FEDERAL INSTITUTE FOR RISK ASSESSMENT
An open-source software framework for food safety analysis and modeling
Matthias Filter, Christian Thoens, Alexander Falenski, Bernd Appel, Annemarie Kaesbohrer, Armin A. Weiser Federal Institute for Risk Assessment (BfR), Germany
Outline: Motivation Introduction to PMM-Lab, FoodProcess-Lab, (FoodChain-Lab) Current work
Matthias Filter, 26 November 2014, EFFoST 2014 Uppsala
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Vision Food safety community resources (containing data, models, tools) supporting state-of-the-art risk assessments along the food chain
animal disease models
Food processing and distribution
Environmental factors
Matthias Filter, 26 November 2014, EFFoST 2014 Uppsala
human disease models
Processing parameters
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Current situation Plenty of predictive microbial models / risk assessment models published A number of predictive microbial / risk assessment software tools (ComBase Predictor, PMP, FSSP, MRV .... / FDA-iRISK, @Risk, R, rrisk …) A number of data, information and model repositories (ComBase, SymPrevius, GroPIN, ICRA, foodrisk.org …)
But • • • • • • •
NO integrated software tools for data management, model generation, scenario simulation and documentation Quality control in documentation of models / data still a major challenge NO harmonized file format for exchange of data / models / scenarios / simulations NO information exchange between predictive microbial modelling / risk assessment software tools FEW open-source software solutions FEW models implemented into tools (compared to number published) => Re-use of existing data, information and models HAMPERED
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Conclusion Extension of
community resources in the field of food safety modeling needed •
Improve transparency, quality control and real information exchange with respect to data, models and the “art” of model generation
•
Support lab scientists / QM professionals to make use of their data and to contribute data and models to the community
•
Support standardization of data / model description and information exchange between tools
•
Support establishment of curated community model repositories
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Open-source food-safety modeling framework
Tracing Analysis and Visualization
Predictive Microbiology
http://silebat.github.io/BfROpenLab
http://sourceforge.net/projects/pmmlab/
DB http://sourceforge.net/projects/foodprocesslab/
www.knime.org
Rind fleisch
Data Mining and Reporting
Matthias Filter, 26 November 2014, EFFoST 2014 Uppsala
Food Process Simulation
Nierenfett
Vorschneiden
Kuttern Froster Kuttern
Verpackungsmaterial
Füller Därme
Lager
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Verschweißen
Reiferaum
Raucherzeugung
What is KNIME (Konstanz Information Miner)?
- free, open source data integration and analysis platform (www.knime.org ) - scientific workflow management system - created and hosted by KNIME.com - community tool for data integration, transformation, modeling and visualization - Development framework for PMM-Lab, FoodProcess-Lab and FoodChain-Lab
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PMM-Lab Predictive Microbiology Modeling-Lab
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PMM-Lab – Database Integrated data management
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PMM-Lab – Use case: model generation
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PMM-Lab – Use case: predictions
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FoodProcess-Lab Collection of information on food processing
Tetra Pak Handbuch der Milch- und Molkereitechnik, Gösta Bylund, 2003, Verlag Th. Mann GmbH & Co. KG
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FoodProcess-Lab Design and run scenarios
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Advantages of proposed software framework •
Free, open-source, transparent
•
Data management integrated (raw data, model generation process, estimated models, food process chains, scenario simulations)
•
Modular, highly flexible, easy-to-extend, easy-to-reuse
•
Integrated into KNIME (provides integration of „R“, MATLAB, Data mining, Report generation etc.)
•
Infrastructure for community contributions available: Code repository, Wiki, File download (e.g.sample files), Ticket system
•
Exchange of workflows -> sharing of knowledge with others
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Current work Predictive Modeling in Food Markup Language (PMF-ML)
Glna Fit GlnaF it
Gro PIN FILT REX
FILT REX
DB DB GroP IN
FISH MAP
DB FISH MAP
Dairy Product Safety Predictor
Dairy Product Safety Predictor
=> Soon available at: http://sourceforge.net/projects/microbialmodelingexchange/ Matthias Filter, 26 November 2014, EFFoST 2014 Uppsala
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FEDERAL INSTITUTE FOR RISK ASSESSMENT
Thanks to the BfR team Armin A. Weiser, Christian Thöns, Alexander Falenski, Arvid Heise, Carolina Plaza-Rodriguez, Annemarie Käsbohrer, Bernd Appel
Thank you for your attention Matthias Filter Federal Institute for Risk Assessment Max-Dohrn-Str. 8-10
10589 Berlin, GERMANY
Tel. +49 30 - 184 12 - 2209
Fax +49 30 - 184 12 - 47 41
[email protected]
www.bfr.bund.de
