1. e-Research Hackfest Experience
and MIPAR
Benjamin Aribisala – Lagos State University - Nigeria
WACREN e-Research Hackfest – Lagos (Nigeria)

2. Overview Introduction Technologies Use Cases Use Case from LASU
Summary and Conclusions
Appreciations

3. The Sci-GaIA Project (www.sci-gaia.eu)
Introduction
The Sci-GaIA Project (
SCI-GAIA is an EU funded project to promote development and use of e-infrastructure in Africa
Research Infrastructures – Coordination & Support Action
Grant Agreement no
EC contribution: ~1.4 MEuro
Start date: 1 May 2015
Duration: 24 Months

4. Catania- July 2016
The e-Research Summer Hackfest was held at the Department of Physics and Astronomy, University of Catania, Italy
the first edition on July, 4-15, 2016
and the second on July, 18-29, 2016
10 instructors and 36 participants from 9 countries (4 African and 5 European) attended the two editions
Co-sponsored by SCI-GaIA, INDIGO-DataCloud and COST ENeL
The focus of the Hackfest was to train participants on technologies that could help them put their tools on the web as services to users
Participants were trained on the following tools – FutureGateway, gLibrary, Kepler, Invenio, OAI-PMH, OneData and Ophidia

5. TRAIN Present IMPLEMENT TPI Model - Hackfest
Hackfest was interactive and in 3 phases
2 days - Instructors trained participants on the different technologies
1 days - Participants presented use cases and the technologies to use
8 days - Participants implemented use cases with support from instructors
TRAIN
Present
IMPLEMENT

6. Technologies
1. FutureGateway – A framework for building science gateway. Allows interaction with remote infrastructure - SAAS. Jobs submitted, processed, retrieved.
2. gLibrary - A service that provides access to existing data collections or for creating new ones
3. OAR (Open Access Repository) – Allows storage of data, users can search and download data, Digital Object Identifier (DOI) will be assigned. You will be introduced to MARCXML tags
4. Liferay -  An open source platform which allows you to create websites.

7. Technologies
5. Kepler – Workflow engine and design platform for analysing and modelling scientific data. Very similar to Amos
6. INDIGO – Enables users to access computing power as a service, e.g. GRID, CLOUD, etc
7. OneData - Allows storage and sharing of heterogeneous data
8. Ophidia - A big data analytics framework for climate change

8. Use Cases from Africa TANZANIA 2. NIGERIA 3. KENYA 4. SOUTH AFRICA
Stephen Mgaya, Tanzania Education and Research Network, - Bioinformatics SG (WEKA Data mining tool)
Aron Kondoro, University of Dar es Salaam , iGrid Portal
Diana Rwegasira, University of Dar es Salaam, Technology Transfer Alliance Collaboration Platform
Damas Makweba, Dar es Salaam Institute of Technology, The Weather Research and Forecasting (WRF) Model for the WIMEA-ICT project
Triphonia Ngailo, Dar es Salaam Institute of Technology, The Weather Research and Forecasting (WRF) Model for the WIMEA-ICT project
2. NIGERIA
Benjamin Aribisala, Lagos State University, Medical Image Analyser
3. KENYA
Dennis Muoki Kimego, Egerton University, Public Health Gateway in Kenya
Charles Muiruri Njaramba, Egerton University, Public Health Gateway in Kenya
4. SOUTH AFRICA
David Risinamhodzi, Northwest University, Reproducible Automatic Speech Recognition workflows

9. Some Testimonies Stephan Mgaya, Tanzania Future Gateway is excellent,
flexible
2. I had access to experts
3. The food was great !

10. Some Testimonies Benjamin Aribisala, Nigeria
Great opportunity to network
Organizers and trainers gave all the support
Learnt many technologies, my favourite was Kepler
The food is great!!!
Italians are very friendly, good culture

11. Some Testimonies Charles Njaramba, Kenya
Science gateway concept is very good
I tried many tools, e.g. FutureGateway
The food was great!!!
Catania is a great city

12. Some Testimonies David Risinamhodzi, South Africa
Really enjoyed FutureGateway and other tools
Opportunity to discuss my use case with experts
The experts were very helpful
The food was great!!!

13. Catania to Lagos
11 Nigerians were expected to attend the Catania Hackfest
10 could not go because of visa issue
LASU, WACREN and EKO-KONNECT discussed with SCI-GAIA on how the remaining 8 Nigerian experts could benefit
Lead to Second Edition of the Hackfest, yet visa delayed
Gave birth to Nigeria Edition
Blessing in disguise – More participants in Lagos, More Use Cases
21 Nigerians
1 South African
2 Ethiopians

14. Medical Image Processor and Repository

15. Medical Image Processor and Repository (MIPAR)

16. Medical Image Processor and Repository
Medical Image Processor and Repository (MIPAR) is an e-infrastructure for sharing and analyzing medical images
The web address of MIPAR is
It was developed by the team of experts in Computer Graphics & Computer Vision group of Lagos State University under the leadership of Professor Benjamin ARIBISALA
We have just completed the implementation of MIPAR
For More information, contact us at

17. When Can I Use MIPAR? You need MIPAR if you
need medical images for your research
have medical images to share
have a case study to share
need an expert to process your medical images
How much will you pay for any of the services above?
Everything is free
I want to collaborate with your team
Just send an to

18. System Analysis and Design
Donate Images
Download Free Images
Download outputs
Process Images
Registered user
Image Types CT
MRI
Doppler
Ultrasound
Anatomy
Brain
Liver
Lung
Chest
Image Format
.hdr/.img
.nii
.nii.gz
(.zip)
Processes
Brain Extraction
Image Segmentation
Image registration

19. System Requirements Software Tools Used for Development
Futuregateway
OAR
PHP
JSON
WAMP
Software Requirement for users
Web browser
Internet
Windows operating system or mac or Linux, etcc
Hardware Requirement for users
Pentium 4, 4GB RAM, 500 GB disk space

20. Modules of MIPAR Registration Donate Images Download Images Process

21. Medical Image Processor and Repository
Home Page

22. Access through Federated Identity
Choose catch-all if in doubt

23. Registration using Federated Identity

24. MIPAR – Image donation (https://mipar.sci-gaia.eu)

25. MIPAR – Image search & download

26. MIPAR – Image search & download & visualize

27. MIPAR – Image processing (brain extraction, segmentation, etc.)

28. MIPAR – Image processing (brain extraction, segmentation, etc.)

29. Summary and Conclusions
The Hackfest was very productive
Science gateway tools were introduced to us
Opportunity to discuss our use cases with experts
Gave Birth to MIPAR
We are expecting more use cases from Lagos Hackfest
The future is bright for all the use cases and new ones

30. Appreciations
A big appreciation to the co-funders - SCI-GAIA, INDIGO-DATACLOUD AND ENEL
We appreciate Eko-Konnect and WACREN for the opportunity to attend and for this meeting
Organizers
Roberto Barbera, sci-gaia
Simon Taylor, sci-gaia
Bruce Becker, sci-gaia
Owen Ivoha, Eko-Konnect
Omo Oaiya, WACREN
Resource Persons
Giacinto Donvito
Riccardo Bruno
Marica Antonacci
Antonio Calanducci
Krzysztof Trzepla
Alessandro D’Anca
Michal Owsiak
Support and Admin staff
Riccardo Bruno
Mario Torrisi (Super!)
Rita Ricceri
Marco Fargetta

31. Thank you!
sci-gaia.eu