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.
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.
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.
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.
The focus will be data management, final product formulations, compliance with GMP guidelines and workflow tracking.
Medicinal Cannabis Manufacturing
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.
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.
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.
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.
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.
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.
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.
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.
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 […]
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.
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. Otherwise, scientists are stuck performing manual […]
Benchling is a life sciences R&D software platform. Our clients include 12 of the top 25 pharmaceutical companies, emerging biotechs, and companies across a variety of other industries. Our goal is to improve their scientists’ productivity with modern software.
Given the world that artificial intelligence promises, our customers are really interested in how advanced data analysis and machine learning techniques can up-level their R&D efforts: from discovery, to lead optimization, process development, pre-clinical, and even IND filings. There’s no lack of enthusiasm to leverage these tools, so how do we get to that world?
The National Institutes of Health (NIH) is our nation’s medical research agency and strives to make scientific discoveries that improve health and save lives. Founded in 1870, the NIH conducts its own scientific research through its Intramural Research Program (IRP), which supports approximately 1,200 principal investigators and more than 4,000 postdoctoral fellows conducting basic, translational and clinical research.
In this blog, we will highlight recent ground-breaking NIH research, while also providing links to upcoming NIH events designed to keep researchers abreast of the latest discoveries.
Welcome to Benchtalk, a journal produced by Benchling. At Benchling, our mission is to accelerate life sciences for the benefit of humanity. As part of that mission, Benchling strives to engage the life sciences community in meaningful discussion and cross-discipline dialogue about the extraordinary goals of the field so that, together, we can work toward a better future. The quarterly Benchtalk Journal showcases the groundbreaking work of brilliant life scientists from academia to industry, facilitates discourse among members of the life sciences community, and connects them to revolutionary ideas.
This season, Benchtalk is all about the impact that breakthrough technologies – from biological techniques, to software, to hardware – are having on life science, and how leading R&D organizations incorporate new tools into their work. In this volume, we showcase the thoughts of leading researchers and software experts (including some of our own) on how these breakthroughs are changing the nature of life science, especially as technological advancement accelerates.