Collaborative Systems Biology: Open Source, Open Data, and Cloud Computing

2011 ◽  
pp. 209-220
Author(s):  
Brian Pratt
Keyword(s):  
Cloud Computing ◽  
Systems Biology ◽  
Open Source ◽  
Open Data ◽  
Collaborative Systems

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic

2021 ◽  
Author(s):  
Shinji Kobayashi ◽  
Luis Falcón ◽  
Hamish Fraser ◽  
Jørn Braa ◽  
Pamod Amarakoon ◽  
...  
Keyword(s):  
Open Source ◽  
Medical Informatics ◽  
Open Source Software ◽  
Collective Intelligence ◽  
Collaborative Work ◽  
Open Data ◽  
Theme Issue ◽  
Health Organizations ◽  
The World ◽  
Civic Technology

Objectives: The emerging COVID-19 pandemic has caused one of the world’s worst health disasters compounded by social confusion with misinformation, the so-called “Infodemic”. In this paper, we discuss how open technology approaches - including data sharing, visualization, and tooling - can address the COVID-19 pandemic and infodemic. Methods: In response to the call for participation in the 2020 International Medical Informatics Association (IMIA) Yearbook theme issue on Medical Informatics and the Pandemic, the IMIA Open Source Working Group surveyed recent works related to the use of Free/Libre/Open Source Software (FLOSS) for this pandemic. Results: FLOSS health care projects including GNU Health, OpenMRS, DHIS2, and others, have responded from the early phase of this pandemic. Data related to COVID-19 have been published from health organizations all over the world. Civic Technology, and the collaborative work of FLOSS and open data groups were considered to support collective intelligence on approaches to managing the pandemic. Conclusion: FLOSS and open data have been effectively used to contribute to managing the COVID-19 pandemic, and open approaches to collaboration can improve trust in data.

scholarly journals Learning Open Science by doing Open Science. A reflection of a qualitative research project-based seminar

2020 ◽  
Vol 36 (3) ◽  
pp. 263-279
Author(s):  
Isabel Steinhardt
Keyword(s):  
Qualitative Research ◽  
Open Source ◽  
Knowledge Society ◽  
Open Data ◽  
Open Science ◽  
Research Project ◽  
Science Practices ◽  
Bachelor's Degrees ◽  
Participatory Technologies ◽  
Digital Knowledge

Openness in science and education is increasing in importance within the digital knowledge society. So far, less attention has been paid to teaching Open Science in bachelor’s degrees or in qualitative methods. Therefore, the aim of this article is to use a seminar example to explore what Open Science practices can be taught in qualitative research and how digital tools can be involved. The seminar focused on the following practices: Open data practices, the practice of using the free and open source tool “Collaborative online Interpretation, the practice of participating, cooperating, collaborating and contributing through participatory technologies and in social (based) networks. To learn Open Science practices, the students were involved in a qualitative research project about “Use of digital technologies for the study and habitus of students”. The study shows the practices of Open Data are easy to teach, whereas the use of free and open source tools and participatory technologies for collaboration, participation, cooperation and contribution is more difficult. In addition, a cultural shift would have to take place within German universities to promote Open Science practices in general.

scholarly journals Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

2011 ◽  
Vol 3 (1) ◽  
Author(s):  
Noel M O'Boyle ◽  
Rajarshi Guha ◽  
Egon L Willighagen ◽  
Samuel E Adams ◽  
Jonathan Alvarsson ◽  
...  
Keyword(s):  
Open Source ◽  
Open Data ◽  
Open Standards

scholarly journals OpenStack: Toward an Open-source Solution for Cloud Computing

2012 ◽  
Vol 55 (3) ◽  
pp. 38-42 ◽  
Author(s):  
Omar Sefraoui ◽  
Mohammed Aissaoui ◽  
Mohsine Eleuldj
Keyword(s):  
Cloud Computing ◽  
Open Source

scholarly journals Scheduling under Open stack – The Current State and Future Enhancements

2019 ◽  
Vol 8 (2) ◽  
pp. 375-382
Keyword(s):  
Cloud Computing ◽  
Open Source ◽  
Task Scheduling ◽  
Computing System ◽  
Important Task ◽  
Shared Resources ◽  
Computing Systems ◽  
Current State ◽  
Cloud Computing System ◽  
Research Findings

Cloud computing is being heavily used for implementing different kinds of applications. Many of the client applications are being migrated to cloud for the reasons of cost and elasticity. Cloud computing is generally implemented on distributing computing wherein the Physical servers are heavily distributed considering both hardware and software, the connectivity among which is established through Internet. The cloud computing systems as such have many physical servers which contain many resources. The resources can be made to be shared among many users who are the tenants to the cloud computing system. The resources can be virtualized so as to provide shared resources to the clients. Scheduling is one of the most important task of a cloud computing system which is concerned with task scheduling, resource scheduling and scheduling Virtual Machin Migration. It is important to understand the issue of scheduling within a cloud computing system more in-depth so that any improvements with reference to scheduling can be investigated and implemented. For carrying in depth research, an OPEN source based cloud computing system is needed. OPEN STACK is one such OPEN source based cloud computing system that can be considered for experimenting the research findings that are related to cloud computing system. In this paper an overview on the way the Scheduling aspect per say has been implemented within OPEN STACK cloud computing system

Sign in / Sign up

Export Citation Format

Share Document