model

Figure 1: 2004 version of a proposed structure for eResearch support service for South Africa -
a governance and management model

The SARIS project team identified the United Kingdom's (UK) Joint Information Systems Committee (JISC) Virtual Research Environment (VRE) project as a prime example of an eResearch application. Because the purpose of a VRE is to help researchers in all disciplines manage the increasingly complex range of tasks involved in carrying out research 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. 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 (all file sizes) and all types of research [2].

The SARIS team members from the University of Pretoria and the CSIR decided to develop a conceptual framework for a South African VRE in support of eResearch.

The Academic Portal project of the University of Pretoria in 2001 investigated the factors that must be considered during the design and development of an academic portal that will support the personal information and knowledge management needs of academics. A model was identified as a conceptual framework for the study. During interviews with academics this model was validated as a sufficient framework to explain the personal management of academic information and knowledge. The knowledge management practices (collection, retrieval, organising, processing, creating, communicating and distributing academic information and knowledge) of these academics were investigated. The results gave an indication of the different academic practices that should be supported by an academic portal. Although the Internet and the Web had the potential to make a huge impact on academics' task performance, in practice the impact had been limited and these academics' Web literacy was actually quite low. These aspects had to be taken into account during the design and development of the academic portal. The concept and functionality of the prototype academic portal were acceptable to these academics and it was possible to develop guidelines for the development of an academic portal. The Infoportal was developed to accommodate these guidelines. The reaction to the Infoportal was very favourable and the launch took place in March 2003 [3]. In practice however it was evident that the portal was used more by management, project and administrative staff than faculty. One of the reasons for this situation is that the University's IT department is focused on the support of administrative functions. With this background it was understood that care would need to be taken that researchers do not perceive the development of a VRE as another initiative to support University administration.

The United Kingdom is an acknowledged leader in the field of VRE development. However, similar undertakings are being initiated in the United States, Europe as well as in Australia. The UK's Integrative Biology VRE (IBVRE) [4] and Building a VRE for the Humanities (BVREH) [5] projects served as two excellent examples, when investigating the requirements of a VRE for malaria researchers in South Africa.

Research Methodology

The most important research designs available to empirical research are the experiment, the quasi-experiment, the survey and the case study [6]. The case study was chosen as the overarching research design for this study, as it can be regarded as the most appropriate research design to answer the research questions. The South African Malaria Initiative (SAMI) Project was identified as the case study. The research design was based on that used for the University of Oxford-based investigation into the Integrative Biology VRE (IBVRE) and the UP Academic Portal projects.

Several data collection methods are available for empirical research, e.g. objective tests and scales, interviews, questionnaires, observations and sociometrics [7]. The exploratory nature of this project meant that it was neither straightforward nor desirable to construct a very rigid, structured interview format. Twenty semi-structured interviews were therefore held with individual malaria researchers and research managers at the following institutions: Council for Scientific and Industrial Research (CSIR) (9 interviews), University of Pretoria (UP) (4), University of Cape Town (UCT) (3), University of Stellenbosch (US) (2) and the Medical Research Council (MRC) (2). These interviewees were selected randomly from a list provided by the SAMI co-ordinators. A basic structured interview framework with two main parts was developed. The first part directed the interviewee to provide an account of the average day in his/her life while the second part required the researchers to describe the research process as well as the tools that they were using while conducting this average day. They were also asked to reflect on the tools they could anticipate using in the future - especially where these tools could support research currently deemed impossible or where the researchers' efficiency could be improved.

A Day in the Life of SA Malaria Researchers

Several informal discussions took place but 20 interviews were captured and analysed. The general distribution in terms of affiliation, gender, main function and age is reflected in table 1 below:

Institution
No. Interviewed
Male
Female
Management
Research
Age group
<30
Age group
30-40
Age group
>40
CSIR
9
6
3
4
5
 
4
5
UP
4
3
1
2
2
 
2
2
Other SAMI
7
4
3
2
5
1
1
5
Total
20
13
7
8
12
1
7
12

Table 1: Demographics of the interviewees

From this detail it is clear that the majority of those interviewed saw themselves primarily as researchers. The majority was male and over the age of 40. It is perhaps necessary to reflect on the age distribution. The majority of interviewees could not be regarded as digital natives. It was however, not possible to establish from this research if a younger group would have responded differently. The age distribution is however, a reality for malaria research and research in general in South Africa and would therefore need to be taken into consideration in the design of a VRE. It also became clear that malaria is very rarely the only field of interest as the respondents' research areas are much wider than just malaria.

The researchers' days are taken up by activities such as:

  • Starting the day with e-mail
  • Wet laboratory work (the largest chunk of day is still spent in the laboratory)
  • Articles written by teams
  • Management of research data: majority of files only traceable via the paper lab book
  • Completing paper lab books (electronic lab books are not used at this stage)
  • Much time is spent on writing progress reports

Research managers' days are focused on:

  • Scheduled meetings (their main activity)
  • Face-to-face communication (it remains their preferred mode of communication)
  • 'Alone time' is spent looking at research agendas, trends and opportunities

The group appeared to understand that the current problems associated with malaria research could only be resolved by multi-disciplinary teams and that a new research paradigm is about to be entered.

Conceptual Framework

The SA Malaria research cycle was developed on the grounds of the researchers' input on how they are doing research. They see research as an iterative and non-linear process rather than a definitive cycle but the research components was summarised in the following graphic (Figure 2):

diagram (88KB) : Figure 2 : The preferred research process for SA Malaria Researchers

Figure 2: The preferred research process for SA Malaria Researchers

The researchers themselves did not identify intellectual property management as a separate component and it was necessary to add that after feedback was given by some of the research managers.

Figure 2 consolidates the current practices of the interviewed SA malaria researchers. The 'agreed-upon' research cycle was used during the interviews to elicit information about the research practices linked to every stage of the research cycle. The importance of face-to-face communication and personal knowledge networks within the research community was stressed by all the researchers. One of the most important discoveries was the lack of knowledge about basic tools / software and the non-integration of those tools into the research cycle as a whole. In terms of the scientific workflow segment of the research cycle, the discrepancy between sophisticated instruments and the use of paper lab books was quite glaring. Obviously paper lab books cannot be used for the purposes of effective collaboration and long-term curation.

Stage No. Stage in Research Process Relevant Resources
1 Identification of research area Personal networks; face-to-face; literature; government documents
2 Literature review & indexing Preferred databases: PubMed, Science Direct, Scopus; Retrieval: Google Scholar, Browser favourites; Filing: manual; database
3 Identification of collaborators Personal networks; EU portal; literature; search engines; ACGT expert list
4 Proposal writing MS Word / Open Office; templates; generic proposal
5 Identification of funding sources Personal networks; funding agencies; institutional resources e.g. SAMI
6 Project management CSIR: formal project management with tools & staff; UP: informal
7 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)
8 Training/mentoring etc Face-to-face; hands on; UP: e-Learning for students
9 Real time communication E-mail; face-to-face; phone; webex; wiki; web site; meetings
10 Dissemination & artefacts High impact traditional & open journals - data sets required by some journals; conferences

Figure 3: SAMI current practices

In terms of the time distribution, it was made clear that at least 75% of all research time was spent on the scientific workflow segment of the cycle. The rest of the activities were done on an ad hoc rather than a daily basis – either at regular intervals (such as once weekly) or when new work is being investigated.

The identified need for tools varied from the relatively simple, e.g. lists of various types, to the quite sophisticated, e.g. electronic collaborative lab books and a repository for experiments (see Figure 4). In general researchers continuously emphasised the need for more sophisticated research equipment.

  Stage in Research Process Identified Need
1 Identification of research area Grouping of information in once place; Access to previous work
2 Literature review & indexing List of search engines; Internal shared database of indexed articles; Person to assist in retrieval of relevant literature
3 Identification of collaborators List of researchers & topics
4 Proposal writing Document management system
5 Identification of funding sources List of funders easily accessible e.g.web site
6 Project management Proper project management system; MS Project
7 Scientific workflow Even more sophisticated instruments; Electronic lab book; Systems biology software; Experiment repository; Labs with in silico screening*; Bio-information specialist
8 Training/mentoring etc e-Learning system for researchers
9 Real time communication Skype; Collaborative tools e.g. e-Lab books; Smart board; Video conference; Project portal
10 Dissemination & artefacts Research output repository

Figure 4: SAMI identified needs

Even though they claimed to be aware of the change in research practice, researchers did not consider the development of collaborative research infrastructure unless they were prompted to do so. It was surprising that they also did not verbalise any frustration in terms of sharing research with peers and partners. Several complaints were expressed that medical modelling software is very expensive. Similarly several respondents remarked how expensive research equipment is. They expressed the need for SAMI members to list the equipment they have available within the pool of research organisations. Several researchers supported the idea of in-silico* experimentation. A proper eLearning system for researchers would, one researcher remarked, increase efficiency because it would address the frustration of continuously having to explain processes/ protocols or to troubleshoot experiments. Several researchers expressed a need for repositories. Needs in respect of repository content ranged from compounds to datasets, to journal articles and to CVs of experts.

A consolidated model (conceptual framework) was created to represent both current and anticipated tools. In the consolidated model (Figure 5) it became clear that some very important aspects of collaborative malaria research were not being supported. It is therefore not surprising that they could not conceptualise the advantages nor visualise the new opportunities that a true collaborative research infrastructure would bring.

  Stage in Research Process VRE components Users
1 Identification of research area Web/wiki/blog: search engines, databases; researchers & topics; funders, portals, communication, projects none
2 Literature review & indexing Internal shared database of indexed articles some
3 Identification of collaborators Expertise lists and commercial services eg Web of Science and Research Africa none
4 Proposal writing Document management system some
5 Identification of funding sources Generic software e.g. MS / Open Office all
6 Project management Project management system some
7 Scientific workflow (Free) Data analysis software all
7 Scientific workflow Access to research networks & super computers some
7 Scientific workflow Sophisticated instruments that generate digital information and data all
7 Scientific workflow Mathematical modelling tools; numerical algorithm tools; simulation software; in silico experiments all
7 Scientific workflow Servers with data files all
7 Scientific workflow Integrated data management system none
7 Scientific workflow (Collaborative) Electronic Lab book none
8 Training/mentoring etc E-learning system for researchers none
9 Real time communication Skype, smart board, video conferences some
10 Dissemination & artefacts Repositories: research results; experiments; literature & documents none

Figure 5: Consolidated model of Malaria VRE components

Figure 5 indicates that:

None of the researchers appear to have access to:

  • A web / wiki / blog containing lists of search engines, databases, researchers, funders, portals, projects, software, instruments
  • Shared repositories for research results (articles, data, etc), experiments and documents
  • An integrated and indexed/ annotated 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 are making use of:

  • An internally shared database of indexed articles. (Private or individual
  • databases (both paper and electronic) are however quite popular.)
  • A document management system (CSIR)
  • A project management system (CSIR)
  • Access to research networks, super-computers and labs with in-silico screening
  • In-silico experiment software
  • Electronic communication tools (Skype, Smart board, Video conferencing etc)
  • Statistical analysis tools ('R' appears to be widely known but commercial products were also mentioned.)

All of the researchers are making use of:

  • Sophisticated instruments that generate digital information and data
  • Servers with data files
  • Mathematical modelling tools
  • Numerical algorithm tools
  • Simulation software
  • Data analysis software (mostly freeware)
  • Generic 'office' type software (e.g. MS Word and Open Write).
  • MS Excel is an application used by all.

While communicating research results it became clear that it would not be sufficient to share just the theoretical understanding of a VRE conceptual framework. It was decided to attempt to build a demonstrator (not a prototype) using Web 2.0 collaboration tools. It was believed that it would not take too much effort to demonstrate the advantages of VRE functions within a secure shared environment.

screenshot (45KB) : Figure 6 : Tools used in Malaria VRE demonstrator

Figure 6: Interface of Malaria VRE demonstrator

The demonstrator was designed around three types of workspaces i.e. the open Internet where anyone could gain access to the information made available, a secure but shared space and a secure private workspace. Tools were identified to deploy in each of these work areas. The interface was designed using a very easy-to-use portal and access to the secure team and personal areas was password-protected. Personal space was facilitated by creating blogs for individual researchers. These blogs served as lab books. The 'researcher' could give access to whom they wanted and they could upload personal material directly into the blog or link to research results and other materials which were placed in the repository. Repository items were indexed in more detail to ensure retrievability and sharability. Obviously, from the organisational perspective, the curation of electronic files within the repository became a more manageable task. (See figures 6, 7, 8).

screenshot (100KB) : Figure 7 : Tools used in Malaria VRE demonstrator

Figure 7: Tools used in Malaria VRE demonstrator

The demonstrator proved to be very successful in transferring concepts and in allowing hands-on experience in what the maintenance of a VRE would require.

screenshot (34KB) : Figure 8 : Relationship between personal and organisational information

Figure 8 : Relationship between personal and organisational information

During this phase of the VRE project (i.e. conceptual framework and demonstrator) it became clear that the development of a VRE is a massive task. Fortunately several developments took place internationally that could ease this process.

As mentioned above, some JISC VRE projects were watched quite closely at the start of the malaria VRE project but an explosion of international VRE-type initiatives took place during the Malaria VRE project that may have a positive impact on the development of a Malaria VRE prototype. Three of these initiatives are therefore discussed briefly:

myExperiment

The myExperiment toolkit enables the research community to share digital items associated with their research — in particular, it enables the researcher to share and execute scientific workflows. It supports individual scientists on their personal projects, forming a distributed community with scientists elsewhere who would otherwise be disconnected, enabling them to share, reuse and re-purpose experiments, to reduce time-to-experiment, share expertise and avoid reinvention — and it does this in the context of the scholarly knowledge lifecycle. Hence myExperiment is marketed as a community social network, a market place, a platform for launching workflows and a gateway to other publishing environments [8].

The British Library's Research Information Centre (RIC)

This project is managed by the British Library and developed by Microsoft Research and it appears to hold much promise. The beta test site was launched mid-June 2008 and malaria researchers were encouraged to participate in the test phase. The biggest advantage of participating in the RIC lies in the 'leapfrog' potential that it holds. South African malaria researchers would be immediately able to start concentrating on the collaborative way of creating content rather than having to struggle with the underlying technologies. At this stage the timeline of the RIC prototype must still be finalised [9].

HUBzero

The HUBzero platform was created by researchers at Purdue University, USA, in conjunction with the NSF-sponsored Network for Computational Nanotechnology. The purpose was to create science gateways for scientific domains. HUBzero allows the developer to create dynamic Web sites that connect a community in scientific research and educational activities. HUBzero sites combine powerful Web 2.0 concepts with a middleware that provides instant access to interactive simulation tools. These tools are not just Java applets, but real research codes that can access the Open Science Grid, and other national Grid computing resources. Seven other science gateways are currently under construction [10]. According to an email communication from Dr. Gerhard Klimeck, Associate Director for Technology Network for Computational Nanotechnology (NCN) and Professor of Electrical Engineering, Purdue University, the HUBzero package will become open source late in 2009. It seems as if the HUBzero platform could inform the design of a malaria VRE – especially then in terms of including the grid technology which is necessary for modelling large datasets. The availability of the code as open source and the possibility of customising specific VREs for different subject fields are added bonuses.

Way Forward

The development of a VRE does not and should not exist in isolation. It is recommended that the development of a prototype is aligned with the South African research cyber-infrastructure development. The improved research infrastructure will address research efficiency improvements - allowing researchers to address the grand challenges in science, engineering, medicine and humanities. It will also improve research effectiveness – allowing multi-disciplinary research and ensuring curation of scientific content. Not only should researchers be able to do the tasks more quickly and collaborate more easily, they should also be assured that their research efforts will be available for future reference.

This research project identified the following as priorities for our future work:

  • The activities carried out to perform scientific experiments i.e. the experimental workflow needs more investigation.
  • The wider context in which the research is conducted needs to be taken into consideration.
  • The tools used by the SAMI researchers have to be embedded for all before they are expanded and enhanced by new tools.
  • The specific collaboration needs of this group have to be the primary focus.

The nanoHUB development at Purdue University is an excellent example of how a VRE could work when placed on top of National Research Network (NREN or grid) infrastructure. It is harnessing the power of grid computing to provide a single entry point to scientific tools, discoveries, and research on the Web without forcing researchers to download a single piece of code [11].

It is important to remember that our researchers are not working on malaria exclusively. This aspect would need to be kept in mind in the design of the VRE and it may just be necessary to build a generic VRE that also caters for other fields of research interest or the VRE could contribute rather than resolve frustrations. In addition the researchers confessed to working at home. A VRE would have to be designed for home access – especially in terms of the collaborative writing component.

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 the SA government and by using software elements of other international VRE-type developments e.g. the British Library's RIC, University of Purdue's HUBzero and JISC's myExperiment.

Conclusion

The question remains: do our researchers need to develop VREs? We are of the opinion that they do, that it would greatly enhance their workflow and improve researcher efficiency and allow South African research organisations to come to grips with the management of its digital research content. The not so obvious advantage is that it would also allow for effectiveness gains especially because our researchers are already working across several areas of expertise. It is clear however, that South Africa, as a developing country with its own particular challenges, would need to think carefully how this development would enhance our research - especially then in research areas such as malaria. It should, for example, not be used as a mechanism to control research output. A further challenge is that it is not yet clear how our newly promulgated Act, on the protection of intellectual property created with public funding [12], will affect developments such as shared work environments. There is therefore an urgency in raising the funding to develop a first pilot project so that challenges could be systematically addressed.

Readers may wish to refer to work associated with this article [13][14] and also to presentations at the African Digital Scholarship & Curation 2009 Conference in Pretoria, South Africa [15].

* Editor's note: in-silico: "performed on computer or via computer simulation."

References

  1. Page-Shipp, RJ, Hammes, MMP, Pienaar, H, Reagon, F, Thomas, G, Van Deventer, MJ, Veldsman, S. (2005). e-Research support services: responding to a challenge facing the South African research and information communities, South African Journal of Information Management, 7/4. Accessed October 2008 from http://www.sajim.co.za/
  2. Fraser, M. (2005). "Virtual research environments: overview and activity". Ariadne, 44. Accessed October 2008 from
    http://www.ariadne.ac.uk/issue44/fraser/
  3. Pienaar, H. (2003). Design and development of an academic portal. Libri, 53/2, 118-129.
  4. Mascord, M. (2007). IBVRE final report. Acccessed October 2008 from http://www.vre.ox.ac.uk/ibvre/IBVRE-FinalReport-1a.pdf
  5. Virtual Research Environments programme (phase 1) Web site. Accessed October 2008 from http://www.jisc.ac.uk/whatwedo/programmes/vre1/bvreh.aspx
  6. Boshoff, AB. (1988). Navorsingsmetodiek in toegepaste geesteswetenskaplike navorsing (Research methodology in applied humanities research). South African journal for library and information science 56,1-6.
  7. Kerlinger. F.N. (1986). Foundations of behavioral research. New York: Holt, Rinehart and Winston
  8. myExperiment Web site. Accessed October 2008 from http://www.jisc.ac.uk/whatwedo/programmes/vre2/myexperiment.aspx
  9. Personal communication with Stephen Andrews of the British Library on 20 October 2008.
  10. HUBzero Web site. Accessed October 2008 from http://www.jisc.ac.uk/whatwedo/programmes/vre2/myexperiment.aspx
  11. Windham, C. (2007) The nanoHUB: Community and Collaboration. Educause Review, 42/6, 144-145. Accessed October 2008 from http://connect.educause.edu/Library/EDUCAUSE+Review/ThenanoHUBCommunityand Col/45232
  12. Republic of South Africa. 2008. Intellectual property rights from publicly financed research and development Act, Act No. 51 of 2008. http://www.info.gov.za/view/DownloadFileAction?id=94343
    This Act has been promulgated and the regulations in preparation are currently the subject of much concern. For one view, see the following blog entry by one South African commentator:
    Gray, E. 2009. The plan for innovation, IPR and public health is adopted at the WHO. How can this be reconciled with the IPR Act?
    http://blogs.uct.ac.za/blog/gray-area/2009/05/28/who-and-sa-ipr-act
  13. Van Deventer, M., Pienaar, H. Advance and attack: technology demonstrator to the rescue …and beyond. International Internet Librarian 2008 Conference. London. 16-17 October 2008
    https://www.up.ac.za/dspace/handle/2263/7878
  14. Van Deventer, M.J., Pienaar, H. Getting Executive Buy-In: The Value of Technology Demonstrators. Ninth Southern African Online Information Meeting. CSIR Conference Centre, Pretoria. 3-5 June 2008
    http://researchspace.csir.co.za/dspace/handle/10204/2263
  15. African Digital Scholarship & Curation 2009 Programme
    http://www.library.up.ac.za/digi/programme.htm

Author Details

Heila Pienaar
Deputy Director
e-Information Strategy & e-Research Enablement Library Services University of Pretoria
South Africa

Email: heila.pienaar@up.ac.za
Web site: http://www.ais.up.ac.za/profile/heila_pienaar/index.htm

Martie van Deventer
Portfolio Manager: CSIR Information Services
CSIR Council for Scientific and Industrial Research
South Africa

Email: mvandeve@csir.co.za
Web site: http://www.csir.co.za/

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Date published: 
30 April 2009

This article has been published under copyright; please see our access terms and copyright guidance regarding use of content from this article. See also our explanations of how to cite Ariadne articles for examples of bibliographic format.

How to cite this article

Heila Pienaar, Martie van Deventer. "To VRE Or Not to VRE?: Do South African Malaria Researchers Need a Virtual Research Environment?". April 2009, Ariadne Issue 59 http://www.ariadne.ac.uk/issue59/pienaar-vandeventer/


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