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
Timeline of investigation
•
South African Research Information
Services (SARIS) project – 2004
–
•
•
Utilising the SERA relationship
between CSIR & UP
–
–
–
–
•
Identified virtual research environments
(VRE’s) as an important component of
current global research – no national
initiative was forthcoming
•
–
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 semi-structured interviews
with 20 malaria researchers in the
SAMI network to establish their
readiness to move to an integrated
VRE
Building of a Malaria VRE demonstrator
(not a prototype) – 2007
Final Report – July 2008 (including
feedback to researchers). This
investigation 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 current tools used by the SAMI
researchers have to be embedded for all
before they are expanded and enhanced
by new tools.
– The collaboration needs of this specific
group needs to drive the priorities for their
VRE’s development
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 VREtype developments e.g. the British Library’s
RIC, University of Purdue’s HUBzero, JISC’s
myExperiment and Australia’s ARCHER eResearch toolkit
A day in the life
• Researchers
– Start the day with e-mail
– Largest chunk of day spent in
wet lab
– Articles are written by teams
– Management of research data:
majority of files only traceable
via the paper lab book
– 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
– Much time spent on report
writing ….
– Whatever ‘assistance’ is added
should not contribute to their
administrative burden
• 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
– Understand that the ‘big
problems’ associated with
malaria could only be resolved by
multi-disciplinary teams ….
Conclusion: the researchers and
their managers are ready for a
changed work environment!
Conclusion: the infrastructure
needs much work to be
converted to an integrated VRE
Repositories:
research results;
experiments;
literature &
documents
Consolidated SAMI VRE components
Identification of
research area
Literature review &
indexing
Dissemination &
artifacts
Skype, smart
board, video
conferences
E-learning
system for
researchers
(Collaborative)
Electronic Lab
book
Integrated
data
management
system
Red: none
Orange: some
Yellow: all
Web/wiki/blog: search engines,
databases; researchers &
topics; funders, portals,
communication, projects
Real time
communication
Identification of
collaborators
Proposal writing
Training / mentoring
etc
Scientific workflow
Servers with
data files
Internal shared
database of
indexed articles
Sophisticated
instruments that
generate digital
information and data
Mathematical modelling tools;
numerical algorithm tools; simulation
software; in silico experiments
Identification of
funding sources
Document
management
system
Generic
software e.g.
MS / Open
Office
Project management
Access to
research
networks &
super
computers;
access to labs
with in silico
screening +
Project
management
system
(Free) Data
analysis
software
Demonstrator Interface
Access and authentication
Library resources
Internet
resources
Alerts and RSS feeds – may help with
info overload
BL / MS RIC: Management of published info
ResearchGate:
research collaboration
OPENWETWARE: Lab
Notebook on Blog
myexperiment:
scientific workflows
HUBzero: access to
interactive simulation
tools
archer e-Research
toolkit: data
management
nanoHUB: subject
gateway built on
HUBzero platform