Merge pull request #52 from keocorak/main

Add sugarcane crossing tool to section 3.5
plantbreeding · Jun 6, 2024 · 507a758 · 507a758
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diff --git a/content/03.05.04.SCT.md b/content/03.05.04.SCT.md
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+#### SCT
+
+The Sugarcane Crossing Tool (SCT) is a lightweight RShiny dashboard application designed to receive, process, and visualize data from a linked BreedBase (https://doi.org/10.1093/g3journal/jkac078) instance. This application is being developed collaboratively with members of the Sugarcane Integrated Breeding System (https://www.amscl.org/sugarcane-integrated-breeding-system/), who have advocated for an application that assists them in designing crosses based on queried information for a list of available accessions. By leveraging existing community resources, the team has been able to develop a simple BrAPI-enabled application without possessing extensive programming knowledge or experience. The SCT is presented as an inspiration for similarly positioned scientists to consider developing custom applications for specific tasks. Modularized code is provided in a GitHub repository for community use (https://github.com/USDA-ARS-GBRU/SugarcaneCrossingTool). The crossing tool utilizes a modified version of a previously described BrAPI implementation in R (https://github.com/CIP-RIU/brapi) to access a compliant database and employs standard R/JavaScript packages to aggregate and visualize data. Modules within the application allow breeders to query information relevant to their decision-making process, such as the number and sex of flowering accessions (since sugarcane flowers have variable male fertility), deep pedigree and relatedness information for each unique flowering accession, summarized trial data, and the prior frequency and success of potential cross combinations. Future versions of this tool will provide additional decision support (e.g. ranked potential crosses) to enhance the accuracy and efficiency of crossing.
diff --git a/content/metadata.yaml b/content/metadata.yaml
@@ -100,6 +100,12 @@ authors:
     email: [email protected]
     affiliations:
       - Clemson University
+   - name: Keo Corak
+    github: keocorak
+    initials: KC
+    email: [email protected]
+    affiliations:
+      - USDA-ARS Genomics and Bioinformatics Research Unit 
   - name: Mariano Crimi
     initials: MC
     email: [email protected]
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		#### SCT

		The Sugarcane Crossing Tool (SCT) is a lightweight RShiny dashboard application designed to receive, process, and visualize data from a linked BreedBase (https://doi.org/10.1093/g3journal/jkac078) instance. This application is being developed collaboratively with members of the Sugarcane Integrated Breeding System (https://www.amscl.org/sugarcane-integrated-breeding-system/), who have advocated for an application that assists them in designing crosses based on queried information for a list of available accessions. By leveraging existing community resources, the team has been able to develop a simple BrAPI-enabled application without possessing extensive programming knowledge or experience. The SCT is presented as an inspiration for similarly positioned scientists to consider developing custom applications for specific tasks. Modularized code is provided in a GitHub repository for community use (https://github.com/USDA-ARS-GBRU/SugarcaneCrossingTool). The crossing tool utilizes a modified version of a previously described BrAPI implementation in R (https://github.com/CIP-RIU/brapi) to access a compliant database and employs standard R/JavaScript packages to aggregate and visualize data. Modules within the application allow breeders to query information relevant to their decision-making process, such as the number and sex of flowering accessions (since sugarcane flowers have variable male fertility), deep pedigree and relatedness information for each unique flowering accession, summarized trial data, and the prior frequency and success of potential cross combinations. Future versions of this tool will provide additional decision support (e.g. ranked potential crosses) to enhance the accuracy and efficiency of crossing.