April 7, 2020 - Importance of Method Validation to Public Health
You can’t escape the knowledge that the world is currently in the midst of a global pandemic of COVID-19, the disease caused by the novel SARS-CoV-2 strain of coronavirus. Tracking and slowing the spread of disease have been on everyone’s mind for much of the year. We know that this will be difficult to do without rapid and accurate testing, which has been in short supply in the United States. The U.S. must produce or acquire accurate tests, quickly and in high volumes, which is why many are pushing to loosen regulations to get more tests into the hands of health care professionals. The laboratory informatics experts at CSols have a unique insight into laboratory testing and data analysis, and we have been discussing—remotely, of course—how our experience with successful LIMS implementations can help experts predict and prevent future pandemics.April 1, 2020 - COVID-19 Testing for the Physician Office Laboratory (POL)
Like it or not, physician or not, the current pandemic is already affecting you in some ways or others. And those physicians on the front line seeing patients cannot avoid being involved. If you have testing equipment of your own, at least you may be able to recoup some of the costs of seeing potential COVID-19 patients, handling specimens and meeting reporting requirements.
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March 31, 2020 - 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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March 31, 2020 - 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.[Read More]
March 31, 2020 - 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.[Read More]
March 31, 2020 - 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.[Read More]
March 31, 2020 - 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.[Read More]
March 31, 2020 - 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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March 24, 2020 - 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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March 23, 2020 - 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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March 23, 2020 - 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.[Read More]
March 23, 2020 - 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.[Read More]
March 23, 2020 - 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.March 17, 2020 - SynBioBeta | Benching & Pairwise – The Future of Agriculture
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. Watch Now:
March 17, 2020 - Tips for Upgrading Your Waters Empower System
Waters Empower 3 is a chromatography data system (CDS) that links to chromatographic instruments to help facilitate management of chromatography test results through data acquisition, processing, reporting and distribution. Empower 3 generates lots of data with complex calculations and detailed reports and has several tools that address compliance and data integrity concerns such as electronic signatures and audit trails. Waters Empower 3 is continuously upgraded to meet the changing needs of laboratories across all industries – pharmaceutical QC/RD, food and beverage, oil and gas, petrochemical, water and environmental, manufacturing, contract labs, and more. Each new feature release of Empower 3 contains new functionality that is built upon feedback and customer input from these sectors and could thus bring significant benefits to the Laboratory user.[Read More]
March 17, 2020 - The Dirty Secret of LIMS Implementations
I’m not going to sugarcoat this…LIMS implementations can suck at first. The vendors may not tell you that in their seamless demos or slick PowerPoint presentations, but business practices will change throughout the whole organization, some things may take longer than they did before, and almost everyone’s likely to hate the new system. These considerable changes can lead to employee confusion, resistance, and a breakdown in communications. This has the potential to lower the system’s value and negatively impact your project’s ROI. So, how do you effectively make the best of the situation? In this blog, we’ll advocate for well-established, effective Organizational Change Management (OCM) practices that can ease the pain of LIMS implementations and manage the changes that go along with a new enterprise application. OCM won’t help you avoid the pain altogether, but at least everyone will know that there’s a plan and it has an end point. [Read More]March 10, 2020 - QLIMS for Cannabis Companies – Part 2 of 3: Research and Analytical Labs
The next part in our series will focus on how QLIMS can help with the extraction, research and testing of medical cannabis, with a focus on data management, quality, inventory, stability testing and regulatory standards.
Medical Cannabis Testing & Quality Assurance
With the large number of cultivation facilities currently set up or in the process of being implemented across the country, Medical Cannabis testing labs will see a massive magnitude of samples that will require testing and processing will be difficult to manage with just spreadsheets or paper-based systems.…
March 10, 2020 - Experience More From Your LIMS Vendor – Part 2: Implementation Phase
It is an understatement to say that the implementation phase of a laboratory information management system (LIMS) is critical to the success of your laboratory. Your LIMS is your lab’s central nervous system, so the implementation must be done right. And, it’s during this phase that the quality of your LIMS vendor partnership will become apparent - either as one that can support your current and future needs or as one that will leave you struggling for years to come.[Read More]
March 10, 2020 - Software as a Biotechnology: How Benchling Extensions and Integrations Drive Life Sciences R&D
Modern life science R&D is producing data of a much greater quantity and complexity than ever before. R&D teams at small biotechs and large pharmas alike need a tech stack that allows them to flexibly extend software tools and and integrate them with one another and with lab hardware.…
