DisplayTitle

2017 APS  Annual Meeting Workshops

Saturday, August 5 • 1:00 - 4:00 p.m.

Organizer: Fulya Baysal-Gurel, Tennessee State University, McMinnville, TN, U.S.A.

Sponsoring Committees: Early Career Professionals Committee, Graduate Student Committee, Committee for Diversity and Equality
Financial Sponsor: Monsanto

Balancing family and career life is a highly personal challenge, and what works for you may not work for others. This workshop will provide training and tips on specific questions that will address APS members' issues (regardless of gender, age, seniority in the professional career, traditional or nontraditional family) to help balance their successful career and family life in our diverse society. The workshop will consist of three parts: 1) addressing a wide variety of topics ranging from the Family and Medical Leave Act (including leave for maternity/paternity, adoption, and care giving), promotion and tenure, and recent changes to the Fair Labor Standards Act; 2) addressing the effective communication skills that help APS members navigate through difficult topics, while guided through pair-up activities and best practices for communicating your difficult issues in person; 3) updating the attendees on APS actions to make the meetings more family friendly and then listening to participants’ comments/suggestions for future needs. This workshop is appropriate for all genders, traditional or nontraditional families, early career professionals, graduate students, and academic and industry professionals. Pre-registration required.

• The Family and Medical Leave Act, promotion and tenure, and recent changes to the Fair Labor Standards Act Stephen Schulze, Texas A&M AgriLife, College Station, TX, U.S.A.
  
• The effective communication skills that help APS members navigate through difficult topics Mike Boehm, Harlan Vice Chancellor of the Institute of Agriculture and Natural Resources at the University of Nebraska, Vice President for Agriculture and Natural Resources of the University of Nebraska system, and Professor of Plant Pathology, Lincoln, NE, U.S.A.
  
• Family-friendly APS meetings Mary E. Palm, PHP, PPQ APHIS, USDA, Riverdale, MD, U.S.A.

Saturday, August 5 • 2:00 - 5:00 p.m.

Organizers: Maya C. Hayslett, University of Wisconsin, Madison, WI, U.S.A.; Brantlee Spakes Richter, University of Florida, Gainesville, FL, U.S.A.; Anissa M. Poleatewich, University of New Hampshire, Durham, NH, U.S.A.

Sponsoring Committee: Teaching Committee

Finacial Sponsor:NIFA

The APS Teaching Committee recently completed a research project to investigate the state of introductory plant pathology curricula nationwide, their alignment with industry needs, and their uses of best practices for learning. This workshop is for instructors of plant pathology courses to discuss in an interactive forum the key findings of the study. What are the core concepts and skills that should be taught in an introductory plant pathology course? What do employers expect of students who have completed an introductory plant pathology course? This workshop brings instructors together with industry representatives to directly discuss the needs and challenges in aligning course content to employer expectations. Attendees will spend time in working groups to plan modifications to their courses (content, structure, delivery, pedagogy) based on the recommendations of the study. Pre-registration required.

Saturday, August 5 • 1:00 - 5:00 p.m.

Organizers: Alissa B. Kriss, Syngenta, Greensboro, NC, U.S.A.; Mizuho Nita, Virginia Tech, Winchester, VA, U.S.A.

Sponsoring Committee: Epidemiology Committee

This workshop will be geared to anyone who has not previously learned about designs (graduate students) or those who would like a refresher course. Registrants will learn the basics of experimental designs that are typically used in greenhouse, lab, and field-based plant pathology, why one would choose to use a certain design for their study, and how to evaluate prior to doing the study that a good choice was made. We will link experimental design and study planning with the analysis of observed data and interpretation of statistical results through several examples given during the workshop and also provide the registrant opportunities for deeper study post-workshop. Code will be provided in SAS and it is recommended (but not required) that registrants have SAS on their computers. No prior in-depth statistics or programming skills will be needed. Pre-registration required.

• Experimental design in lab, greenhouse, and field settings
  Alissa Kriss, Syngenta, Greensboro, NC, U.S.A.

Saturday, August 5 • 1:00 - 4:00 p.m.

Organizers: Beth Carroll, Greensboro, NC, U.S.A.; Sheila Corley, USDA National Agricultural Statistics Service, Washington, DC, U.S.A.

When agricultural statistics make the headlines, the focus is usually on the latest statistics that help to minimize the uncertainties and risks associated with the production and marketing of commodities. NASS reports are often used directly and indirectly by farmers, producer organizations, agribusinesses, researchers, policymakers, and government agencies. This training will also be used to enhance the understanding of the phytobiome and in continuing APS’s commitment to enabling sustainability of agricultural production. This workshop will provide training on the NASS Survey Programs, Quickstats use demonstrations, and a new, guided interface to Quickstats 2.0. Experts from NASS will provide understanding and skills to help users get commonly requested statistics from the online database. Workshop participants may submit specific questions to be addressed by the NASS experts during the training. These questions can cover virtually every U.S. agriculture, including production and supplies of food, feed, and fiber; pricing; chemical use; demographic data and much more. Pre-registration required.

Saturday, August 5 • 10:00 a.m. - 5:00 p.m.

Organizers: Laurence V. Madden and Pierce Paul, Ohio State University, Wooster, OH, U.S.A.

Sponsoring Committee: Epidemiology Committee

Meta-analysis is the analysis of results of multiple independent studies, which is performed in order to synthesize the evidence from many possible sources in a formal quantitative manner. In the most common case, the outcome of each study becomes a single observation in the meta-analysis of all available studies. The discipline developed originally in the social sciences in the 1970s and has now been embraced within many scientific disciplines. This workshop will cover basic concepts and approaches in meta-analysis and show how to estimate parameters and interpret results. Methods for expanding the meta-analytical model to account for study-level characteristics (so called moderator variables) and for multiple treatments per study will be reviewed. Methods will be explained primarily using SAS software, and also with R. Lunch is not included in this fee, time is allotted for a lunch break. Pre-registration required.

Saturday, August 5 • 9:00 a.m. - 4:00 p.m.

Organizer(s): Lindsey D. Thiessen, North Carolina State University, Raleigh, NC, U.S.A.; Megan K. Romberg, USDA APHIS PPQ NIS, Beltsville, MD, U.S.A.

Sponsoring Committee(s)/Sponsor(s): Mycology Committee

While molecular techniques can help clarify relationships between fungi and provide for diagnostics of cryptic species or nonsporulating fungi, these techniques may not be rapid enough for diagnosticians or extension specialists to quickly and efficiently diagnose disease in the clinic or in the field. In addition, the lack of sequences for many fungi in public databases means that, even if molecular techniques can be employed, the identity of a fungus may still elude the diagnostician. This workshop is geared toward improving the skills of plant pathologists in morphological identification of fungi. Morphological identification of several groups of fungi, including tips for sample preparation, will be addressed as well as important events in fungal taxonomy and nomenclature. Fee in includes light lunch. Pre-registration required.

• Morphological ID of phytopathogenic fungi
  Megan K. Romberg, USDA APHIS, Beltsville, MD, U.S.A.

Saturday, August 5 • 8:00 - 11:30 a.m.

Organizer: Niklaus Grunwald, USDA ARS, Corvallis, OR, U.S.A.

Sponsoring Committee: Evolutionary Genetics and Genomics Committee

Analysis of population genetic data remains challenging, particularly in the genomics era. High-throughput sequencing has resulted in the opportunity to sequence variants (SNPs, indels, etc.) at the genome scale. However, application of these technologies for the characterization of pathogens provides unique challenges. This workshop will focus on the kinds of analyses typically conducted by plant pathologists. It will cover analyses of 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 will focus on the processing and filtering of variants obtained by tools such as TASSEL, SAMtools, or GATK. Participants will gain hands-on experience with analysis of variant calling format (VCF) data in R using datasets provided by instructors. We will use R packages such as adegenet, poppr, and vcfR. Basic familiarity with R is required. Pre-registration required.

• Population genomics in R
  Niklaus Grunwald, USDA ARS, Corvallis, OR, U.S.A.


• Population genomics in R
  Javier Tabima, Oregon State University, Corvallis, OR, U.S.A.


• Population genomics in R
  Brian J. Knaus, USDA ARS, Corvallis, OR, U.S.A.

Satruday, August 5 • 8:00 a.m. - 5:00 p.m.

Organizers: Kitty F. Cardwell, Oklahoma State University, Stillwater, OK, U.S.A.; James P. Stack, Kansas State University, Manhattan, KS, U.S.A.; Laurene Levy, USDA APHIS PPQ CPHST, Riverdate, MD, U.S.A.; Arif Mohammad, Kansas State University, Manhattan, KS, U.S.A.; Carla D. Garzon, Oklahoma State University, Stillwater, OK, U.S.A.; Jacqueline Fletcher, Oklahoma State University, Stillwater, OK, U.S.A.

Sponsoring Committee(s)/Sponsor(s): Forensic Microbiology Interest Group, Plant Pathogen and Disease Detection Committee, Diagnostics Committee, Emerging Diseases Committee
Financial Sponsor: agdia, PathSensors, Inc.

A 1-day workshop to develop a conceptual framework to discuss and define the principles of diagnostic assay validation. The vocabulary of assay validation is only loosely understood in our discipline. Specifications of confidence, defined by metrics of specificity, inclusivity, sensitivity, and exclusivity, and then robustness of an assay in the hands of multiple users are not standardized. We propose to look at confidence across a range of stringency requirements; bioforensic analysis by law enforcement, discriminatory analyses for regulators and PPQ, and diagnostic tools used by NPDN and industry clinics for local sample triage and assessment.

EXPECTED OUTCOMES:
1. The diagnostic community and assay developers will have a common understanding of the language and metrics of validation.
2. A Framework for Discussion about validation protocols will be proposed in advance of a 2018 International Symposium on assay validation standards.
3. A Position Paper will be developed and published that will provide a potential framework for review of APS journal articles on diagnostic assay development.
Fee includes breaks and lunch. Pre-registration required.

• Aspects of assay validation across a range of stringency and outcome expectations
  Jim Stack, NPDN, Manhattan, KS, U.S.A.


• Validation for quarantine and regulatory verification
  Laurene Levy, APHIS, Beltsville, MD, U.S.A.


• Validation for forensics
  Nick Bergmann, NBFAC, Ft Deterick, MD, U.S.A.


• Validation for commercial assays
  Debi Groth-Helms, AgDia, Elkhart, IN, U.S.A.


• Intro to specificity/exercise 1
  Mohammad Arif, University of Hawaii, Oahu, HI, U.S.A.


• Intro to sensitivity/exercise 2
  Francisco Ochoa, Oklahoma State University, Stillwater, OK, U.S.A.


• Intro to inclusivity-exclusivity/exercise
  Carla D. Garzon, NIMFFAB - Oklahoma State University, Stillwater, OK, U.S.A.


• Intro to repeatability & robustness/exercise
  Patrick J. Shiel, APHIS CPHST, Raleigh, NC, U.S.A.


• Intro to precision, accuracy, and confidence statistics/exercise
  Geoffrey Dennis, APHIS PPQ, Raleigh, NC, U.S.A.


• Introduction to validation research planning for diagnostic assay development
  Geoffrey Dennis, APHIS PPQ, Raleigh, NC, U.S.A.