>Magister Scientiae - MSc / The generation of biomedical research data on the African continent is grow-
ing, with numerous studies realizing the importance of African genetic diver-
sity in discoveries of human origins and disease susceptibility. The decrease in
costs to purchase and utilize such tools has enabled research groups to produce
datasets of signi cant scienti c value. However, this success story has resulted
in a new challenge for African Researchers and institutions. An increase in
data scale and complexity has led to an imbalance of infrastructure and skills
to manage, store and analyse this data. The lack of physical infrastructure has
left genomic research on the continent lagging behind its counterparts abroad,
drastically limiting the sharing of data and posing challenges for researchers
wishing to explore secondary analysis, study veri cation and amalgamation.
The scope of this project entailed the design and implementation of a proto-
type genome archive to support the e ective use of data resources amongst
researchers. The prototype consists of a web interface and storage backend
for users to upload and browse projects, datasets and metadata stored in
the archive. The server, middleware, database and server-side framework are
components of the genome archive and form the software stack. The server
component provides the shared resources such as network connectivity, le
storage, security and metadata database. The database type implemented in
storing the metadata relating to the sample les is a NoSQL database. This
database is interfaced with the iRods middleware component which controls
data being sent between the server, database and the Flask framework. The
Flask framework which is based on the Python programming language, is the
development platform of the archive web application.
The Cognitive Walkthrough methodology was used to evaluate suitabil-
ity of the software for its users. Results showed that the core conceptual model
adopted by the prototype software is consistent and that actions available to
the user are visible. Issues were raised pertaining to user feedback when per-
forming tasks and metadata term meaning. The development of a continent
wide genome archive for Africa is feasible by utilizing open source software
and metadata standards to improve data discovery and reuse.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:uwc/oai:etd.uwc.ac.za:11394/8108 |
| Date | January 2021 |
| Creators | Southgate, Jamie |
| Contributors | Christoffels, Alan |
| Publisher | University of the Western Cape |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Rights | University of the Western Cape |
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