Network meta-analysis in R

R4PlantPath

Meta-analysis (MA)has gained more popularity in Plant Pathology. Among the methods, network meta-Analysis has been thoroughly presented to plant pathologists in a recent paper. In this post, I reproduce part of the analysis shown in that paper which was conducted using SAS. Although the results are not identical, they are very similar.

Seminar: Rubber leaf drop - in defence of Pestalotiopsis

CCH-USQ Seminars

Seminar given by Dr. Anthony Young for the CCH-USQ Seminar Series. Dr. Young is a Senior Lecturer in Crop Protection at The University of Queensland, Gatton Campus. In this seminar, he will explore the epidemiology of rubber (Hevea brasiliensis) leaf drop in Sumatra and Malaysia, presenting field work undertaken in 2019 and with reference to real-world examples of the role of climate in what we term ‘disease.’

An interview with Dr. BananaMan García: on being bananas about bananas

Interviews

Get to know our newest member of the OPP team, Dr. Fernando Alexander García-Bastidas, a Colombian researcher in Wageningen (NL) at KeyGene leading banana breeding program focusing on Panama Disease. He is also known as Dr. Bananaman, the creator of the #bananatoons. Fernando will be responsible for creating open digital art useful for plant pathology teaching and outreach.

A multi panel figure for coffee leaf rust

R4PlantPath

In scientific publishing, it is a good visualization practice to present more than one plot (graph, chart or images) in the same figure, not only to improve communication and comparison but also decrease the number of total figures referenced in papers. I use a coffee leaf rust data set to demonstrate how to make these multi panel figures, using the R package patchwork to produce the most common multi panel figures for scientific papers.

The elusive long-read fungal sequence: how to minION like a pro (when you’ve never done it before)

CCH-USQ Seminars

Research seminar presented by Ms. Lauren Huth to the Center for Crop Health, University of Southern Queensland. The rapid development of microbial genome sequencing methods in the last decade has revolutionized whole genome sequencing and has become the standard for many molecular typing applications in research. Largely driven by the development of high-throughput, low cost, second generation sequencing methods, the industry has become familiar with Illumina as the most widely used sequencing platform for microbial genomics.

Deciphering the origin of powdery mildews in Australia. Implications for plant biosecurity

CCH-USQ Seminars

Seminar given by Dr. Levente Kiss (University of Southern Queensland). Powdery mildews are widespread obligate biotrophic fungal plant pathogens, comprising over 900 species that infect more than 10,000 plant species globally. The symptoms caused by these fungi are easy to spot, but the fungi themselves are difficult to handle, and some are difficult to identify.

A tale of two crop diseases

CCH-USQ Seminars

Seminar given by Dr. Araz Solman from the Queensland Department of Agriculture and Fisheries. Short abstract: Research into plant-pathogen interactions has historically taken a simplified approach involving a single host and a single disease. However, in natural and agroecosystems, plants are frequently co-infected with several pathogen species or genotypes, exhibiting complexities not captured by the widely used single disease approach. In this seminar, I will address the complex dynamics of plant co-infection by focusing mainly on a tripartite pathosystem consisting of wheat as the host and two major fungal pathogens: _Pyrenophora tritici-repentis_ (Ptr) and _Parastagonospora nodorum_ (Pan).

Effectiveness and expression of resistance in maize to isolates of Puccinia sorghi from Eastern Australia

CCH-USQ Seminars

CCH-USQ seminar given by Ms. Aurelie Quade from the University of Southern Queensland. The vulnerability of the Australian maize industry to Puccina sorghi is currently unknown. Maize is grown across a range of agro-ecological regions in Australia and the effectiveness and stability of deployed Rp genes has not been examined.

Cristal structure of Tox3 - a unique effector fold and insights into Kex2 protease processing of fungal effectors

Virtual seminars

Virtual seminar given by Dr. Simon Williams from Australian National University. Plant pathogens cause disease through secreted effector proteins, which act to modulate their hosts physiology and promote infection. Typically, the sequence of effector proteins provides little functional information and further targeted experimentation is required. We look to utilise structural biology and biochemical approaches to help us understand effector function.

OPP Interviews: Dr. Sally Mallowa from Augustana University

Interviews

Post seminar interview with Dr. Sally Mallowa, an Assistant Professor of Biology at Augustana University (South Dakota, USA). Sally delivered a talk on, Technology driven cassava pest management on the 4th of May 2020

cpn60UT: the perfect marker to identify and characterize phytoplasmas?

Virtual seminars

Seminar given by Dr. Edel Pèrez-Lòpez - Université Laval. Abstract: Phytoplasmas taxonomy is very complex. Besides genus ('_Candidatus_ Phytoplasma'), phytoplasmas are also classified into groups and subgroups based on the RFLP pattern obtained after digesting the F2nR2 sequence (into the 16S rRNA operon) with 17 restriction enzymes. Many other taxonomic markers have been suggested in order to simplify this classification scheme.

OPP Interviews: Prof. Gert Kemma from Wageningen University & Research

Interviews

Post seminar interview with Dr. Gert Kema (Wageningen University & Research), is the professor leading research at the Laboratory of Phytopathology. A focus on septoria tritici blotch of wheat for ~25 years set Gert on a path to work on banana as a result of the relationship between the causal fungi, _Mycosphaerella graminicola_, now known as _Zymoseptoria tritici_ and _Mycosphaerella fijiensis_ now known as _Pseudocercospora fijiensis_, associated with black sigatoka.

Evolution of mini-chromosomes in Fusarium

Virtual seminars

Seminar given by Dr. Luigi Faino (University of Rome La Sapienza) on Fusarium verticillioides, a maize pathogen that causes millions of dollars in loss every year due to the production of mycotoxins, namely the neurotoxic and carcinogenic fumonisins. Dr. Faino investigated the F. verticillioides (Fv) strain 10027 which is an Italian isolate and it produces high amount of fumonisin B1.

Technology driven cassava pest management

Virtual seminars

In the recent past, a priority of many national research programs, international research institutions, non-governmental organizations, and funding agencies, has been focused on finding novel solutions to the complex constraints to cassava production.

Post-seminar interview: Dr. Peter Solomon from The Australian National University

Interviews

A post-talk interview with Dr. Peter Solomon, a specialist in the field of wheat biosecurity. Peter is a dedicated researcher, committing over twenty years of research to dissect the intricate interactions of effector and host defence proteins.

The ongoing pandemic of Tropical Race 4 threatens global banana production

Virtual seminars

Dr. Kema reviews their research on the understanding of the phylogeography of TR4, and discuss on the broad genetic potential of the crop for breeding as well as options for disease management to avoid a repetition of history.

How the study of necrotrophic effectors advanced our understanding of the enigmatic PR-1 protein

Virtual seminars

Seminar given by Dr. Peter Solomon (The Australian National University). Abstract: It had long been thought that necrotrophic plant pathogenic fungi use a barrage of lytic enzymes to break down host cells releasing nutrients for growth. However, in recent years it has emerged that some necrotrophic fungi facilitate disease through a strict gene-for-gene mechanism as observed in biotrophic pathogens.

Research Compendium: High-Resolution Satellite Imagery for the Detection of Soybean Sudden Death Syndrome

Research compendia

In this inaugural post, we showcase a reproducible example of research conducted by Dr. Muhammad Mohsin Raza, a recent graduate from Iowa State who worked under the supervision of Dr. Leonor Leandro, describes his research, the tools he used and how to reproduce his work. His project is a wonderful narrative, and one of many ways to build a research compendium to encourage reproducibility of the analysis and communication of the findings.

Evolution is not static: understanding factors that govern pathogen-host diversity

Interviews

A post-talk interview with Dr. Remco Stam, a specialist on host-pathogen genetic diversity and (co)evolution. Remco is a forward-thinking researcher, with a humble yet passionate approach to understanding (co)evolution between host plants and their pathogens.

What are Brazilian plant pathologists doing? A text-analysis of scientific poster titles

R4PlantPath

A short description of the post.

The diversity and molecular evolution of plant defence against pathogens in nature

Virtual seminars

Virtual seminar given by Dr. Remco Stam (Technical University of Munich). Abstract: Plant pathogen defence responses are often studied in model systems or in agricultural settings. However, in nature plants also encounter a large variety of pathogens. Interestingly, in natural systems this seldom leads to epidemics. One possible reason for this is the high amount of genetic variation that can be found in natural plant populations.

Clubroot of brassicas, an old but still poorly understood disease on the rise!

Interviews

Dr. Susann Auer a postdoc at Technische Universität Dresden (Dresden, Germany), delivered the first OPP Virtual Seminar on the 31st of March on the molecular response of Clubroot infected plants to the endophytic fungus Acremonium alternatum. I had the privilege to get to know her and her work a little better. Dr. Auer is a passionate researcher, who shows care towards her students and is thoughtful in considering her fellow researchers.

OPP Virtual Seminar: delivering scientific talks without barriers

General

After two years promoting and supporting openness, transparency and reproducibility in our field, we are very proud to announce a new exciting project: the Virtual Seminars (aka science webinars), a new venue for delivering scientific talks in plant pathology-related topics. The idea was brought up by Dr. Benjamin Schwessinger (Australian National University), a prominent representative of scientists advocating for urgent changes in scientific meetings, including replacement of the current model by digital conferences. We had a quick chat with Benjamin who further stressed why he believes the timing is perfect to start experiencing virtual talks in plant pathology, a trend that is spreading into other scientific communities

Molecular response of clubroot infected plants to the endophytic fungus Acremonium alternatum

Virtual seminars

In our first OPP Virtual seminar we have Dr. Susann Auer - Postdoc Technische Universität Dresden, speaking about the clubroot, a disease that continues to cause economic losses in Brassica crops worldwide, sustainable control measures are not in sight. The clubroot pathogen persists in soils in the form of durable resting spores which infect new crops every consecutive year.

Reproducible Reports and Research Using R

Workshops

Workshop taught by Adam H. Sparks, Nick Tierney, Paul Melloy, and Nirodha Weeraratnee at the Australasian Plant Pathology Society Conference 2019

Are you getting ready for ensuring reproducibility in Plant Pathology? We want to hear!

General

We are calling for participation in a survey. Please donate only five minutes of your time to answer a survey questionnaire with 16 multiple choice questions about your current practices related to organisational procedures, data management, analytical workflows and sharing of scientific information.

Get your research project organized, shareable and reproducible using R

Workshops

The importance of sharing data and computational code has been highlighted extensively to promote transparency and replication of scientific results. Data and code sharing practices are rare in the plant pathology, but they are expected to increase in the near future. It is urgent that plant pathologists get training in how to organize their research in a way that promotes effective project management, reproducibility, collaboration and sharing of results.

Breaking down barriers between remote sensing and plant pathology

Preprints

This is a preprint of a Letter to Editor of Tropical Plant Pathology by Heim _et al._ on the challenges and potential solutions in the context of application of remote sensing in plant pathology.

Modeling tools and techniques using R

Workshops

In this workshop, we will present an overview of different modeling approaches that are available in the R language and environment for statistical and graphical computing. We will focus on using a hands-on approach that explores different aspects of statistical modeling ranging from exploratory data analysis to model development, validation, and prediction.

Reproducible Reports and Research Using R

Workshops

As scientists, we often read about or hear about reproducible research, but we may not be sure where to start or how we can make our research reproducible. Sharing code, scripts and data that make up your analysis with others such that they are able to easily reproduce your results can make it easy to obtain feedback and improve the quality of your work. This workshop will introduce participants to ways that R and related tools, such as RMarkdown.

OPP Interviews: Jade d’Alpoim Guedes and Ben Marwick

Interviews

In our third OPP Interview we have the privilege to chat with two prestigious computational scientists, representatives of the field of archaeology, about their experiences on the use, tool development and promotion of reproducible research practices in science.

A Plant Pathologist's Guide to Writing Your First R Package

R4PlantPath

So you want to write your first R package, but you don't know where to start? We can help with that! Writing an R package is not difficult, but it can be intimidating for a first timer. Why would you want to write an R package? Read more to find out!

OPP Interviews: Sophien Kamoun

Interviews

In this OPP series we will be interviewing scientists in Plant Pathology or related areas who has embraced open science and contributed knowledge and tools to advance the field. Our first interviewee is Prof. Sophien Kamoun, a senior scientist with the Sainsbury Laboratory, Norwich, UK. Dr. Kamoun is known for his prolific tweeting but, also importantly, for his work with oomycetes, effectors, genomics and evolution.

OPP Interviews: Niklaus J. Grünwald

Interviews

In this OPP series we will be interviewing scientists in Plant Pathology or related areas who has embraced open science and contributed knowledge and tools to advance the field. Our first OPP interview features Dr. Niklaus Grünwald, a plant pathologist with USDA ARS, Corvallis, OR, USA. Nik is well recognized by his research on population genetics and genomics of plant pathogens - mainly on oomycetes of major importance to global agriculture.

Workshop: Network Analysis in Plant Pathology

Workshops

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.

Workshop: Population Genomics in R

Workshops

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.

Establishing a community for supporting and fostering adoption of reproducible research using R

Talks

Lightning talk presented at useR!2018 in Brisbane, Queensland, Australia by Adam Sparks who discuss our methods of community building and what has worked and what has not for others that may wish to pursue similar efforts

Workshop: Introduction to Multivariate Statistics Using R

Workshops

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.

Open ideas, data and code sharing: epidemiologists should be in front!

Talks

Talk given by OPP Founder, Emerson M. Del Ponte, at the 12 International Epidemiology Workshop on June 12 2018 (Lillehammer, Norway) to promote the initiative among plant disease epidemiologits

The fall of an empire

R4PlantPath

I recently tweeted an animated GIF that depicted the yearly variation in efficacy of tebuconazole, a DMI fungicide, evaluated in field trials, for the control of soybean rust in a major soybean region of Brazil (Mato Grosso state). The Tweet got a lot of attention, not only because of the important issue, but I think also because of the nice way to visualize the data. So I decided to share the R code use to produce the animation for others' presentations.

What is going on in OPP? a quick summary of the first five months

General

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.

Are you a scientist dealing with computational plant pathology? Then let's connect and code together!

General

We propose to develop a community that values the sharing of knowledge, ideas and data; building capacity; and promotes open and reproducible research to benefit plant pathologists.

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Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/openplantpathology/OpenPlantPathology, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".