Overview and objectives
The WACREN e-Research Hackfest was held at the Computer Science Department of the Lagos State University (Nigeria) on November, 21-30, 2016. In total, 9 instructors, 20 selected candidates and 2 of the organisers from Ethiopia, Ghana, Italy, Nigeria and South Africa participated to the hackfest.
The event was locally organised by WACREN, Eko-Konnect and the Lagos State University and supported by the European Commission through the WACREN participation in the Horizon 2020 Sci-GaIA and AfricaConnect2 projects.
The WACREN e-Research Hackfest was the first “in-Africa” replica of the e-Research Summer Hackfest and its main objective was to integrate African scientific use cases through a pervasive adoption of web technologies and standards and make them available to their end users through Science Gateways(1). Overall, 13 use cases where selected to be developed during the hackfest in Lagos: 12 where new and 1 was an extension of an use case already selected for the e-Research Summer Hackfest held in Catania (Italy). Promoting and fostering open and reproducible research was the ultimate goal of the WACREN e-Research Hackfest.
Note: the WACREN e-Research Hackfest allowed the selected candidates from Nigeria, who could not come to either of the two editions of the hackfest held in Catania due to visa issuance delay, to come to Lagos and implement their use cases.
The following topics were tackled during the WACREN e-Research Hackfest:
- Distributed computing services
- Distributed storage services
- Programmatic access to Open Data repositories
- Semantic federation of Open Access repositories
- User interfaces (web, desktop, mobile, etc.)
- Open courseware
Education e-Library and MOOC Platform
Ethiopian Education Roadmap Project is a research project that studies about the current education system ranging from pre-school to the tertiary education. Until now, comprehensive literature reviews are conducted and hundreds of artifacts have been analyzed. The huge documents collected during this study process need to be turned into an e-library that will eventually be utilized as an African Education Library comprising of research publications, books, journals and other related materials. The e-library will be based on a clone of the Sci-GaIA Open Access Repository and each artifacts will be assigned a DOI in order to ensure citability and authorship (this through the connection with ORCID – http://orcid.org). The e-library will be also exposing an OAI-PMH endpoint and a RESTful API endpoint to allow automatic harvesting of metadata by machines. The use case also includes the installation and customization of a web based environment for MOOCs, the MOOCs platform, the Sci-Gaia Online Courses server (http://courses.sci-gaia.eu), based on OpenEdx, will be considered.
Presentation – Intermediate report – Final report Yoseph Abate, EthERNet, and Behailu Osro, Education Strategy Center – Ethiopia
Addis Ababa Rivers and Riversides Monitoring System (AARRMS)
Rivers in Addis Ababa have suffered an incessant degradation for so many years that they ended up as waste disposal bins and sewers. The need to revitalize the rivers and riversides within the city has been a priority for the Addis Ababa City Government for quite some time. Currently, researchers for the fields of Environmental Protection, Biology and Urban Planning are engaged in studying the current statuses of all rivers and riversides and follow-up their conditions in the years to come. The data acquisition, analysis and reporting need to be automated using mobile and web applications. For this purpose, I have volunteered to build a mobile and web application in order to assist these researchers whose study eventually help the City Government make a proper decision concerning the rivers and riversides. During this Lagos Hackfest, I have planned to complete the web application and the backend database.
Presentation – Final report Yoseph Abate, EthERNet – Ethiopia
An Adaptable e-Service Communication Model for Rural Agricultural Extension (e-AgriSERVICOMM)
Agricultural extension finds itself at a time of crisis. Many of today’s agricultural extension services are suffering under bureaucratic centralised management structures. Squeezed by decentralization policies, diminishing public funds and the privatization of public services, they are urgently in need of change. The design is to come up with communication model using mobile technology to reinvent agricultural extension to improve the kind of information that is being disseminated to farmers.
Presentation – Intermediate report – Final report Olutayo Ajayi and Oluwaseyi Babarinde, Federal University of Agriculture – Nigeria
Development of a SGW-based Plant Tissue Culture Micropropagation Yield Forecasting Application (Plantisc2)
Plant tissue culture is a collection of techniques used to maintain or grow plant cells, tissues or organs under sterile conditions on a nutrient culture medium of known composition. Plant tissue culture is widely used to produce clones of a plant in a method known as micropropagation. During the UNESCO-HP Brain Gain Initiative (BGI) project (2009-2013), the University of Nigeria team conducted series of plant tissue culture experiments and developed a stand-alone application, Plantisc. A Plant Tissue Culture micro propagation simulation software, which achieved over 67% predication accuracy whose result was published in a peer-reviewed journal.
Presentation – Intermediate report – Final report Collins Udanor, University of Nigeria Nsukka – Nigeria
Valorization of Open Data Archive and Documentation of the University of Ibadan Research Metadata Platform (UI-NADA)
The University of Ibadan data archive and documentation (UI-NADA) platform (http://nada.ui.edu.ng/) was established in April 2015. It signaled the piloting of a web-based open access metadata archiving and documentation of survey datasets in any Nigerian University. The UI-NADA has recorded phenomenal hits since it was launched. This phenomenal success is the motivating factor for the proposed project on the valorization of the research metadata platform. The valorization will avail end-users a more user-friendly platform with the incorporation of citation tracking through digital object identifier (DOI) and linkage to other open access repository (OAR) platforms, including social media platforms (Facebook and Twitter). It will enable more visibility and impact through the tracking, re-use and re-analysis of the research metadata.
Presentation – Intermediate report – Final report Olawale Olayide, AbdulAzeez Adelopo, Rising Osazuwa, University of Ibadan – Nigeria
ACEPRD Plant Repository
The Africa Centre of Excellence in Phytomedicine and Research Development (ACEPRD), University of Jos Nigeria has noticed a paradigm shift from traditional pharmaceuticals to plant derived medication in the treatment of diseases. This paradigm shift has led to a global demand for plant-derived medicines (phytomedicines) as a primary and complementary medical tool. Within the region, traditional medicine has not been fully integrated into the modern healthcare delivery system due to the following challenges such as the safety, efficacy and stability of traditional remedies have not been fully documented, Inadequate authentication, documentation and comprehensive database of flora in the sub region, Poor academia- industry relationship and so on. ACEPRD aims to overcome these challenges by developing the field of Phytomedicine that includes the development of ACEPRD Plant Repository to aid the integration of Phytomedicine research into the healthcare delivery system in the African sub-region.
Presentation – Intermediate report – Final report David Oguche and Uchechukwu Ohaeri, University of Jos – Nigeria
A Near Real-Time Meteorological Data Depository for Atmospheric Research in Africa (OAU-MET)
Development of a remotely accessible meteorological data depository from an online server located at Obafemi Awolowo University (OAU). Using resources based on existing RENs this facility will allow researchers anywhere in the world to download reliable atmospheric data (in near real-time) from an array of low-cost automatic (and autonomous) weather stations to be deployed across Nigeria. This online database will be useful for the study of the atmospheric phenomena (regional climate modelling, aerosol loading and pollution, etc.).
Presentation – Final report Segun Oyeyiola, Obafemi Awolowo Univerisity – Nigeria
A framework for Large NGS data analysis: Metagenomics (HPC416S)
Next-Generation Sequencing (NGS) provides a lot of platforms to sequence DNA and samples at a cheaper and faster rate. Genomic research is benefiting from this, thus making various analysis and interpretations possible. Despite the benefits of NGS, large data handling is a challenge in the area of whole genome/exome sequencing. The analysis of this large data is complex and requires high performance computing (HPC) to remote users. Here, were describe a framework that uses HPC to address large NGS data processing, incomplete data (no sample metadata information) and reduce the task complexity. We use technologies from Sci-GaIA Open Science Platform to make this analysis available for remote users. This framework proposes to ease research in metagenomics and microbial diversity analysis.
Presentation – Final report Trust Odia, Covenant University – Nigeria
Development of an interactive pipeline for Genome wide Association study (GWAS-TOOL)
The need for tailoring healthcare and treatment therapies to individual patients based on their genetic-makeup and other biological features is becoming more and more crucial in today’s clinical practice. Genome Wide Association Study (GWAS) has been applied extensively to uncover several variations and genes in our DNA that are related to different diseases, traits and clinical symptoms. However, a typical GWAS analysis requires the use of numerous complex commands, codes and analysis from different languages. This makes research projects complex and time consuming for researchers. GWAS also requires the use of large computing and storage resources to perform state of art data analysis, which might not be available for most developing country researchers. We aim to develop an e-infrastructure web application that will provide state-of-the art GWAS analysis to local researchers. Back-end Web technologies to be used include JSP for business logic, JAX-RS for programmatic access to web application, nextflow, a workflow language, Liferay, FutureGateway, gLibrary etc. This solution will make GWAS analysis easier to perform, by requiring limited understanding of the computational needs and from researchers. This will also allow researchers focus mainly on research problem and give better and intuitive biological interpretation to the results.
Presentation – Final report Oluwadamilare Falola and Taiwo Adigun, Covenant University – Nigeria
Drug Design, Discovery and Development Platform and Repository (D4PR)
Presentation – Intermediate report – Final report Ikemefuna Uzochukwu, Ekene Ezeasor, Tochukwu Eze, Nnamdi Azikiwe University, Nigeria
Web based predictive defuzzifier
Defuzzification is a method of converting membership functions generated from linguistic variables into usable numerical values. Defuzzification is an important process in the fuzzy inference engine but in its present state, there are more than 50 (fifty) deffuzication method however, there are no methods to help known method for linking a defuzzification method with a particular type of data. Our system will allow users to upload their data in .xls and .csv and get it processed by the defuzzifier, who would have predicted the best defuzzification method for the class of data recived. The systems build knowledge from the submitted data by learning and using it for training in other to perform better while processing similar data.The work will leverage on the the open science using FG, Kepler, OLAP cube to build the defuzzifier and use PHP for the front end to enable users upload data for processing.
Presentation – Final report Oluwatoyin Enikuomehin, Lagos State University – Nigeria
IBIS, A Framework For the Interoperability Of Bio-repository Information System In Africa
This solution tackles the challenges of data and information scarcity in the midst of abundance of biological data for research, especially in Africa. It is a rich Enterprise application with several imbued Java technologies in its architecture. It also implements ontology for the smooth integration of abstract knowledge models, and data mining algorithms for real time knowledge discovery and predictive decision making. Microsoft internationalization API will be used to make the system intelligibly adapt to various languages and regions without need for engineering changes. This system provides real time access to bio-specimens stored in isolated bio-repositories scattered all around Africa hereby enhancing collaboration, exchange of data, and aiding researchers in the genomic analysis of the samples as well as identifying new ways of preventing, diagnosing and treating diseases irrespective of their geographic locations.
Presentation – Final report Abayomi Mosaku and Boladele Akanle, Covenant University – Nigeria
MIPAR Portal Extension
Medical images are used for clinical diagnosis, treatment and patient management. There are many methods of acquiring medical images and each technique has its own application area, strengths and weaknesses. The recent advancements in medical image analysis has given birth to image guided therapy, virtual reality and augmented reality, all these among other innovations have greatly improved health delivery, improved quality of life and also saved lives. The high cost of image acquisitions and limited availability of medical image analysts plus the need to share expertise amongst clinical experts have led to the development of Medical Image Processor and Repository (MIPAR). MIPAR is a web based tool which allows users to donate, download or process images. However, MIPAR does not have any module for statistical analysis. The aim of this project is to extend MIPAR to include statistical analysis. It is our hope that the proposed statistical features of MIPAR will allow users to get useful information from their data.
Presentation – Intermediate report – Final report Benjamin Aribisala and Olusola Olabanjo, Lagos State University – Nigeria
Federal University of Agriculture – Nigeria
Lagos State University – Italy
University of Catania – Italy
CSIR – South Africa
University of Catania – Italy
Lagos State University – Nigeria
Brunel University London – UK
Eko-Konnect – Nigeria
WACREN – Ghana
Lagos State University – Nigeria
University of Catania – Italy
1A Science Gateway (also known as a Virtual Research Environment or a Virtual Laboratory) is a “community-development set of tools, applications, and data that is integrated via a portal or a suite of applications, usually in a graphical user interface, that is further customized to meet the needs of a specific community“ [TeraGrid/XSEDE].