What is Open Plant Pathology?

A community of modelers and computational researchers involved in plant pathology, plant disease epidemiology, pathogen population biology, microbial ecology and genomics, that supports the several forms of Open Science practices in Plant Pathology. We support efforts from individuals or groups to develop and deliver next-generation databases and tools for plant pathology-related subjects and applications using open source software, data and repositories.

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Recent Posts

Updates on our recent work, projects, tutorials and viewpoints

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Our second OPP interview features Professor Sophien Kamoun, a senior scientist and professor of biology with the Sainsbury Laboratory, Norwich, UK. Dr. Kamoun is known for his prolific Tweeting but more importantly for his work with oomycetes (#notafungus), effectors and evolution. Prof. Kamoun is well recognized for his efforts to champion data sharing and other open science practices. It is a great pleasure to have Prof. Kamoun answering six questions about open science.

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Our first OPP Interview features Dr. Niklaus J. Grünwald, a plant pathologist with USDA ARS, Corvallis, OR, USA. Nik has made significant scientific contributions to the understanding of the population biology and evolution of Phytophthora infestans worldwide. His lab has developed R packages which have contributed considerably to advance and facilitate the analysis of genetic and genome sequence data with applications in taxonomy and evolution, beyond the field of plant pathology.

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OPP was created in early January and we had no idea how OPP would be received and whether it would catch interest and be sustainable. In this post, we provide a brief summary of major achievements during the first five months of OPP.

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OPP Notes

Teaching notes peer-reviewed by community members.

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This teaching note recreates the fit of linear and quadratic models using R for the population response of Pratylenchus thornei in Queensland, Australia wheat to temperature as described in the original paper.
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Workshops & Talks

Get access to presentations and instructional materials produced by OPP members

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This Workshop will prepare participants to interpret network analyses, and will provide participants with experience in network analysis for several representative data sets. The workshop will use the R programming environment, and will provide a brief introduction to R.


This Workshop will combine lectures on concepts with practical computer exercises to allow participants to learn to calculate key information quantities that are important in understanding how DSS’s and diagnostics work, fundamentally, by capturing information from the world and making it available for use in decision-making


This Workshop cover analyses of plan pathological data from tools such as whole-genome variant calling and genotyping-by-sequencing or RADseq once variant call data are in hand. This workshop will not cover genome assembly, read mapping to reference genomes or the calling of variants.


This Workshop aims to introduce new users to several different and useful multivariate analysis methods available in the R statistical computing language. It is focus will be on application rather than background theory.

A Growing Global Community!

Check detailed information about the members, institutions, knowledge domains and the global map of Open Plant Pathology

Knowledge domains

General Plant Pathology, Epidemiology, Geophytopathology, Modeling, Population Biology, Genomics, Microbial Ecology, Programming, Embedded Systems.

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Leadership

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Adam Sparks

Founder. Plant pathologist and epidemiologist. University of Southern Queensland, Australia

Emerson Del Ponte

Founder. Plant disease epidemiologist. Universidade Federal de Viçosa, Brazil

Neil McRoberts

Plant disease epidemiologist and modeller. University of California - Davis, USA

Nik Cunniffe

Mathematical modeller. University of Cambridge, UK

Nik Grunwald

Plant pathologist. USDA, Oregon, USA

Paul Esker

Plant disease epidemiologist and modeller. Pennsylvania State University, USA

Sydney Everhart

Plant disease epidemiologist and population biologist. University of Nebraska, USA

Mladen Čučak

Phd student Maynooth University, Ireland. Disease modeling and forecasting.

Rene Heim

Phd student University of Hamburg/Macquarie University. Germany/Australia. Remote sensing and spectroscopy