scholarly journals Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

2019 ◽  
Vol 1 ◽  
pp. 9
Author(s):  
Azza E. Ahmed ◽  
Phelelani T. Mpangase ◽  
Sumir Panji ◽  
Shakuntala Baichoo ◽  
Yassine Souilmi ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Heterogeneous Computing ◽  
Lessons Learned ◽  
Technical Expertise ◽  
Research Projects ◽  
Pan African ◽  
Genomic Analyses ◽  
Standard Operating ◽  
Computing Environments ◽  
Scientific Expertise

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network’s Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.

scholarly journals Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

2018 ◽  
Vol 1 ◽  
pp. 9 ◽  
Author(s):  
Azza E. Ahmed ◽  
Phelelani T. Mpangase ◽  
Sumir Panji ◽  
Shakuntala Baichoo ◽  
Yassine Souilmi ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Human Health ◽  
Heterogeneous Computing ◽  
Lessons Learned ◽  
Technical Expertise ◽  
Research Projects ◽  
Pan African ◽  
Computing Environments ◽  
Scientific Expertise

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous compute environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. To address this need, in 2016 H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon, with the purpose of building key genomics analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on quay.io.

scholarly journals H3ABioNet genomic medicine and microbiome data portals hackathon proceedings

Database ◽  
2021 ◽  
Vol 2021 ◽  
Author(s):  
Faisal M Fadlelmola ◽  
Kais Ghedira ◽  
Yosr Hamdi ◽  
Mariem Hanachi ◽  
Fouzia Radouani ◽  
...  
Keyword(s):  
Ethnic Groups ◽  
Genomic Medicine ◽  
Lessons Learned ◽  
Team Work ◽  
Significant Progress ◽  
Team Members ◽  
Pan African ◽  
Scientific Expertise ◽  
Microbiome Data ◽  
Made In

Abstract African genomic medicine and microbiome datasets are usually not well characterized in terms of their origin, making it difficult to find and extract data for specific African ethnic groups or even countries. The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate their development. The two portals were designed and significant progress was made in their development during the hackathon. All the participants worked in a very synergistic and collaborative atmosphere in order to achieve the hackathon's goals. The participants were divided into content and technical teams and worked over a period of 6 days. In response to one of the survey questions of what the participants liked the most during the hackathon, 55% of the hackathon participants highlighted the familial and friendly atmosphere, the team work and the diversity of team members and their expertise. This paper describes the preparations for the portals hackathon and the interaction between the participants and reflects upon the lessons learned about its impact on successfully developing the two data portals as well as building scientific expertise of younger African researchers. Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal].

Challenges and Cloud Computing Environments Towards Big Data

2014 ◽  
pp. 203-208
Author(s):  
Kiran Kumar S V N Madupu
Keyword(s):  
Data Mining ◽  
Cloud Computing ◽  
Big Data ◽  
Technology Development ◽  
Computing Environments ◽  
Modern Technologies

Big Data has terrific influence on scientific discoveries and also value development. This paper presents approaches in data mining and modern technologies in Big Data. Difficulties of data mining as well as data mining with big data are discussed. Some technology development of data mining as well as data mining with big data are additionally presented.

Sign in / Sign up

Export Citation Format

Share Document