20 Open-source Tools can Help COVID-19 Cure Research

Governments, scientists and analysis establishments are utilizing expertise and innovation to sort out COVID-19.

Open supply instruments have been developed, and a few are nonetheless being examined, to help efforts to attenuate the influence of this lethal virus.

A variety of open-source instruments exist already to assist researchers be taught extra concerning the illness, establish its unfold, forestall its unfold, and reduce additional unfold and deaths. A sequence of initiatives can be found on the Schooling Ecosystem that define how completely different instruments can be utilized.

This text appears to be like at a few of the open supply instruments and libraries used within the monitoring, prevention and containment, prognosis and remedy of COVID-19.

COVID-19 monitoring map

In January, the JHU’s Heart for Techniques Science and Engineering launched a COVID-19 World Monitoring Map that rapidly grew to become an internationally trusted supply of real-time knowledge on the evolving pandemic.

The map is open supply and has been used to help analysis and visualization efforts by prime media organizations, small organizations and native governments.

DXY-COVID-19 crawler

DXY-COVID-19-Crawler is without doubt one of the first open supply initiatives developed in January to answer COVID-19.

The builders used knowledge from DXY.cn, a website utilized by Chinese language medical doctors to report and monitor circumstances. They developed an online crawler that collected knowledge from the positioning and made it accessible by way of an API and an information warehouse. The code is obtainable on Github.

Open knowledge package

Open Information Equipment (ODK) just isn’t a brand new instrument. It has beforehand been used in the course of the Ebola outbreaks in West Africa in 2004 and the newer outbreak within the Democratic Republic of the Congo in 2019.

Primarily, it helps customers acquire, handle and use knowledge involved tracing, strategic mapping, choice help, neighborhood consciousness and case administration.

The ODK neighborhood has additional developed its use in response to the COVID-19 by making a reporting kind accessible with its implementation. The shape is designed in line with the World Well being Group’s protocol for case investigation and phone tracing and investigation.

The lead builders are additionally offering free help for any group that has deployed the ODK in response to COVID-19.

Subsequent sort

Nextstrain tracks the evolution of pathogens. It has beforehand been used to work out the household historical past of a illness, permitting for the prediction of illness development.

It has been used efficiently in previous epidemics, reminiscent of Ebola. Via genetic knowledge from the World Initiative on Sharing All Influenza Information (Gisaid), Nextxtrain is getting used to sort out COVID-19.

DIS2

You most likely already know DHIS2. It’s the world’s largest well being data administration system. It’s utilized in greater than 70 nations. As a part of the response to COVID-19, DHIS2 has launched a digital knowledge bundle that accelerates the detection, reporting, surveillance and remedy of the illness.

The DHIS2 digital knowledge bundle makes use of customary metadata aligned with WHO’s protocol on COVID-19 case definition and surveillance to allow speedy deployment and response.

Pikobar West Java

The Indonesian Illnesses and Disasters Data and Coordination Heart is a disaster response heart established to mitigate and reply to COVID-19 in Indonesia’s West Java province.

As a part of the response, the Jabar Digital Service has developed an open-source net instrument and app that can permit customers to entry the most recent COVID-19 knowledge.

OpenMRS

OpenMRS is a affected person care system utilized in many growing nations around the globe. The pliability of the OpenMRS system permits nations the place their healthcare assets are beneath strain to make use of it for surveillance, screening and remedy of COVID-19.

The system may help them broaden their capability by giving them entry to evidence-based data on easy methods to take care of the disaster.

OpenLMIS

The OpenLMIS undertaking makes use of a community-based tactic to develop an open supply and customizable logistics administration data system. The OpenLMIS system strives to enhance knowledge accuracy, enhance accountability, enhance knowledge timeliness and visibility.

The OpenLMIS system goals to enhance healthcare provide chains and medical system stock to offer a transparent image of obtainable medical provides, together with take a look at kits and PPE (private protecting tools). This instrument can be utilized successfully to help choice makers in allocating assets in response to COVID-19.

Well being websites

The World Healthsites Mapping Mission is a undertaking that goals to map each healthcare facility on the earth and make the main points of each hospital simply accessible. The info about healthcare establishments has been made accessible by way of an API.

Working with customers, the healthsites.io workforce captures and validates the situation and phone data of every healthcare facility, making the information freely accessible and accessible by way of an Open Information license.

DON’T ASK

SORMAS (Surveillance Outbreak Response Administration and Evaluation System) is an open-source cell e-health system. It has been deployed to implement each illness management and outbreak administration procedures.

It has been successfully deployed in a number of nations together with Ghana, Nigeria, Nepal and Fiji for COVID-19 surveillance and early detection.

SORMAS is a free, open supply system that follows knowledge safety requirements.

Tokyo COVID-19

In contrast to many different cities and governments, the Tokyo Metropolitan Authorities has developed an open-source web site that informs its residents about COVID-19. By making the positioning open-source, the positioning has obtained contributions from over 200 customers. Three different cities, Chiba, Nagano and Fukuoka, recreated the web site.

OpenELIS

The aim of the OpenELIS well being system is to enhance healthcare by offering a complicated, standards-based laboratory data administration system that can be utilized by varied well being initiatives to enhance remedy choices.

The COVID-19 outbreak has introduced a world problem by way of contact tracing and mass testing of suspected circumstances. The OpenELIS system might be successfully deployed within the administration of COVID-19 to facilitate monitoring of lab assessments and outcomes.

Group well being toolkit

The Group Well being Toolkit is a set of open supply instruments and open entry assets targeted on constructing and deploying digital instruments to be used in neighborhood well being initiatives in hard-to-reach areas.

The Group Well being Toolkit developer neighborhood has mobilized to develop instruments and assets geared toward supporting neighborhood well being employees in addressing COVID-19.

CALL

The COVID-19 Hospital Influence Mannequin for Epidemics (CHIME) is an open supply software developed by knowledge scientists at Penn Medication – College of Pennsylvania. It’s a web-based instrument that permits hospitals to foretell the influence of the virus on healthcare assets.

It’s developed utilizing Python and Panda’s open supply dependency.

COVID care card

The COVID Care Map helps map current healthcare assets and predict shortages in hospital beds, ventilators, medical provides and employees. All strategies, knowledge processing instruments, visualizations and supply code are free and open supply.

The COVID Care Map undertaking seeks to anticipate and take motion to collect help for efficient look after the quickly rising variety of COVID-19 infections and people in want of intensive care.

Locale.ai

Locale.ai has developed an open-source, interactive visualization of all confirmed circumstances of COVID-19 around the globe. It queries the John Hopkins College open-source dataset.

Locale.ai developed the COVID-19 visualization web site utilizing Vue.js, a well-liked framework that helps builders create fashionable net apps.

COVID-19 around the globe

This app makes use of a map visualization to trace the unfold of COVID-19, the confirmed circumstances and the event of the illness around the globe. It makes use of knowledge from John Hopkins CSSE.

Corona tracker

It is a Shiny app developed by John Coene. It tracks the unfold of COVID-19 utilizing knowledge from John Hopkins, DXY knowledge, and Weixin. The app exhibits the variety of suspected, confirmed and recovered circumstances by time and area. The code is obtainable on Github.

World circumstances of COVID-19

COVID-19 World Instances is a shiny app developed by Christoph Schoenenberger that exhibits the developments of COVID-19 in a map, plots, abstract tables and figures. The code is obtainable on Github.

Governments and COVID-19

It is a shiny app developed by Sebastian Engel-Wolf. It charts the exponential progress of COVID-19, the variety of days to double infections, the confirmed circumstances, the dying price and the variety of confirmed circumstances per 100,000 individuals in several areas. The code is obtainable on Github.

To dam

The open supply neighborhood has responded rapidly and successfully to the COVID-19 pandemic. Many initiatives have been and are nonetheless being constructed to sort out the unfold of the illness. This text describes some initiatives. There’s nonetheless uncertainty concerning the course of the illness within the coming weeks. Extra initiatives that may make use of current open supply applied sciences will discover a place within the combat in opposition to this lethal illness.

Thoughts your security!

Article by dr. Michael J. Garbade, CEO, Schooling Ecosystem

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