Open source tools have been developed, and some continue to be tested to support the efforts that have been deployed to minimize the outcomes of this deadly virus. A range of open-source tools is already in place, helping researchers learn about the disease, identifying the spread, preventing the spread, and minimizing further spread and deaths. A range of projects is available at the Education Ecosystem that outlines how to use different tools. This article looks at some of the open-source tools and libraries that are being used in monitoring, prevention and containment, diagnosis, and treatment of COVID-19.
COVID-19 Tracking Map
In January, the JHU’s Center for Systems Science and Engineering launched a COVID-19 Global Tracking Map that quickly became an internationally trusted source of the evolving pandemic’s data in real-time. The map is open source and has been used to power research and visualization efforts by top media organizations, small organizations, and local governments.
DXY-COVID-19-Crawler
DXY-COVID-19-Crawler is one of the earliest open-source projects developed to respond to COVID-19 in January. The developers made use of data from DXY.cn, a site that was used by Chinese medical practitioners to report and track cases. They developed a web crawler that collected data from the site and made it available through an API and a data warehouse. The code is available on Github.
Open Data Kit
Open Data Kit (ODK) is not a new tool. It has been used before during the Ebola outbreaks in West Africa in 2004 and the more recent outbreak in the Democratic Republic of Congo in 2019. It mainly helps users collect, manage, and use data in contact tracing, strategic mapping, decision support, community sensitization, and case management. The ODK community has further advanced its use in response to the COVID-19 by making available a reporting form in its deployments. The form is designed according to the World Health Organization’s protocol for investigating cases and contact tracing and investigations. The lead developers are also offering free support for any organization that has deployed the ODK in response to COVID-19.
Nextstrain
Nextstrain tracks the evolution of pathogens. It has previously been used to work out the family history of a disease, hence enabling prediction of the disease progression. It has successfully been used in previous epidemics, such as Ebola. Through genetic data from the Global Initiative on Sharing All Influenza Data (Gisaid), Nextxtrain is being used to tackle COVID-19.
DHIS2
You probably already know DHIS2. It is the world’s largest Health Information Management System. It is used in more than 70 countries. As part of the response to COVID-19, DHIS2 has released a digital data package that accelerates infection detection, reporting, surveillance, and treatment of the disease. The DHIS2 digital data package makes use of standard metadata that is aligned with the WHO’s protocol on COVID-19 case definition and surveillance to enable rapid deployment and response.
Pikobar West Java
Indonesia’s Information and Coordination Centre for Disease and Disaster is a crisis response center formed to mitigate and respond to COVID-19 in the West Java province of Indonesia. The Jabar Digital Service has, as part of the response, developed an open-source web tool and app that allows users to access the latest COVID-19 data.
OpenMRS
OpenMRS is a patient care system used in many developing countries across the globe. Owing to the flexibility of the OpenMRS system, countries that have had their healthcare resources strained can use it for surveillance, screening, and treatment of COVID-19. The system can help them expand their capacity by giving them access to scientific-based information on dealing with the crisis.
OpenLMIS
The OpenLMIS project makes use of a community-focused tactic to develop an open-source and an adjustable logistics management information system. The OpenLMIS system seeks to improve data accuracy, increase accountability, improve data timeliness, and visibility. The OpenLMIS system seeks to enhance health supply-chains, the inventory of medical resources to provide a clear picture of the available medical supplies, including test kits, and PPEs (personal protective equipment). This tool can effectively be deployed to support decision-makers in allocating resources as a response to COVID-19. Healthsites The Global Healthsites Mapping Project is a project aimed at mapping every health facility in the world and making the details of every hospital easily accessible. The data on health facilities has been made accessible through an API. By collaborating with users, the healthsites.io team captures and validates the location and contact details of each health facility and makes the data freely available and accessible through an Open Data License.
SORMAS
SORMAS (Surveillance Outbreak Response Management and Analysis System) is an open-source mobile e-health system. It has been deployed to implement disease control as well as outbreak management procedures. It has been effectively deployed in several countries, including Ghana, Nigeria, Nepal, and Fiji, for COVID-19 surveillance and early detection. SORMAS is a free, open-source system that follows data protection standards.
Tokyo COVID-19
Unlike many other cities and governments, the Tokyo Metropolitan Government has developed an open-source website that informs its residents about COVID-19. By making it open-source, the site has seen contributions from over 200 users. Three other cities, Chiba, Nagano, and Fukuoka, have recreated the website.
OpenELIS
The purpose of the OpenELIS health system is to improve healthcare by providing a progressive, standards-based laboratory information management system that can be used by various health initiatives to improve treatment options. The COVID-19 outbreak has presented a global challenge of contact tracing and mass testing of suspected cases. The OpenELIS system can effectively be deployed in tackling COVID-19 to facilitate tracking of laboratory tests and results.
Community Health Toolkit
The Community Health Toolkit is a collection of open-source tools as well as open access resources that targets to build and deploy digital tools for use in community health initiatives in areas that are hard to reach. The Community Health Toolkit developer community has mobilized to develop tools and resources that aim at supporting community health workers to tackle COVID-19.
CHIME
The COVID-19 Hospital Impact Model for Epidemics (CHIME) is an open-source application developed by data scientists at Penn Medicine – University of Pennsylvania. It is an online tool that allows hospitals to predict the impact of the virus on healthcare resources. It is developed using Python and the pandas open-source dependency.
COVID Care Map
The COVID Care Map helps in mapping the already existing healthcare resources and in forecasting gaps in hospital beds, ventilators, medical supplies, and staffing. All the methods, data processing tools, visualizations, and source code are free and open-source. The COVID Care Map project seeks to anticipate and act to summon support to effectively care for the rapidly growing number of COVID-19 infections and those in need of intensive care.
Locale.ai
Locale.ai has developed an open-source, interactive visualization of all confirmed cases of COVID-19 across the globe. It queries the open-source dataset from John Hopkins University. Locale.ai developed the COVID-19 visualization website by the use of Vue.js, which is a popular framework that allows developers to create modern web apps.
COVID-19 across the world
This app makes use of a map visualization to monitor the spread of COVID-19, the confirmed cases, and the development of the disease across the globe. It makes use of data from John Hopkins CSSE.
Coronavirus tracker
This is a Shiny app developed by John Coene. It tracks the spread of COVID-19 by the use of data from John Hopkins, DXY data, and Weixin. The app shows the number of suspected, confirmed, and recovered cases by time and region. The code is available on Github.
COVID-19 Global Cases
COVID-19 Global Cases is a Shiny app developed by Christoph Schoenenberger that shows the developments of COVID-19 on a map, plots, summary tables, and figures. Its code is available on Github. Governments and COVID-19 This is a Shiny app developed by Sebastian Engel-Wolf. It maps the COVID-19 exponential growth, days to double infections, confirmed cases, mortality rate, and the number of confirmed cases per 100,000 people in different regions. The code is available on Github.
Wrapping Up
The open-source community has responded quickly and effectively to the COVID-19 pandemic. Many projects have been built and continue to be built to tackle the spread of the disease. This article describes some of the projects. There is still uncertainty about how the disease will progress in the coming weeks. More projects that can leverage the existing open-source technologies will find a place in the fight against this deadly disease. Stay safe! Article by Dr. Michael J. Garbade, CEO, Education Ecosystem
