diff --git a/build/pandoc/defaults/common.yaml b/build/pandoc/defaults/common.yaml index bfa5d97..8fa2aba 100644 --- a/build/pandoc/defaults/common.yaml +++ b/build/pandoc/defaults/common.yaml @@ -9,5 +9,6 @@ filters: - citeproc wrap: preserve metadata: - csl: build/assets/style.csl + #csl: build/assets/style.csl + csl: https://www.zotero.org/styles/nature.csl link-citations: true diff --git a/content/03.02.02.DArTView.md b/content/03.02.02.DArTView.md index 05fbb22..899d4f5 100644 --- a/content/03.02.02.DArTView.md +++ b/content/03.02.02.DArTView.md @@ -1,4 +1,6 @@ #### DArTView - -DArTView is a desktop application for visualizing genotype variant data and looking for trends or correlations. It is newly BrAPI compatible and can use BrAPI as an input data source. + +DArTView is a desktop application for marker data curation via metadata filtering. DArTView enables genotype variant data visualization and users can easily identify trends or correlations within their data using the tool. Its primary goal is to overcome tedious manual calculation of marker data through common spreadsheet applications like Excel. Users are able to import marker data from csv files, but DArTView has been recently enhanced to be BrAPI compatible. Users can now use any BrAPI compatible server as an input data source. BrAPI provides a consistent data standard across databases and data resources. DArTView's compatibility with BrAPI also ensures easy integration with other tools and pipelines that would use DArTView for marker filtering and exploration. + +Initially developed by Diversity Arrays Technology (DArT), the tool is gaining popularity within the breeding community, especially in Africa. Future releases will focus on enhancing the BrAPI compatibility, making it accessible to more breeders and researchers in the region. A web enabled version of DArTView is in development. This new version will allow for further collaboration opportunities with other interested partners who would like to integrate it as part of their pipelines. diff --git a/content/03.05.04.SCT.md b/content/03.05.04.SCT.md index 7b71c26..02c19cd 100644 --- a/content/03.05.04.SCT.md +++ b/content/03.05.04.SCT.md @@ -1,3 +1,6 @@ #### 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. + +The [Sugarcane Crossing Tool (SCT)](https://github.com/USDA-ARS-GBRU/SugarcaneCrossingTool) is a lightweight RShiny dashboard application designed to receive, process, and visualize data from a linked BreedBase [@doi: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 from 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. The modularized, open source code is available in a [GitHub repository](https://github.com/USDA-ARS-GBRU/SugarcaneCrossingTool) for community reference and reuse. + +The crossing tool utilizes a modified version of the [BrAPI-R](https://github.com/CIP-RIU/brapi) library to access a compliant database, and it employs standard R/JavaScript packages to aggregate and visualize data. Modules within the application allow breeders to query the database (through BrAPI) for information relevant to their decision-making process. This includes the number and sex of flowering accessions, deep pedigree and relatedness information, 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.