A list of tools for predictive modeling in food and quantitative microbial risk assessment
| Tool/Resource | Description | Topic | |
|---|---|---|---|
| @Risk | Excel add-in that uses Monte Carlo simulation to analyze risk and uncertainty in decision-making, showing the probability of various outcomes and supporting risk analysis. | Quantitative Microbial Risk Assessment (QMRA) | |
| A swift Quantitative Microbiological Risk Assessment tool (sQMRA) | Simplified Excel-based Quantitative Microbiological Risk Assessment tool for comparing pathogen-food risks from retail to illness, including cross-contamination and food preparation stages. | Quantitative Microbial Risk Assessment (QMRA) | |
| biogrowth (R package) | R package for modeling microbial growth under static and dynamic conditions in predictive microbiology, offering model fitting and growth predictions. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| biogrowth-web (Shiny app) | Web app for microbial growth modeling using an interactive interface, allowing users to predict microbial growth and fit models under static and dynamic conditions. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| Bioinactivation (R package) | R package for microbial inactivation modeling, supporting predictions and model fitting under isothermal and non-isothermal conditions for use in predictive microbiology. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| Bioinactivation (Shiny app) | Web app for microbial inactivation, providing interactive tools for fitting inactivation models and making predictions under static and dynamic conditions. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| Bioinactivation FE | Web interface for microbial inactivation modeling, offering easy model fitting and prediction generation under both isothermal and non-isothermal conditions. | Predictive Microbial Modeling (PMM) Fitting Tool Prediction Tool | |
| Cardinal Fit (Shiny app) | Shiny app for fitting cardinal parameter models in predictive microbiology, estimating microbial growth conditions like temperature and pH from challenge study data. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| ComBase | Online resource for quantitative and predictive food microbiology, featuring a database of microbial growth and survival data, aiding in risk management and food safety modeling. | Predictive Microbial Modeling (PMM) Model Repository Quantitive Microbial Risk Assessment (QMRA) | |
| Control Measures Validation (FSO) Tool | Spreadsheet tool to explore the ICMSF Food Safety Objective (FSO) equation for determining product compliance in processes affected by variability, useful for validating food safety control measures. | Other Resources | |
| D-database microbial inactivation data in foods | Database compiling over 2,000 microbial inactivation models from peer-reviewed studies, emphasizing variability in microbial responses and providing tools like meta-regression with mixed-effects models. | Other Resources | |
| DMFit | Application for fitting bacterial growth curves, allowing users to visualize microbiological growth/survival data and apply models, with nonlinear least squares and regression coefficient calculations. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| DMRI – predictive models for meat | Predictive models for meat safety and shelf life, simulating bacterial growth based on user input. Offers consultancy services and predictive modeling courses on topics like Listeria and pathogen inactivation. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| E. coli Inactivation in Fermented Meats Model | Excel-based tool for calculating E. coli inactivation in fermented meat products by inputting fermentation and maturation conditions, supporting isothermal and dynamic scenarios with easy data entry. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| EFSA Comprehensive European Food Consumption Database | Database offering detailed food consumption data across the EU, essential for food hazard risk evaluation and exposure estimation, helping tailor risk assessments based on dietary surveys by age and food group. | Other Resources | |
| EFSA Knowlege Junction (KJ) | Open repository for sharing food and feed safety risk assessment evidence and materials, promoting transparency and reuse, with submissions receiving DOIs and metadata for tracking. | Other Resources | |
| EFSA zoonoses, antimicrobial resistance and food-borne outbreaks | Directive-mandated data collection on zoonoses, antimicrobial resistance, and foodborne outbreaks across the EU, analyzed and published by EFSA in annual reports in collaboration with ECDC. | Other Resources | |
| Emerging Zoonoses Information and Priority systems (EZIPs) | Resource for prioritizing emerging zoonoses based on threat criteria, featuring a ranked database of zoonotic pathogens and an interactive tool for exploring and adding new pathogens. | Other Resources | |
| FDA’s Fresh Produce Risk Ranking Tool | Semi-quantitative tool identifying high-risk pathogen-produce combinations in the U.S. food supply, based on outbreak data, customizable in Microsoft Access with guidance and peer review support. | Other Resources | |
| FDA-iRISK | Web-based risk-assessment tool for comparing and ranking microbial and chemical hazards in food, simulating food safety scenarios across the supply chain, with advanced features like Monte Carlo simulations and predictive microbial models. | Quantitative Microbial Risk Assessment (QMRA) | |
| FISHMAP | Software that predicts spoilage bacteria growth in fish products under modified atmosphere packaging (MAP), comparing experimental data with models, and saving results in Excel format for easy analysis. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| fitdistrplus (R package) | Statistical package for fitting univariate parametric distributions to censored/non-censored data, offering functions for estimation, goodness-of-fit assessment, and uncertainty quantification, useful in risk assessment and data analysis. | Quantitative Microbial Risk Assessment (QMRA) | |
| Food and Ecological Systems Modelling Journal (FESMJ) | Open-access journal publishing models, datasets, and software solutions in agriculture, food systems, bioeconomy, and environmental sciences, emphasizing research outcomes like model validation and data analytics pipelines. | Other Resources | |
| Food Commodity Intake Database (FCID) | U.S. EPA database translating food consumption into defined commodities, enhancing dietary exposure assessments for pesticides, supporting risk assessment models for the U.S. population. | Other Resources | |
| Food Spoilage and Safety Predictor (FSSP) | Free software for predicting microbial growth and shelf-life under various conditions, including spoilage and pathogens in food, with customizable inputs like temperature, pH, and salt content. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| FoodProcess-Lab | Open-source extension for microbial modeling integrated into food and feed industry processes, tracking microbial growth and inactivation to support risk assessment and industry monitoring. | Other Resources | |
| foodrisk.org Tutorials | Tutorials on risk analysis in food safety, featuring FDA-iRISK webinars and risk communication/assessment tutorials, offering practical guidance and accessible resources for food safety professionals. | Tutorial | |
| FOSCOLLAB: a global platform for food safety data and information | Collaborative platform offering access to risk assessment reports, food consumption data, and raw contamination data from global sources like JECFA and FAO/WHO, aiding risk analysis and decision-making. | Other Resources | |
| FRISBEE | European initiative enhancing refrigeration technologies in the food cold chain, integrating food quality, safety, energy efficiency, and environmental impacts, supported by the open-access ColdBase database. | Other Resources | |
| FSK-Lab | Open-source KNIME extension for working with FSKX food safety models, supporting model creation, editing, import/export, and running models in R or Python. Developers can contribute via GitHub. | Quantitative Microbial Risk Assessment (QMRA) | |
| GInaFiT | Free Excel add-in for testing nine microbial survival models, offering automatic statistical reports and model comparisons based on experimental data, with built-in safeguards for accurate use. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| GroPIN | Predictive modeling database featuring microbial growth and inactivation models for pathogens and spoilage organisms, with models considering intrinsic and extrinsic factors, regularly updated for scientific and industrial use. | Predictive Microbial Modeling (PMM) Prediction Tool Model Repository | |
| growth rates (R package) | R package for estimating microbial growth rates from batch or plate reader data, using multiple methods for model fitting, including linear regression, nonlinear models, and smoothing splines. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| Heavy Metal Screening Tool | Risk assessment tool for evaluating public health risks from heavy metals in food, providing hazard characterization, dietary exposure assessment, and risk characterization using publicly available data. | Other Resources | |
| Interactive online Catalogue on Risk Assessment (ICRA) | Downloadable tool for comparing microbial risk assessment models, offering a wide range of pathogen and commodity comparisons for microbial risk analysis. | Quantitative Microbial Risk Assessment (QMRA) Model Repository | |
| IPMP | User-friendly software for analyzing microbial growth and inactivation data, supporting a range of models for predictive microbiology, and evaluating temperature effects on growth rates. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| Lis-RA (Excel spreadsheet) | Risk assessment model for estimating listeriosis cases in the EU based on RTE foods, featuring Excel-based inputs and outputs, requiring @Risk software for optimal performance. | Quantitative Microbial Risk Assessment (QMRA) | |
| Listeria Cardinal Model | Cardinal parameter model for Listeria monocytogenes growth, estimating temperature, pH, and water activity thresholds for growth, developed using broth data from growth experiments. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| Listeria monocytogenes generic Quantitative Microbiological Risk Assessment (gQMRA) model | Excel-based model assessing Listeria contamination in ready-to-eat foods, supporting uncertainty evaluation and dose-response variability, developed using flexible inputs for different food categories. | Quantitative Microbial Risk Assessment (QMRA) | |
| mc2d (R package) | R package for two-dimensional Monte Carlo simulations (Second-Order Monte Carlo), supporting various distributions such as pert, triangular, and empirical. Requires R version 2.10.0 or higher, with dependencies on libraries like stats and ggplot2. | Quantitative Microbial Risk Assessment (QMRA) | |
| Microbial Responses Viewer (MRV) | Database focused on microbial growth/no-growth data for 19 microorganisms. Provides access to growth rates influenced by temperature, pH, and water activity, modeled with generalized linear models. | Predictive Microbial Modeling (PMM) Prediction Tool Model Repository | |
| Microbiological Sampling Plan Analysis Tool (JEMRA) | Tool for designing and evaluating microbiological sampling plans, assessing risk reduction and detection effectiveness for contaminated product lots. | Other Resources | |
| Microbiological Sampling Plans Tool (ICMSF Spreadsheet) | Spreadsheet tool for exploring ICMSF microbial safety recommendations, calculating acceptance probabilities using a lognormal distribution, with support for three-class sampling plans. | Other Resources | |
| MicroHibro | Risk assessment tool integrating microbial kinetics and dose-response models to predict microorganism growth or inactivation in food, supporting food safety and hygiene evaluations. | Predictive Microbial Modeling (PMM) Prediction Tool Model Repository Quantitative Microbial Risk Assessment (QMRA) | |
| Microrisk Lab (Shiny app) | Online freeware for microbial kinetic analysis, offering modules for fitting isothermal and non-isothermal models, as well as deterministic and stochastic simulations. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| MLA Refrigeration Index Calculator | Predictive model for E. coli growth on meat, based on temperature, pH, water activity, and lactate concentration. Allows users to enter product temperature data to estimate E. coli growth. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| ModelAssist | Free risk analysis training tool offering practical examples, a searchable database, and instructional videos to support consistent risk analysis practices. | Other Resources | |
| nlsMicrobio (R package) | R package for nonlinear regression in predictive microbiology, providing models and data sets for microbial growth analysis. Built on the stats and nlstools packages, tailored for microbiology research. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| openFSMR | Community-driven search engine for predictive microbial models, offering models for various microorganisms, including growth and inactivation data gathered from multiple repositories. | Predictive Microbial Modeling (PMM) Model Repository Prediction Tool | |
| OptiPa | MATLAB-based GUI for simulating and calibrating ordinary differential equation (ODE) models, designed for food research. Simplifies parameter estimation, sensitivity analysis, and confidence interval generation, accessible to researchers with minimal programming skills. | Predictive Microbial Modeling (PMM) Fitting Tool | |
| Pathogen Modeling Program (PMP) | Predictive models for foodborne bacteria growth and inactivation under various environmental conditions. The tool is continuously updated, and validation is encouraged for accurate use. | Predictive Microbial Modeling (PMM) Prediction Tool Model Repository | |
| Pathogens in Foods (Database) | Web application aggregating and analyzing microbial hazard occurrence data in foods across Europe, with around 6,000 observations. Offers summary statistics, meta-analyses, and regular usability updates. | Other Resources | |
| Perfringens Predictor | User-friendly simulation tool for predicting Clostridium perfringens behavior during the cooling of bulk cooked meats. Allows inputs for pH, salt concentration, and product type (cured or uncured). | Predictive Microbial Modeling (PMM) Prediction Tool | |
| PMM-Lab | Open-source extension for KNIME, providing tools for microbial data analysis, predictive model development, and storage of experimental data in an HSQL database. | Predictive Microbial Modeling (PMM) Fitting Tool Prediction Tool | |
| Praedicere | Free web-based tool offering predictive microbiology modules for modeling pathogen growth and probability under varying conditions, with results exportable in CSV, Excel, or PDF. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| PredOxyPack | Software simulating oxygen evolution in custom packaging, allowing users to compare packaging designs, materials, and temperatures. Generates graphical results and exports to Excel or PDF. | Other Resources | |
| Process lethality determination spreadsheet | Model for validating heat treatment effectiveness in food processing, helping users determine microbial destruction throughout heating and cooling cycles to ensure safety. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| QMRA Wiki | Comprehensive resource for Quantitative Microbial Risk Assessment (QMRA), offering data and tools for hazard identification, dose-response, exposure assessment, and risk management. Open to contributions from the community. | Tutorial | |
| RAKIP -Web Model Repository | Portal for downloading risk assessment models and data in standardized formats, facilitating knowledge exchange and integration with various software tools, part of the RAKIP initiative. | Predictive Microbial Modeling (PMM) Prediction Tool Model Repository Quantitative Microbial Risk Assessment (QMRA) | |
| Risk Ranger | This tool assists with microbial food safety risk assessments by adjusting hazard severity and serving frequency to improve accuracy. Primarily used for teaching and ranking pathogen-product risks, it relies on the quality of input data. | Quantitative Microbial Risk Assessment (QMRA) | |
| Salmonella in eggs (Shiny app) | A model that estimates salmonellosis cases per million servings of table eggs and the probability of illness per serving. It describes potential Salmonella Enteritidis contamination from farm to fork, accounting for time/temperature storage and consumption practices. | Quantitative Microbial Risk Assessment (QMRA) | |
| Shelf Stability Predictor | Predicts the growth of Listeria monocytogenes and Staphylococcus aureus on fully cooked, ready-to-eat (RTE) meat products. It bases its predictions on pH and water activity and applies only to products that are fully cooked and dried for shelf stability. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| Sym’Previus | A decision support software for predicting bacterial growth, growth/no-growth boundaries, and thermal inactivation. This tool includes modules for fitting microbiological data and simulating pathogen and spoilage organism behavior. The free version provides fitting tools for growth curves and inactivation parameters. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| The European Surveillance System (TESSy) | A data collection and analysis platform for communicable diseases in EU and EEA countries, launched in 2008. It consolidates previous systems into a single resource for high-quality public health analysis and actionable insights. | Other Resources | |
| Therm 2.0 | Predictive tool for assessing food safety risks in raw meat and poultry, especially during temperature abuse, focusing on Salmonella and Staphylococcus aureus. It evaluates products like pork, sausage, beef, and poultry intended for thorough cooking, including seasoned items. | Predictive Microbial Modeling (PMM) Prediction Tool | |
| Webinar QMRA Better food safety control in the food chain | This one-hour webinar provides a comprehensive overview of risk assessment and explores predictive modeling of microbial growth, with an emphasis on Quantitative Microbial Risk Assessment (QMRA) and its food safety applications. | Tutorial |