​The Plant Health workshops will take ​place in the months following the online conference. Registration will be structured per workshop. If you register for the Unlimited Plant Health 2020 Online registration price, you will receive complim​entary access to each workshop. Workshop registration fees are $49 (APS Member rate) / $89 (Nonmember rate). 

Plant Health Workshops

Dates and times TBD

• Basic bioinformatics and command-line tools for phytopathologists: How to handle, explore, and organize big biological data
  
• High-throughput sequencing technologies have significantly improved the generation of large data sets of omics information (genomes, transcriptomes, proteomics and microbiomes). Administration and analysis of big data in the omics-era to understand complex biological systems present a new challenge for plant pathologists. Analysis of big and complex data sets requires use of computational tools that interact with databases and computer servers. The command line interface allows users to interact with computers both locally and in server to conduct computationally intensive analyses. In this workshop, we will explore different usages of command line interface for bioinformatic analyses. We will introduce the cluster computing system, Linux shell, and shell scripting. We will use unix commands to parse sequence and text files followed by application of local BLAST and data parsing. Different genome data analyses and de novo assembly using command line interface will be discussed.
  
• Data visualization in R​
  
• High quality visualizations, such as graphs and maps, are critical for effectively communicating science. In this workshop participants will gain an understanding of the workflow and data-wrangling necessary for creating publication ready graphs and maps in R. Participants will become familiar with various graph types (including boxplots, scatterplots, violin plots, networks, and heatmaps) and their best use cases through motivating, plant-pathology related examples and hand-on exercises. Participants will also be introduced to non-traditional and interactive visualizations as well as an overview of visualization packages, including ggplot2 and ggpubr. Attendees will learn the basics of not only selecting the correct graph, but also proper design elements such as labeling, sizing, legends, and coloring. Additionally, participants will be introduced to the basics of working with geospatial data in R. This workshop will be introductory level, previous R experience is welcome but not required.
  
• Improving and increasing awareness to the National Plant Disease Recovery System*
  
• The National Plant Disease Recovery System (NPDRS) is mandated under a Presidential Directive to ensure that the tools, infrastructure, communication networks, and capacity required are in place to mitigate the impact of high consequence plant disease outbreaks.  A product of NPDRS is a Recovery Plan that is a published collection of information on a targeted disease or pathogen.  These Recovery Plans were discussed at previous APS meetings and USDA workshops starting in 2006 and tie in with the APS Emerging Pathogens Initiative. The purpose of this workshop will be to assemble attendees who are interested in new and emerging diseases and pathogens with the intention to review the purpose of the Plan, discuss how to improve its content and propose diseases/pathogens for new plans with recommended contributors.
  
• Know your roots: introduction to root phenotyping for plant pathologists
  
• Many plant pathogens and beneficial microbes cause changes in root structure, whether from direct tissue loss, growth restriction, or repatterning caused by microbe-​in​duced hormonal changes. By quantifying these effects, pathologists can reveal ways in which biotic interactions affect belowground plant health. This workshop is aimed at providing a broadly accessible, hands-on introduction to quantitative measurement of root traits. Attendees will participate in excavation of roots, identification and sampling of different root types, and the acquisition and analysis of root images using the open-source Rhizovision program to quantify root length, diameter, topology, and other traits in healthy and diseased samples. Demonstrations will introduce the benefits and drawbacks of platforms for root phenotyping in the context of plant disease, such as field shovelomics, rhizoboxes, and agar plate methods, as well as options for imaging and analysis. We will facilitate a discussion of how knowledge of root phenotypes could be better applied and standardized in plant pathology research. The workshop will be led by Dr. Larry York of the Noble Foundation.
  
• Scientific Communication in the Year of Plant Health: Let’s Talk/Text/Tweet about it!
  
• From the digital to the spoken word, learn how to communicate your science in a way that will leave a lasting impact! How do you capture your audience and cater to their specific interests? How do you tell a story that will be attention-grabbing and unforgettable? How do you create a narrative that will leave the audience wanting more? The Office of Public Relations and Outreach brings you this workshop, the first half of which will host speakers who will address the creativity, timing and tools needed to communicate science effectively in both a digital and spoken format. The second part will be break-out sessions; the participants will split up to work with an expert in each category to brainstorm ideas on how to effectively communicate their science to a general audience. In the final 20 minutes of our workshop, participants will have a chance to practice their new skills in front of other workshop attendees and receive feedback.
  
• Taking MPMI Discoveries to the Field​
  
• In celebration of the 2020 International Year of Plant Health, the International Society for Molecular Plant Microbe Interactions (IS-MPMI) is hosting this satellite meeting to bring together scientists who are taking molecular advances in plant science and translating these discoveries to develop disease resistant crops that will impact global food security. The meeting will highlight technical advances, progress in the field, and challenges for bridging the foundational research – translation gap. The goal of this meeting is to capitalize on the expertise of the IS-MPMI and APS communities to exchange ideas and strategies to bridge this gap to promote plant health around the world. The format will include presentations by MPMI scientists that are successfully bridging this gap and discussions. We encourage broad participation of students, post-doctoral scholars, principle investigators and policy makers to provide diverse perspectives.
  
• ​Unmanned Aerial Vehicles For Making Plants Healthy- Do We Have a Winner? ​
  
• Efficient management of plant diseases is dependent on accurate and timely detection. In the past century we have seen tremendous diagnostic advances from a traditional, field-walk scouting, to the deployment of Unmanned Aerial Vehicles (UAVs) for real-time mapping of crop, soil and environment variables. UAVs are a powerful deployment tool for a number of newly developed technologies for early management intervention, and cut across the traditional boundaries of pest detection through the combination of automation and on-board data analysis. UAVs offer a number of unique, interdisciplinary opportunities to excite and engage the next generation of farmers and researchers. The use of UAVs has become more widespread due to increased affordability and safety, evolution of imaging sensors, and “on-board” image processing coupled with machine learning tools for data acquisition and processing. In the last decade, UAVs became a valuable decision making tool. The use of UAV systems to deploy novel sensor systems could facilitate quick and accurate field detection, thus improving disease management efficacy through timely and site-specific applications. In the International Year of Plant Health (2020), this workshop session will give the attendees an opportunity to learn about the technology, its current and future applications.​
  
• ​Using Spore Trapping in Research and Disease Forecasting ​
  
• Foliar diseases spread by airborne spores include some of the most important plant diseases worldwide. Growers can benefit from early warning of the presence of infectious spores in their local environment and reduce potential yield and quality losses by applying management options. Recent advances in several technologies have facilitated the development of spore trap systems that can report in real-time or near real-time. The last few years have seen spore detection systems emerge from the use of various Burkard samplers coupled with qPCR, low cost passive spore traps such as the Spornado (Sporometrics), integrated systems such as the SporeSentry (OptiSense), the DNA Auto spore trap (Burkard), and more recently, image recognition systems like the SporeCam (Scannit Techno​logies). Several knowledge gaps exist such as the geographic scale data from each trap is valid for, the significance of an individual detection event, thresholds for disease development and how this data can be integrated with weather-based disease models. This workshop aims to bring together various technology providers with plant pathology research and extension professionals to seek ways to utilise this technology in plant pathology.