AG2PI Workshop #23 - Wednesday July 12, 2023
CartograPlant Workshop: Integrating, Visualizing and Analyzing Genotype, Phenotype, and Environmental Data from Geo-Referenced Plants
Wednesday July 12, 2023
10:00 - 12:30 PM
(US Central Time)
Purpose
Hands-on training on how to utilize the CartograPlant app for data searching, visualization, and plant population analysis.
Registration
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Climate change, invasive plants, and pathogens are threatening plant health and productivity at all spatial scales. Future plant health and productivity will depend on the identification of genes controlling traits which provide plant resilience to these biotic and abiotic stresses. This identification requires the integration of diverse data: genotypic, phenotypic and environmental. Existing public repositories struggle to provide frameworks that can integrate across these complex data types. CartograPlant is the first web-based application that integrates genotype and phenotype data for model and non-model plant systems with global environmental layers. This Tripal-based (tripal.info) field to analysis framework connects data collection, data submission, ontology-based metadata annotation, and analytics directly to high performance computing resources. Environmental data is available through advanced integration of global and regional layers. Genotype and phenotype metrics are collected through direct submission of studies at the time of publication via the FAIR data submission module TPPS, or through the biocuration efforts of the affiliated databases (TreeGenes, BIEN, Dryad). Georeferenced trait data can be also submitted using WildType (wildtypeapp.org) or TreeSnap (treesnap.org), mobile apps for field-based data and sample collection. After data selection, users are able to choose from a menu of appropriate workflows that are completed on CartograPlant computational resources using the Galaxy platform (galaxyproject.org). This workshop will provide hands-on training with data search, visualization, and plant population analysis: CartograPlant Introduction Data Submission with TPPS Data Collection and Mobile Phenotyping with TreeSnap/WildType CartograPlant Backend: Environmental Layers and Data Analytics with CartograPlant – GWAS and GEA
** This workshop is a product of an AG2PI seed grant **
View AG2PI Funded Seed GrantAbout Presenters
Dr. Irene Cobo-Simón holds a Ph.D. in Biology (Complutense University of Madrid, Spain). She led the development of the web-based application CartograPlant during her first postdoc at UConn (Storrs, USA), focusing on the development of integrative and robust analytical workflows. She is currently a postdoctoral fellow at the Institute of Forest Science (ICIFOR-INIA, CSIC, Spain)
Gabriel Barrett is currently pursuing a MSc. degree in biology and engages in the CartograPlant project. His work focuses on the development of bioinformatic workflows like NextFlow and Galaxy that make data analysis more streamline and efficient. He mentioned that working on the CartograPlant project has been a captivating experience and presents unique challenges and opportunities to understanding plant genomics.
Emily Grau is an independent Genomics Data Curator and Web Developer working with forest tree community database, TreeGenes. Her interests include collaborative Tripal software development and developing automated and manual curation pipelines for genomic data and metadata.
Risharde Ramnath holds a MSc. in Engineering Management and BSc. Computer Science from the University of the West Indies, Trinidad and Tobago. He is the lead developer at TreeGenes continuing to further develop CartograPlant.
Dr. Margaret Staton earned her Ph.D. in plant and environmental science from Clemson University. Currently she is an Associate Professor of Bioinformatics in the Entomology and Plant Pathology Department at the University of Tennessee, Knoxville. Her interests include plant computational genomics, transcriptomics and epigenomics, as well as developing cyberinfrastructure platforms for genomics research data and supporting citizen science (e.g. TreeSnap)
Dr. Jill Wegrzyn is an Associate Professor of Ecology and Evolutionary Biology in the Department at the University of Connecticut where she leads the Plant Computational Genomics Lab. She is also the director of the Computational Biology Core within the Institute of Systems Genomics. She develops web-based applications that integrate data across domains to facilitate the plant geneticist or ecologist's ability to analyze, share, and visualize their data. Such integration requires the implementation of semantic technologies and ontologies to connect genotype, phenotype, and environmental data.
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