Open Source Technology Essential in Facing COVID-19 Challenges

[This is a repost of a CROSS blog post.]

The COVID-19 pandemic has led to increased focus on the need for collaboration and openness to develop effective means to fight the spread of the virus and to minimize the societal damage of pandemic countermeasures. Open source technologies, along with open science efforts, have been in the forefront of the global response from the earliest stages of the COVID-19 outbreak, and crucial in tracing the coronavirus’s spread, mapping its genome, analyzing infection trends, manufacturing of needed medical equipment and serving communities most impacted by the outbreak. Open source contributors reacted quickly to the outbreak and, according to one estimate, over 10,000 individuals have contributed to the multitude of open source projects aimed at mitigating the health and social impacts of the pandemic. A search for COVID-19 on Github shows more than 3,700 repositories; a curated list of these repositories highlights the work of open source communities on topics including: global data, healthcare toolkits, machine-learning data sets, data visualization, stay at home help, hardware and local responses. Volunteer opportunities are also highlighted on this list, including assisting with large scale research through the crowdsourced computing project Folding@Home. This project is speeding up the rate at which researchers can obtain information about the coronavirus proteins and the forms they can take by tapping “ over four million CPUs and half a million GPUs” from contributors donating their computer power since late March.

Open source communities have also been effectively leveraging their human resources and reach through the creation of needed medical equipment and hardware, the establishment of disease tracking platforms, and facilitating the sharing and analysis of large data sets. Academic-based open source contributors have been particularly helpful in these areas. For example, numerous universities including the Massachusett Institute of Technology and University of Minnesota have developed open source designs for inexpensive ventilators with automated resuscitation bags to push oxygen into a patient’s lungs. The data repository and COVID-19 dashboard developed by John Hopkins University (JHU) provides researchers, public health officials and the general public with a hands-on, user friendly tool to track the pandemic in real-time. The JHU project quickly became “ one of the canonical sources of data on the outbreak” used by scientists, journalists and statisticiations from all over the world.
UCSC’s Genomics Institute (GI) created the Genome Browser for SARS-CoV-2 in order to continuously update “ access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared.” This new browser platform was adapted from GI’s existing open source genome browser visualization tool and inputs molecular data from published studies and database submissions in order to map to the viral genome. The SARS-CoV-2 browser aims to support the development of therapeutics and vaccines against the virus. UCSC faculty researchers are also developing an open source 3D browser that will gamify crowdsourcing of coronavirus data. This project, recently funded by CITRIS Seed Funding, will create a platform that will enable experts to post challenges, allow crowdsourced annotations and data manipulation, leverage 3D rendering and virtual reality, and utilize gamification to stimulate data analysis and collaboration.

The Center for Research in Open Source Software (CROSS) affiliated researchers are likewise working on projects aimed at supporting pandemic mitigation efforts. CROSS incubator fellow Ivo Jimenez, who leads the Black Swan project, is collaborating with the University of Sonora (Mexico) on a dashboard that displays daily summaries of COVID-19 data for the state of Sonora. Dr. Jimenez and his collaborators will be building a prediction model using unsupervised learning in order to estimate the location of new cases, based on geographical information that is available in the data provided by the Mexican government. Professor Gabriel Elkiam, advisor to CROSS’s newest research project Open Source Autonomous Vehicles, is working with a team to develop a small, soft robot that extends via eversion (a so-called vine robot) that will be used for automated naso-pharyngeal swabbing to test for presence of the virus. The robot will carry a swab through the nostril back to the pharynx and retract depositing the swab in an appropriate collection container, allowing the test to be carried out without endangering healthcare workers. Open source communities, particularly contributors based in universities and research institutions, have been active in the global effort to fight the COVID-19 pandemic, and have increased the level of collaboration and speed at which data and resources are shared internationally. As the research, developer and medical communities continue to work collectively to develop effective solutions to end the pandemic and preserve publich health, open source projects and communities will continue to be vital to these efforts.

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Stephanie Lieggi
Assistant Director of CROSS

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