ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis
In this brief article published in Cytometry Part A, researchers at the Austrian Centre for Industrial Biotechnology present their open-source multiplex fluorescence in situ hybridization (M‐FISH) software for chromosome painting. The tool—ChromaWizard—acts as a free and open-source option for hybridization analysis, integrating "image processing, multicolor integration, chromosome separation, and visualization with false color assignments." The software can handle images in TIFF, PNG, and JPEG formats and provides robust visualization tools. The authors conclude that ChromaWizard "allows direct inspection of the original hybridization signals and enables either manual or automatic assignment of colors, making it a functional and versatile tool that can also be used for other multicolor applications."
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Haves and have nots must find a better way: The case for open scientific hardware
Open-source software has been a topic of discussion for decades, both as a model of software development and distribution and as a potential for what could be done with it. But the concept of open-source hardware, particularly in the field of science, has been more challenging to address. In this brief perspective article by University of Tübingen's André Maia Chagas, he discusses the benefits of open science hardware to address the growing concern of "haves and have nots" in the scientific research community. Citing high prices, the overall closed-source nature of equipment, businesses that can close without warning, and poor customer support, Chagas attempts to demonstrate that advances in modern design—such as the smartphone—and organizational efforts to implement and promote open hardware philosophies provide opportunity for more people to engage in scientific endeavors. He concludes we "need to reassess our relationship to knowledge and technology, how it determines our role in society, and how we want to spend grant money entrusted to us by the people," and by focusing on making hardware more open and accessible, we'll shrink the divide and improve scientific research as a result.
Laboratory Informatics Weekly Update – Volume 17, Issue 50
December 17, 2019 Laboratory Informatics Weekly Update Volume 17, Issue 50 In This Issue Upcoming Webinars 01/28/2020 - Astrix Webinar – Supporting Your Laboratory Informatics Ecosystem with Laboratory Informatics as a Service (LIaaS) Featured Books LIMSpec 2019-r1 Edition Journal Articles Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registryThe clinical registry is an important tool in assisting those affected by rare diseases. Using observational study methods, the registry collects and assists with analysis of data related to a particular disease or condition, helping to serve researchers and their policies towards helping…CytoConverter: A web-based tool to convert karyotypes to genomic coordinates
In this brief article published in BMC Bioinformatics, Wang and LaFramboise address the topic of cytogenetic data and their genomic coordinates, which the authors describe as "precisely [specifying] a chromosomal location according to its distance from the end of the chromosome." The authors note that despite changes in techniques over the years, the use of karyotype and cytogenetic nomenclature was the primary way of characterizing aberrations in chromosomes, and those methods are still being used today. Additionally, archival data used karyotypes and cytogenetic nomenclature. Given the lack of a maintained, robust tool for converting that nomenclature to genomic coordinates, the authors address their creation, CytoConverter, and explain how it accomplishes such conversions. They conclude that the tool should have "considerable value to the community for analyzing archival patient samples, as well as samples for which higher-resolution copy number data is unavailable."
Benefits and Best Practices for Integrating Laboratory Instruments with LIMS
Due to technological advances in laboratory instruments and higher throughput processes, data volumes in modern analytical laboratories have increased dramatically over the last several decades. While this increased data volume presents the opportunity to improve innovation and enable timely and effective business decisions, it also presents significant data management and processing challenges. In order to meet the challenge of turning this data into knowledge, laboratories are looking to automate and integrate laboratory operations and processes as much as possible in order to provide digital continuity throughout the product lifecycle.
Integrating laboratory instruments with Laboratory Information Management Systems (LIMS) is one of the best ways to automate laboratory processes. Instruments that are commonly integrated with LIMS in laboratories include:
- GC
- GCMS
- HPLC
- LCMS
- ICP
- Particle Counters
- DNA Sequencers
- Balances
- Titrators
- AA Analyzers
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Roche and Fortelinea to co-market software solutions in US to improve workflow in histology research labs
Roche announced today that it has signed a joint marketing agreement in the United States with Fortelinea Software Systems that allows for the linking of Roche's VENTANA Connect middleware with Fortelinea's Prima lab tracking and management system to improve workflow for automated immunohistochemistry (IHC) and in-situ hybridization (ISH) testing in U.S. research laboratories.Experience Convenience Like Never Before with the Verso® Q20 Automated Sample Storage System
The new Verso® Q20 Automated Sample Storage System from Hamilton Storage lets you take control of your time – and your samples – with hands-free sample storage and access. Discover all the exciting benefits this compact powerhouse offers during its market debut in Booth #805 at the SLAS 2020 International Conference & Exhibition, January 25-29 at the San Diego Convention Center.Biosero Acceleration Lab Demonstrates Most-Advanced Lab Automation Experiences in Pharmaceutical, Life Science and Research
Acceleration Lab in San Diego Showcases AI, Machine Learning, Robotics, Voice Command and Real-Time Data to Show Potential of Automated Lab Management.Intermountain Healthcare Selects PierianDx Clinical Genomics Solution
PierianDx, a leading clinical genomics informatics company, today announced that Intermountain Healthcare has selected the PierianDx Clinical Genomics Workstation to advance their precision medicine program, Intermountain Precision Genomics.Autoscribe Informatics Announces New President, North American Operations
Autoscribe Informatics, a leading provider of Laboratory Information Management Systems (LIMS), is delighted to announce the appointment of Claude Hatfield as President, North American Operations. Claude assumes responsibility for leading the North American operation to achieve its revenue, profit and cashflow objectives while encouraging global teamwork.
Thermo Fisher Scientific to Bring One-Day Genomic Profiling to Hematology Oncology
Thermo Fisher Scientific announced that the Ion Torrent Oncomine Myeloid Research Assay* will be available in 2020 to run on the newly introduced Ion Torrent Genexus System*, the first fully integrated next-generation sequencing (NGS) platform featuring an automated workflow that delivers results economically in a single day with minimal user intervention and tissue sample input.
IDBS expands operations in India to capitalize on R&D growth
IDBS, a software informatics solution provider for biotech and pharma, has expanded its global reach in India and made two strategic hires in the region.Proscia® and Johns Hopkins School of Medicine Collaborate to Bring Artificial Intelligence Applications to Several High-Impact Diseases and Specialties in Pathology
Proscia, a leading provider of AI-enabled digital pathology software, and Johns Hopkins School of Medicine, one of the leading academic medical centers in the U.S., will collaborate on the development of computational applications that incorporate artificial intelligence (AI) to advance the practice of pathology for multiple diseases.LIMS Vs. QMS
Most laboratories generate massive volumes of data on a day-to-day basis and have to follow regulatory guidelines. Laboratories must determine if they need a LIMS or a QMS or both. Managing a plethora of laboratory data efficiently and assuring quality is crucial for all laboratories. To make a decision, it is important to understand the differences between a LIMS and a QMS.
To read the complete blog, please visit: https://cloudlims.com/blog/lims-versus-qms.html
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Laboratory Informatics Weekly Update – Volume 17, Issue 49
December 10, 2019 Laboratory Informatics Weekly Update Volume 17, Issue 49 In This Issue Featured Books Laboratory Information Management for Cannabis Quality Assurance Journal Articles Fast detection of 10 cannabinoids by RP-HPLC-UV method in Cannabis sativa L.In this 2019 article published in Molecules, Mandrioli et al. detail the process they developed for detecting 10 cannabinoids in Cannabis sativa L. using reversed-phase high-performance liquid chromatography with an ultraviolet detector (RP-HPLC-UV). Citing numerous other published methods, many of them requiring more expensive mass spectrometry detectors, the authors sought to "identify and titrate cannabinoids in a simple way" using a method that…Implementing a novel quality improvement-based approach to data quality monitoring and enhancement in a multipurpose clinical registry
The clinical registry is an important tool in assisting those affected by rare diseases. Using observational study methods, the registry collects and assists with analysis of data related to a particular disease or condition, helping to serve researchers and their policies towards helping the afflicted. While studies have been performed on the "fit for use" nature of registry data, data quality studies of registries using specific quality improvement approaches have been fewer. Pratt et al. give their take on a quality improvement scheme for registries in this 2019 paper, tapping into the significant data generated by the ImproveCareNow (ICN) Network and its goal of improving outcomes of pediatric and adolescent inflammatory bowel diseases. After going through their methodology, the authors conclude that data quality improvement campaigns, particularly those that include support for training and tools, can improve "the completeness and consistency" of registry data, and by extension resulting "in a higher level of confidence when accessing the data for various purposes, including clinical decision making."
Evaluating Legacy LIMS Part 2: LIMS Migration
Whether due to increases in data volume, regulatory constraints, M&As, globalization, outsourcing, or a myriad of other reasons, legacy LIMS are becoming extremely costly to manage, and many companies are finding themselves in a situation where their legacy system is not able to adequately keep up with changing business requirements.
Organizations looking to address deficiencies in their legacy LIMS have two options – re-architect/re-engineer their legacy system or purchase and migrate to a new LIMS. In part 1 of this blog series, we discussed the steps involved in re-architecting your legacy system, as well as the benefits of doing so. In this article, we’ll explore the other option – purchasing and migrating to a new LIMS.
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Agile Development in Laboratory Informatics
Agile development is one of those buzzwords that you’ve heard a lot if you’ve spent any time at all in the business world. Like Lean Six Sigma, it’s one of those secret handshake-type terms that will have everyone nodding in recognition, even if they’re not really sure what it’s about. But in laboratory informatics—particularly in…
