Build A Dashboard To Track The Spread of Coronavirus Using Dash: Real-time view of globally confirmed, recovered and deaths coronavirus (COVID-19) cases
Last month, I published four posts to share with you my experience in using matplotlib. Benefit from its full control of elements on a given graph, matplotlib is deemed as a fundamental python library for data visualisation and used by many other libraries (e.g. seaborn and pandas) as plotting module. This is also why I think learning matplotlib is an essential part for being a practitioner in data science, which helps to build up in-depth understanding about logic behind data visualisation tools.
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LabLynx Joins the COVID-19 Fight by Introducing New CovidLiMS
ATLANTA – LabLynx, Inc., long-time leader in enterprise-level cloud-hosted LIMS/LIS, today announced it has developed the world’s first LIMS (Laboratory Information Management System) dedicated specifically to COVID-19 diagnostic testing. Called "CovidLIMS”, its main features include, crucially, swift setup-to-live time: 2-5 days, including training, according to LabLynx President John H. Jones.
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How biotechs are racing to develop COVID-19 tests
The novel SARS-CoV-2 virus and the disease it causes (COVID-19) are sweeping the world. The US’s ability to rapidly and accurately test patients, not to mention their health care providers, is critical to containing the virus. That said, it has proved to be one of the biggest challenges for our country in recent weeks.
Much has already been written about what initially went wrong with the coronavirus testing in the US and why the US government and CDC lagged behind other developed nations in deploying diagnostics. This article will instead focus on the remarkable companies, institutions, and clinical labs that are rising to the challenge by working around the clock to produce high volumes of accurate and reliable tests.
In addition to the COVID-19 tests that are already in use, companies are prototyping groundbreaking new diagnostics. These new tests have the potential to revolutionize COVID-19 detection now and chart the course for the future of infectious disease diagnostics.
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Pittcon 2020 – Covid-19 Changes Everything
The Pittcon 2020 roundup for those that didn't make there.
Pittcon 2020, the annual laboratory science conference, had a very different feel to it this year. If the show had been held just two weeks later, with much of the USA and Europe in lock-down, it would not had gone ahead. Although the USA had not at that stage seen many cases of Coronavirus this was the word on everyone’s lips as they walked the exhibition hall and conference. Several booths were left empty with signs saying the exhibitor was “Absent due to travel restrictions”. Certainly the most popular thing on the Autoscribe stand were individual packets of antimicrobial hand wipes which we had bought along to give-away.
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A place to share COVID-19 resources with the scientific community
In the midst of the COVID-19 outbreak, the world is looking to the scientific community for help. We know that scientists everywhere are mobilizing to characterize the virus, to replicate and study it in lab, to perform testing and analyze results, to develop next-gen diagnostics, and to quickly develop vaccines and antiviral treatments.
To support these efforts, we have set up a COVID-19 resources webpage that points to sequences, protocols, and other work that has been shared by scientists for public use. Our hope is that these resources will be beneficial to the greater scientific community, especially to scientists who are actively addressing this challenge.
We are accepting submissions from scientists and will be updating the page regularly. You may share data in Benchling — protocols, sequences, experimental results. You may also share an existing resource with us — a pre-print, a published protocol. Please find instructions for contributing below.
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Tips for Using Pipeline Pilot as an Integration Platform
One of the most common integration platforms used in laboratory informatics is Pipeline Pilot from BIOVIA. Whether part of a large enterprise software implementation or a project to pass data between two applications, integration projects always present challenges. In the laboratory environment, achieving integration goes beyond merely exchanging data between applications. Laboratory equipment/automation, specialized data sets, and validation complicate an already difficult task and create unique challenges. In addition to the goals of streamlining business operations, eliminating data silos and minimizing redundant data entry, integration also has to be done in such a way that supports regulatory compliance and promotes data integrity.
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QLIMS for Cannabis Companies – Part 3 of 3: Medicinal Cannabis Manufacturing
The final part of this series will focus on how QLIMS supports the manufacturing of medicinal cannabis products.
The focus will be data management, final product formulations, compliance with GMP guidelines and workflow tracking.
Medicinal Cannabis Manufacturing
A large number of medicinal cannabis facilities set up across Australia are focused on manufacturing for local and exporting. As such the sampling numbers are going to be very high so a system to effectively manage all that data, maintain traceability and help keep compliant with GMP will be important.
As seen from our previous posts, no matter what data you are looking to record and track a LIMS can help.
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Point-of-care RNA-based diagnostic device for COVID-19
In this brief editorial article published in the journal Diagnostics, Tiawanese researchers Yang et al. provide their insights into a more convenient at-home point-of-care (POC) testing method for the COVID-19 illness. Noting the urgency of the associated pandemic and the various costs associated with traditional testing methodologies such as lateral flow immunoassays and molecular-based assays, the authors suggest the blending of several tools: a paper-based result and common mobile devices. A patient at home could take a nasal swab and use a POC device to return a colorimetric result, which could then be captured by mobile phone and rapidly sent to a clinician for analysis. They conclude that such a method could "provide new insights into designing POC COVID-19 diagnostics and ultimately improve the health care system to combat this and similar diseases."
Italian Researchers Identify New SARS-CoV-2 Gene Variants That Provide Clues to Coronavirus’s Epidemiology
Two teams of infectious disease researchers in Italy say they have further analyzed the SARS-CoV-2 genome from samples acquired locally to generate early data that reveal a level of genetic variability suggesting the rapidly spreading virus's genome is stable. The findings were developed using a new next-generation sequencing (NGS) research assay from Thermo Fisher Scientific.
Laboratory Informatics Weekly Update – Volume 18, Issue 12
March 25, 2020 Laboratory Informatics Weekly Update Volume 18, Issue 12 In This Issue Blogs LIMS and COVID-19 Testing & ReportingKnown variously as coronavirus, COVID-19, novel coronavirus, 2019-nCoV and SARS-CoV-2, the current global pandemic has been reported in 191 Countries and Territories around the world as of March 23, 2020, with over 350,000 confirmed cases and more than 15,000 deaths. These figures are being tracked in real time by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University. [Read More] Disaster Management for the LabDisaster management is, in a nutshell, about preparedness. Of course, the primary…Policy for diagnostic tests for Coronavirus Disease-2019 during the public health emergency
This is the third of a series of interim guidance documents, this one originating from the U.S. Food and Drug Administration (FDA). Issued on March 16, this guidance document provides insight into FDA policy for the development, validation, and use of diagnostic tests for Coronavirus Disease-2019 (COVID-19), particularly those tests issued an Emergency Use Authorization (EUA). This guidance applies to not only manufacturers developing and distributing test kits but also CLIA laboratories cleared for high-complexity testing that develop and validate their own tests. The FDA provides background on the topic and then discusses the policy in detail, before closing with its validation study recommendations.
LIMS and COVID-19 Testing & Reporting
Known variously as coronavirus, COVID-19, novel coronavirus, 2019-nCoV and SARS-CoV-2, the current global pandemic has been reported in 191 Countries and Territories around the world as of March 23, 2020, with over 350,000 confirmed cases and more than 15,000 deaths. These figures are being tracked in real time by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University.
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Laboratory biosafety guidance related to coronavirus disease (COVID-19): Interim Guidance, 19 March 2020
Again, not a journal article, but here rather we have another interim guidance document by the World Health Organization (WHO), this time in regards to laboratory biosafety related to COVID-19 testing. Effective March 19, 2020, this guidance document, complete with references, addresses laboratory biosafety principles to consider when handling and testing specimens believed to contain the COVID-19 virus. The WHO provides a bit of background, provides an overview of the key points, and then discusses those points in further detail. They also include two annex items: the core requirements of good microbiological practice and procedure (GMPP) and a risk assessment template for laboratories to borrow from.
Disaster Management for the Lab
Disaster management is, in a nutshell, about preparedness. Of course, the primary challenge in preparedness is anticipating just what it is for which you are preparing. In the case of disaster management, the possible scenarios vary a great deal – with some being virtually impossible to foresee – so any management plan faces potential failure right from the outset.
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Starburst Announces Free Software To Accelerate COVID-19 Data Discovery & Analytics
Starburst today announced a free offer aimed at helping healthcare professionals stop the spread of COVID-19. The offer is available for the duration of 2020 and is specifically for universities, hospitals, and healthcare research organizations, including government and non-government organizations (NGOs) that have teams dedicated to analyzing COVID-19 data.A Conversation with Dr. Nigel Mouncey, Director of the Joint Genome Institute: The next frontier of genomic breakthroughs
Nigel Mouncey, PhD is the Director of the Joint Genome Institute (JGI), a U.S. Department of Energy Office of Science National User Facility located at Lawrence Berkeley National Laboratory in Berkeley, California. Previously, Dr. Mouncey held increasing leadership roles at Dow AgroSciences, most recently as the Director of R&D for Bioengineering and Bioprocessing. Before that, he led research groups at DSM Nutritional Products and Roche Vitamins. We sat down with Dr. Mouncey to discuss the most exciting ongoing developments in genomic research and how data will continue to shape life science R&D.
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Generating FAIR — Findable, Accessible, Interoperable, Reusable — Resources with Marchantia, a Prototype for Plant Synthetic Biology
“Classic!” That’s a veteran lab member’s response when a new PhD student recognizes that a plasmid doesn’t have the expected sequence. I have personally heard this, and I have seen it happening around me many more times. DNA constructs from other labs, or even from former members of your own lab, can often be poorly documented. As a result, scientists waste time and resources by having to recheck or redo previous work. And that’s just the tip of the iceberg when it comes to data management challenges in a highly dynamic and resource-limited academic environment. In this environment, working practices and structural constraints have tended to prioritize innovation before documentation. Fortunately, this has been changing for some time, as data-driven biology and society have demanded well-characterized research and open science in order to make research more reproducible and more transparent.
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Meeting ISBER Recommendations for Biobank Management
LIMS can contribute significantly to the efficient management of any biobank facility. With every aspect of specimen handling from collection through storage, processing, distribution, and eventual disposal to be considered as well as the need to manage all the associated data and information, ISBER (International Society for Biological and Environmental Repositories) has published a set of recommendations (the ISBER Best Practices: Recommendations for Repositories Fourth Edition) for the most effective practices for managing biological and environmental specimen collections and repositories. ISBER has also created a very useful self-assessment tool to allow biobanks to evaluate how well their facilities already comply with the best practices. In a recent webinar Autoscribe Informatics explained how the Matrix Gemini Biobank Manager configuration addresses the recommendations from ISBER. This webinar is still available to view.
Laboratory testing for coronavirus disease (COVID-19) in suspected human cases: Interim Guidance, 19 March 2020
Breaking from the norm, rather than a journal article, this document represents official interim guidance on laboratory testing for COVID-19 from the World Health Organization (WHO), effective March 19, 2020. This guidance document, complete with references, addresses laboratory testing guidance principles for testing patients who meet the case definition for being infected with the COVID-19 virus. The WHO provides a bit of background, then addresses specimen collection and shipment, laboratory testing procedures, and reporting. They also include where further research must tread, as well as an ISO 15189:2012-compliant COVID-19 laboratory test request form. WHO closes by encouraging "the sharing of data to better understand and thus manage the COVID-19 outbreak, and to develop countermeasures."
SynBioBeta | Benching & Pairwise – The Future of Agriculture
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Through SynBioBeta's webinar series, Benchling and Pairwise came together to discuss how gene editing allows the production of new and improved crops that are more sustainable, more nutritious, and more affordable. We also covered the challenges and opportunities for using gene editing to bring better food to market.
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