e-Research Hackfest Experience a nd MIPAR

1. e-Research Hackfest Experience and MIPAR Benjamin Aribisala – Lagos State University - Nigeria (benjamin.aribisala@lasu.edu.ng) WACREN e-Research Hackfest – Lagos (Nigeria)

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

3. Introduction The Sci-GaIA Project(www.sci-gaia.eu) 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. 654237 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. 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 • 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 • DamasMakweba, Dar es Salaam Institute of Technology, The Weather Research and Forecasting (WRF) Model for the WIMEA-ICT project • TriphoniaNgailo, 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 MuokiKimego, Egerton University, Public Health Gateway in Kenya • Charles MuiruriNjaramba, 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 https://mipar.sci-gaia.eu 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 Benjamin.aribisala@lasu.edu.ng

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 email to Benjamin.aribisala@lasu.edu.ng

18. System Analysis and Design Donate Images Process Images Download outputs Registered user Download Free Images 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 Images

21. Medical Image Processor and Repository Home Page https://mipar.sci-gaia.eu

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 Resource Persons • GiacintoDonvito • Riccardo Bruno • MaricaAntonacci • Antonio Calanducci • Krzysztof Trzepla • Alessandro D’Anca • Michal Owsiak Support and Admin staff • Riccardo Bruno • Mario Torrisi (Super!) • Rita Ricceri • Marco Fargetta Organizers • Roberto Barbera, sci-gaia • Simon Taylor, sci-gaia • Bruce Becker, sci-gaia • Owen Ivoha, Eko-Konnect • OmoOaiya, WACREN

31. Thankyou! sci-gaia.eu info@sci-gaia.eu benjamin.aribisala@lasu.edu.ng