GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology.

SUMMARY: GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the 'tcpl' core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate PDF reports for quality control and data processing. AVAILABILITY AND IMPLEMENTATION: GladiaTOX R package (bioconductor). Also available via: git clone https://github.com/philipmorrisintl/GladiaTOX.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AI-driven laboratory workflows enable operation in the age of social distancing.

The COVID-19 (Coronavirus disease 2019) global pandemic has upended the normal pace of society at multiple levels-from daily activities in personal and professional lives to the way the sciences operate. Many laboratories have reported shortage in vital supplies, change in standard operating protocols, suspension of operations because of social distancing and stay-at-home guidelines during the pandemic. This global crisis has opened opportunities to leverage internet of things, connectivity, and artificial intelligence (AI) to build a connected laboratory automation platform. However, laboratory operations involve complex, multicomponent systems. It is unrealistic to completely automate the entire diversity of laboratories and processes. Recently, AI technology, particularly, game simulation has made significant strides in modeling and learning complex, multicomponent systems. Here, we present a cloud-based laboratory management and automation platform which combines multilayer information on a simulation-driven inference engine to plan and optimize laboratory operations under various constraints of COVID-19 and risk scenarios. The platform was used to assess the execution of two cell-based assays with distinct parameters in a real-life high-content screening laboratory scenario. The results show that the platform can provide a systematic framework for assessing laboratory operation scenarios under different conditions, quantifying tradeoffs, and determining the performance impact of specific resources or constraints, thereby enabling decision-making in a cost-effective manner. We envisage the laboratory management and automation platform to be further expanded by connecting it with sensors, robotic equipment, and other components of scientific operations to provide an integrated, end-to-end platform for scientific laboratory automation.

Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure.

The US FDA defines modified risk tobacco products (MRTPs) as products that aim to reduce harm or the risk of tobacco-related disease associated with commercially marketed tobacco products.  Establishing a product's potential as an MRTP requires scientific substantiation including toxicity studies and measures of disease risk relative to those of cigarette smoking.  Best practices encourage verification of the data from such studies through sharing and open standards. Building on the experience gained from the OpenTox project, a proof-of-concept database and website ( INTERVALS) has been developed to share results from both in vivo inhalation studies and in vitro studies conducted by Philip Morris International R&D to assess candidate MRTPs. As datasets are often generated by diverse methods and standards, they need to be traceable, curated, and the methods used well described so that knowledge can be gained using data science principles and tools. The data-management framework described here accounts for the latest standards of data sharing and research reproducibility. Curated data and methods descriptions have been prepared in ISA-Tab format and stored in a database accessible via a search portal on the INTERVALS website. The portal allows users to browse the data by study or mechanism (e.g., inflammation, oxidative stress) and obtain information relevant to study design, methods, and the most important results. Given the successful development of the initial infrastructure, the goal is to grow this initiative and establish a public repository for 21 st-century preclinical systems toxicology MRTP assessment data and results that supports open data principles.