Feature Articles

A Web-native Approach to Open Source Scientific Publishing

This summer, eLife was pleased to launch Executable Research Articles (ERAs) in partnership with Stencila, allowing authors to post computationally reproducible versions of their published papers in the open-access journal. The open source ERA technology stack delivers a truly web-native format that treats live, interactive code as a first-class asset. It was developed to address current challenges around reproducing and reusing published results-challenges mostly caused by the lack of infrastructure for publishers to showcase the richness and sophistication of the computational methods used by researchers in their work.

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Resilience must be Blind to the Catalyst

On October 29 William Stemper, Forbes Councils Member put forth a thoughtful piece titled Three Steps To Building Resilience Through Technology.The article goes a long ways towards solidifying why resilience has a more urgent place in our businesses. I commend the article to the readers of this post. While Mr. Stemper focuses primarily on technology at his job at Comcast, he tees up some further, more holistic insights. Read More »

The Ransomware Attacks on Hospitals Are (Cyber) Criminal

One of the redeeming aspects of crises is that, amidst all the confusion, suffering, and loss, there are usually moments of grace, of humans showing their best nature... Unfortunately, crises also tend to bring out the worst of our natures... And then there are the cyberattacks. Last week the federal Cybersecurity & Infrastructure Security Agency, the FBI, and HHS issued a joint alert Ransomware Activity Targeting the Healthcare and Public Health Sector, warning that they have "credible information of an increased and imminent cybercrime threat to U.S. hospitals and healthcare providers." I'll spare you the technical details of the expected attack strategies or suggested mitigation efforts, but I will note that they warned: "CISA, FBI, and HHS do not recommend paying ransom." Read More »

Open Source Tools Provide An Economic Advantage For Science

Free and open source software (FOSS) and the distributed digital manufacturing of free and open source hardware (FOSH) have shown great promise for developing custom scientific tools. For some time now, FOSH has provided scientists a high return on investment. In fact, my previous research in the Open Source Labreported substantial economic savings from using these technologies. However, the open source design paradigm has since grown by orders of magnitude; now, there are examples of open source technology for science in the vast majority of disciplines, and several resources, including the Journal of Open Hardware, are dedicated to publishing them.

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Data Management for Large-scale COVID-19 Immunization: This is all not as simple as it seems

There is a global race for the development of a vaccine for the SARS-CoV-2 virus that causes COVID-19. Finding a vaccine that works and receives approval is only part of the process. There are a series of other steps that need to be taken so that the vaccine can be delivered. These include the mass production of the vaccine, shipment, administration and record-keeping. This may be even more complex as there may be several vaccines. In this article we review some of these issues with a particular focus on the United States.

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How Breaking My Back Led Me To Open Source

Open source gave a voice and a community to someone coping with the aftermath of a major injury, and eventually led to a new career...Breaking my back was a pivotal experience on many fronts. It scared the hell out of me. But the road to recovery helped me become a more resilient, courageous, and patient human being. Interestingly, it was this incident that also led me to the world of open source. Living with chronic pain is lonely, but I found my voice and a community via WordPress. Now, nearly eight years later, I'm working for the number one open source company in the world.

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Report on ONC’s Working Session on Patient Identity and Matching

On Monday, August 31, I attended the final Working Session on Patient Identity and Matching. This virtual event was hosted by the Office of the National Coordinator for Health IT (ONC). This Working Session was a followup to an earlier session back in June 2020. The event last week had over 300 attendees and covered a wide range of topics and technologies related to patient identity and matching. These ONC Working Sessions are being driven by requirements that are part of the 21st Century Cures Act as well as a Congressional request from December 2019 to continue to "...evaluate the effectiveness of current [patient identity and matching] methods and recommend actions that increase the likelihood of an accurate match of patients to their health care data." Much of the focus of this study has been on whether a national patient identifier should be implemented in the US.

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The Wrong Legacies of Health Information Technology

I read two articles this week that got me thinking, Robert Charette's "Inside the Hidden World of Legacy IT Systems" (IEEE Spectrum) and Douglas Holt's "Cultural Innovation" (Harvard Business Review). Both deal with what I'll call legacy thinking. It's a particular problem for healthcare...If you are in healthcare and rely on legacy systems, you're in trouble. If you are in healthcare and are not acutely aware of what your Achilles heel is, someone else is going to exploit it. Even if you are a new healthcare entrant with more modern technologies but still based on the current ideology, your impact is going to be limited.

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Extreme Wildfires Can Create Their Own Dangerous Weather, Including Fire Tornadoes - Here's How

It might sound like a bad movie, but extreme wildfires can create their own weather - including fire tornadoes. It happened in California as a heat wave helped to fuel hundreds of wildfires across the region, many of them sparked by lightning. One fiery funnel cloud on Aug. 15 was so powerful, the National Weather Service issued what's believed to be its first fire tornado warning. So, what has to happen for a wildfire to get so extreme that it spins off tornadoes? As professors who study wildfires and weather, we can offer some insights.

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Approval Of A Coronavirus Vaccine Would Be Just The Beginning - Huge Production Challenges Could Cause Long Delays

The race for a SARS-CoV-2 vaccine is well underway. It's tempting to assume that once the first vaccine is approved for human use, all the problems of this pandemic will be immediately solved. Unfortunately, that is not exactly the case. Developing a new vaccine is only the first part of the complex journey that's supposed to end with a return to some sort of normal life. Producing hundreds of millions of vaccines for the U.S. - and billions for the world as a whole - will be no small feat. There are many technical and economic challenges that will need to be overcome somehow to produce millions of vaccines as fast as possible.

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ONC Tech Forum 2020: An Attendee's Perspective

I attended the ONC summer Tech Forum in August 2020 which brought together over 1,500 industry experts and Federal partners to discuss technical innovations in health information technology and their potential impacts on the healthcare ecosystem...One of the most interesting parts of the conversation was focused on the efforts made by Honk Kong to develop an open source digital health platform. Over the past 20+ years, Hong Kong has been pursuing a "one system, one record" policy primarily built on open source components. Though they had little money to invest at the beginning, for them open source is more about retaining control than about controlling cost (though the lower price tag certainly got them started down this path)...

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An Epic Fight For the Metaverse—Fortnite Takes on the Big Tech Oligopolies

You might have missed it amongst all the headlines about the U.S.P.S., the 2020 elections, and, of course, that little thing we call the pandemic, but Fortnite got kicked off Apple's App Store (and subsequently Google Play). I'm not a gamer, but I am fascinated by gaming, because, as Steven Johnson put it, "The Future is where people are having the most fun." Tim Sweeney, the founder and CEO of Epic Games, Inc., which makes Fortnite, seems to be having a lot of fun. And he thinks the future is the Metaverse. Healthcare, take note. The tech giants were reacting to Epic allowing "permanent discounts" on developer fees for in-game purchases made directly, rather than going through Apple or Google. Developers thus avoid the 30% commission charged in those Stores. Mr. Sweeney has been railing about the commission level for some time, leading to the recent decision.

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Why openly available abstracts are important - overview of the current state of affairs

The value of open and interoperable metadata of scientific articles is increasingly being recognized, as demonstrated by the work of organizations such as Crossref, DataCite, and OpenCitations and by initiatives such as Metadata 2020 and the Initiative for Open Citations. At the same time, scientific articles are increasingly being made openly accessible, stimulated for instance by Plan S, AmeliCA, and recent developments in the US, and also by the need for open access to coronavirus literature. In this post, we focus on a key issue at the interface of these two developments: The open availability of abstracts of scientific articles. Abstracts provide a summary of an article and are part of an article's metadata. We first discuss the many ways in which abstracts can be used and we then explore the availability of abstracts. The open availability of abstracts is surprisingly limited. This creates important obstacles to scientific literature search, bibliometric analysis, and automatic knowledge extraction.

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Open Source Solutions For Public Health Case Reporting and COVID-19

The United States is continuing its slow emergence from a nation-wide shut down imposed to slow down the spread of COVID-19. Most states have started to reopen, with bars, restaurants, and many workplaces starting to fill. As people begin to spend more time together again, it is critically important that public health agencies do everything they can to help prevent further spread of the infection and continue to monitor the level of infection within the population. Data is an important tool that public health has to understand what is going on in the country. Years of limited government investment and neglect of current systems has limited public health's ability to meet the challenges of managing both localized outbreaks and pandemics.

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And We Thought Pandemics Were Bad...Time to Examine The Threat from Microplastics

The ocean full of microplastics, and fish are as well. They're in our drinking water. Indeed, "There's no nook or cranny on the surface of the earth that won't have microplastics," Professor Janice Brahney told The New York Times. Dr. Brahney was coauthor on a recent study that found microplastics were pervasive even in supposedly pristine parts of the Western U.S. They estimated that 1,000 tons of "plastic rain" falls every year onto protected areas there; 98% of soil samples they took had microplastics. Dr. Brahney pointed out that, because the particles are both airborne and fine, "we're breathing it, too." She admitted: "It's really unnerving to think about it."

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