1. GWAS-TOOL – Final report
Falola Damilare & Taiwo Adigun
WACREN e-Research Hackfest – Lagos (Nigeria)

2. Work done during the Hackfest Results Summary and conclusions
Outline
Scientific problem
Work done during the Hackfest
Results
Summary and conclusions

3. Scientific Problem, Aim and benefits
A typical GWAS analysis involves
the use of numerous complex commands from different languages, which makes research work complex for researchers.
Use of large computing and storage resources to perform state of art GWAS data analysis which might not be available for most African or developing country researchers.
AIM
The aim of this project is to develop and implement an e-infrastructure that will provide state-of-the art GWAS analysis to local researchers. This tool will include all tools.
Benefits
This allows users focus mainly on the research problem, by making the analysis process a black box technique, which will bring about better and accurate research results.
This solution also brings in user interactivity providing better visualization of results, swift comparison of results from different types of analysis, and management of several projects.

4. Computational & Data model

5. Computational & Data model

6. Objectives and milestones
User interface design
Develop User Interface and user interactivity using Hypertext Mark-up Language (HTML) and Java scripting
Develop javascript modules to ensure input data integrity and enforcing client side user validation.
Implement SAML (Security Assertion Markup Language) for Federated Authentication.
Implement back end using Java Enterprise Programming Technologies (JSP, Servlet, JDBC)
Install apache tomcat on own HPC.
Have working directory on server.
Have working development environment on local machine

7. Objectives and milestones
Install Future Gateway on own HPC.
Install Flask API (Pyhton)
develop Java Servlets & Java API for RESTful Web Services (JAX-RS)
Install and implement glibrary and globus api on HPC or implement FTP in JSP to handle large file transfers.
Install all required tools and packages for analysis.
Download reference genomes needed for some phases of the analysis e.g. HapMap, 1000 genomes.

8. Work done during the Hackfest
Set-up all required tools and packages for analysis.
User interface design
Develop User Interface and user interactivity using Hypertext Mark-up Language (HTML) and Java scripting
Develop javascript modules to ensure input data integrity and enforcing client side user validation.
Working Implementation back end using Java Enterprise Programming Technologies (JSP, Servlet, JSTL, JDBC)
Install apache tomcat on own HPC.
Have working directory on server.
Have working development environment on local machine

14. Install Future Gateway on own HPC.
Future plans (until end of July and until the Workshop in Dar es Salaam on 5th of September - duplicate this slides as many time as needed)
Implement SAML (Security Assertion Markup Language) for Federated Authentication.
Complete UI design. This will allow clients manage and run analysis via the web page.
Install glibrary and globus on HPC or implement FTP in JSP to handle large file transfers.
Install Future Gateway on own HPC.
Install Flask API (Pyhton)
develop Java Servlets & Java API for RESTful Web Services (JAX-RS)

15. Summary and conclusions (tell us your experience about the Hackfest)
Good exposure and a platform to network with other researchers.
Educational and practically oriented (learnt a lot)

16. Thank you! Gratitude goes out to:
To the organizers of this Hackfest. I had a very wonderful experience!
Mr Abayomi Mosaku for assistance in the implementation.
Bruce Becker and Mario Torrisi for their assistance in designing the architecture of the application.
To all my colleagues from CU at this hackfest.
To every participant at the hackfest.
Lastly to wonderful guys at the Kitchen for the lovely meals.
Thank you!
sci-gaia.eu