Wednesday, Dec. 1, 2021 | 1:00–3:00 p.m. (Central US Time) 
Ruchir Shah, Alex Sedykh, Vijay Gombar, and Austin Ross—Sciome LLC 

Zoom Details: Will be emailed to registrants on the morning of the session

EXPERIMENTS ARE TOO HARD: HOW TO USE ONLINE RESOURCES FOR PREDICTIVE TOXICOLOGY

Only a small fraction of compounds in the commerce (TSCA, US; ECHA, EU; DSL, CA) has been experimentally assayed for toxicity evaluation to support hazard and risk assessment. Given the large number of chemicals that lack experimental toxicity profile, coupled with the cost, time, and animal sacrifice it takes to generate those profiles, NAMs – New Approach Methodologies – are a prudent recourse. Predictive models have been recognized as a first go-to NAM and their importance has been highlighted in all four previous sessions of this series. 

In our workshop, we will discuss some publicly available tools for accessing data and/or predicting various properties relevant to hazard and exposure assessment, namely ICE (Integrated Chemical Environment), OPERA (OPEn (q)saR App), and OrbiTox – a newly designed tool for translational discovery through an interactive, concerted view of multi-domain data and predictive models that provide chemistry-backed reasoning based on our recently published set of structural features, Saagar.

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Wednesday, Nov. 3, 2021 | 1:00–3:00 p.m. (Central US Time) 
Caroline Ring—US Environmental Protection Agency 

Zoom Details: Will be emailed to registrants on the morning of the session

PLACING TOXICOLOGY DATA IN THE CONTEXT OF EXPOSURE

“The dose makes the poison” – in other words, risk is a function of both hazard and exposure.

New approach methodologies (NAMs) for hazards, such as in vitro high-throughput screening assays, can rapidly estimate hazards for thousands of chemicals. But those thousands of chemicals may have little or no measured exposure data.

How can we estimate exposures – and meaningfully compare them to in vitro hazard data?

This session will present an overview of exposure NAMs in US EPA’s ExpoCast project to inform exposure estimation from source to receptor, and a discussion of the high-throughput toxicokinetics approach used to place in vitro HTS hazard data in the context of in vivo exposures.

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Wednesday, Oct. 6, 2021 | 1:00–3:00 p.m. (Central US Time) 
Fred Wright—North Carolina State University, Burcu Beykal—University of Connecticut, and Allison Dickey—North Carolina State University 

Zoom Details: Will be emailed to registrants on the morning of the session

MANIPULATING AND DISPLAYING BIG(ISH) DATA IN R 

This session will provide a tutorial on commonly used and useful aspects of R, using the RStudio interface. Example datasets will be used that are relevant to bench scientists and environmental researchers. We do not assume any prior familiarity with R.

• Introduction to R
  • An introduction to RStudio and installation of packages
  • Reading data into R in various formats
  • Exploring data types and dimensions
  • Extracting data and identifying missing data
  • Sorting data and using the apply function
  • Merging data frames
• Data visualization and analysis
  • Plotting/graphics in base R (scatterplots, histograms, boxplots, etc.)
  • Basic summary statistics
  • Basic inferential statistics (e.g. t-tests, ANOVA, multiple test correction)
  • Clustering and dimensional reduction (e.g. PCA)
• More Advanced Visualization
  • Using ggplot2
  • Customizing plots
  • Spatial displays and maps in ggplot2
  • Interactive plots using plotly

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Download Slide Deck (PPTX)

Wednesday, Aug. 18, 2021 | 1:00–3:00 p.m. (Central US Time)
Antony Williams—US Environmental Protection Agency  

Zoom Details: Will be emailed to registrants on the morning of the session

“NEW APPROACH METHODS”—WHAT IS THAT? 

• An introduction to New Approach Methods
  • What’s a NAM?
    • In silico – QSAR and read-across
    • In vitro assays
    • In vitro  toxicokinetics
    • Computer modeling
• Short introduction to QSAR model data in the Dashboard
  • TEST predictions
  • OPERA predictions
  • Calculation reports
  • Realtime prediction
• An introduction to ToxCast and Tox21
• An overview of assay endpoints and biology
• What can be done using ToxCast in vitro data?
  • Bioactivity for weight-of-evidence and biological questions
  • Screening level endocrine bioactivity assessment
• High throughput toxicokinetics
• IVIVE high-throughput toxicokinetic data and models
• Bioactivity-Exposure Ratio
• Short introduction only to Exposure Modeling (this will be a separate session with Caroline Ring)

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Wednesday, July 14, 2021  | 1:00–3:00 p.m. (Central US Time) 
Antony Williams—US Environmental Protection Agency

HOW TO PLACE YOUR RESEARCH QUESTIONS OR RESULTS
INTO THE CONTEXT OF THE “LEGACY” TOXICOLOGY DATA? 

Chemicals/structures/properties; ToxRefDB, ToxValue, etc.

• An introduction to the dashboard
  • Substances vs structures
  • Structure formats for data exchange and connectivity (SMILES, InChIs, molfiles)
  • Identifiers – CASRN, chemical names, systematic names
  • Data curation approaches: substance-structure ambiguity
  • ChemReg: substance registration
  • Data gathering for systematic reviews
  • Curated lists
  • Properties/Fate and Transport
  • Access to Exposure Data
  • Hazard data in the dashboard – ToxVal data (sourced from >40 databases, >50,000 chemicals, >900,000 data points)
  • Access to in vitro bioactivity data (ToxCast/Tox21)
  • The Executive Summary of data
  • Single chemical searches vs Batch searches

CASE STUDIES

• Specific examples – disinfectant by-products,
• Approaches to “prioritizing” a set of chemicals

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