pmm-lab - an open source community resource for creating...

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PMM-Lab - an open source

community resource for creating,

collecting, sharing and applying

predictive microbial models (PMM)

Matthias Filter, Christian Thöns, Jörgen Brandt,

Armin A. Weiser, Alexander Falenski, Annemarie

Käsbohrer, Bernd Appel

Matthias Filter

Locations: Berlin (Marienfelde, Jungfernheide)

BfR staff: appr. 750 employees (550 working in the scientific field)

Annual budget: appr. 65 Mio €

Research budget: appr. 6 Mio €

Established 1 November 2002 (its predecessor founded in 1876)

Main areas of work: Feed and Food Safety

Safety of Substances and Preparations

Safety of Consumer Products

Risk-Communication etc.

Federal Institute for Risk Assessment

Matthias Filter

Community resources - predictive microbiology

Ready-to-use models

• Pathogen Modeling Program (locked, web+local)

• ComBase Predictor / Perfringens Predictor (locked, only web)

• Sym’Previus (locked, only web)

• Seafood Spoilage and Safety Predictor (locked, local)

• Refrigeration Index Calculator (locked, local)

• Shelf Stability Predictor (locked, only web)

• Microbial Response Viewer (locked, only web)

• (Scientific Literature no implementation)

• PMM-Lab open, (web)+local

Model generation tools

• GInaFiT (Geeraerd et al., 2005)

• DMFit (Baranyi et al., 1994)

• The R Project for Statistical Computing

• Commercial modeling software packages (Matlab, SAS etc.)

• PMM-Lab

Data:

• ComBase (open, only web)

• (industry) data collections (proprietary, local)

• Scientific literature

Matthias Filter

BfR Conclusion

It would be valuable to extend

community resources in the field of

predictive microbiology

• 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

• Support establishment of a community model database

Matthias Filter

Solution

A locally installable software “toolbox” which is

free of charge AND open source

• Open to joint development by the predictive microbiology community

• Make use of already existing open-source initiatives (KNIME, R-project, Apache, Java)

• Leave room for commercialization (tailor-made application, consulting etc.)

Matthias Filter

BfR concept -

Integrated community tools for (microbial) exposure assessments

DB

Food Chain

& disease

modeling

Data

analysis

Predictive

Microbiology

Food

Process

Simulation

Matthias Filter

What is KNIME (Konstanz Information Miner)?

- free, open source data integration and analysis platform (www.knime.org )

- created and hosted by KNIME.com

- first version released in 2006

- “scientific workflow management system”

- community tool for data integration, transformation, modeling and visualization

- strongly applied in pharmaceutical research (virtual drug design & cheminformatics)

http://www.knime.org/

Matthias Filter

What is PMM-Lab ?

A library of Java software modules for predictive

microbial model generation and application

An extension to the open-source scientific workflow

management and data analysis platform KNIME

www.knime.org

An integrated, locally installed database for microbial

data and models (including meta data, e.g.

references)

A community software project hosted at

http://sourceforge.net/projects/pmmlab

http://www.knime.org/

Matthias Filter

PMM-Lab –

How does it look like?

Matthias Filter

PMM-Lab – DB

integrated data management

Matthias Filter

PMM-Lab –

use case: data integration

Matthias Filter

PMM-Lab –

use case: model generation

Matthias Filter

PMM-Lab –

use case: predictions

Matthias Filter

What are the advantages of PMM-Lab ?

All relevant information saved (raw data, data

modifications, model generation workflow, estimated

models)

Modular, “easy to use” software

Integrated into data analysis package KNIME

(integration with other libraries: „R“, „Matlab“, Data

mining, Report generation etc.)

Open community resource incl. Wiki, Ticket system

http://sourceforge.net/projects/pmmlab

Database integration

Allows exchange of models and model generation

workflows -> opportunity to provide best practice

Matthias Filter

“Business model” Free and Open

Community Resources

(e.g. licensed under GPL)

domain experts authorities

universities

research institutes

food safety consultants

software companies

…

Taylor-made software /

consulting service etc.

€ £ ¥ $

free of charge free of charge

Matthias Filter

PMM-Lab –

areas of community contribution

Jointly improve PMM-Lab software

(not necessarily need programming skills)

Establish / develop standards (e.g. data / model exchange)

Announcement

BfR / FDA - workshop series on tools for food defense and safety

Incl. plenary discussion –

“Towards a community library of food safety models - synergy generation and joint initiatives”

4th to 6th September 2013, Berlin

www.bfr.bund.de

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Thank you for your attention

Matthias Filter

Federal Institute for Risk Assessment

Diedersdorfer Weg 1 D-12277 Berlin

Tel. +49 30 - 184 12 - 2209 Fax +49 30 - 184 12 - 2952

[email protected] www.bfr.bund.de

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