3d Cassavabase workshop: manage field-trial
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This document provides instructions for managing field trials in Cassavabase, including: 1) Exporting and importing existing trial files 2) Creating new trials using accession lists 3) Accessing and editing information for existing trials, including the field map, design, accessions, plots, and phenotypic traits 4) Uploading and downloading phenotypic trait data using Field Book
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Musabase PAG 2018
Musabase is a phenotyping and breeding database for bananas that aims to connect data within and between banana breeding projects. It digitizes field data collection through tools like barcoding and digital forms. The database integrates data from various sources like field trials, surveys, sequencing data and tissue culture. It links this in situ breeding data to ex situ conservation resources to create a "digital ecosystem" for banana breeders and researchers. Future work will expand collaboration and train local partners to continue developing open-source tools to improve banana improvement for smallholder farmers.
Cassavabase workshop ibadan March17
This document outlines an agenda for a Cassavabase workshop to be held in Ibadan, Nigeria in March 2017. It provides details on the workshop objectives, audience, attendees, an overview of Cassavabase, and exercises for days 1 and 2. The objectives are to train attendees on using Cassavabase for data loading, visualization, analysis and breeding management through hands-on examples. The audience includes trial managers, data curators/analysts, and scientists/PhD students. Details are provided on checking accounts, tablets, and websites for training. The agenda covers searching, downloading accessions, list management, barcoding, fieldbook use, phenotype analysis including selection indices and genomic selection, and solving issues.
Improvements in the Tomato Reference Genome (SL3.0) and Annotation (ITAG3.0)
The document describes improvements made to the tomato reference genome sequence (SL3.0) and its annotation (ITAG3.0). Over 1,000 BAC sequences were integrated which reduced contig gaps by 11 Mb. Optical maps from BioNano helped assemble the genome into 57 scaffolds with an N50 of 25.4 Mb. The ITAG3.0 annotation includes over 5,800 novel genes identified through RNA sequencing evidence and ab initio prediction. The updated annotation shows improvements in gene structures and functional annotations compared to the previous version.
SolGS Hyderabad conference 2016
This document describes solGS, a web-based tool for genomic selection analysis. solGS allows users to store phenotypic and genotypic data, perform pre-modeling data processing like handling missing values, build prediction models using methods like RR-BLUP and GBLUP, estimate breeding values of selection candidates, and conduct additional analyses like estimating genetic correlations and calculating selection indices. The tool aims to make genomic selection more accessible for plant breeders by providing a platform for organizing and analyzing genomic data.
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2) Designing fieldbook layouts and trait lists for phenotyping
3) Using the Android Fieldbook app to record phenotypes in the field
4) Uploading the exported phenotype data into Musabase
SolGS workshop 2016
solGS is a web-based tool for genomic selection analysis that allows users to store data, build prediction models, and estimate breeding values. It offers three options for composing a training population: searching by trait, searching for trials, or using a custom list. Models can then be applied to estimate breeding values for selection candidates, analyze genetic correlations, and calculate selection indices. The tool aims to advance genomic selection in plant breeding.
Cassavabase workshop IITA oct2016
The document summarizes a NextGen Cassava workshop held at IITA Ibadan in October 2016. The workshop aimed to train attendees in using Cassavabase for cassava breeding data management and analysis. Over two days, participants learned how to search and manage data, design trials, record phenotypes using Fieldbook, analyze data, and utilize genomic selection and crossing tools. Hands-on exercises helped attendees practice the various Cassavabase functions. Support was provided for using the tool and participants received homework assignments.
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This document provides a cheat sheet for using SQL commands to interact with PostgreSQL databases, schemas, tables, and data. It lists commands for connecting to databases (\c) and schemas (\dn), viewing table details (\d), and sending output to a file (\o). It also summarizes commands for data manipulation like INSERT, UPDATE, DELETE, and transactions using BEGIN and COMMIT. Finally, it outlines common SQL queries using SELECT, WHERE, ORDER BY, LIMIT, JOIN and other clauses.
Cassavabase general presentation PAG 2016
CASSAVABASE is a central data store for genomic and phenotypic data from the NEXTGEN CASSAVA project, which aims to accelerate breeding of African cassava through genomic selection. It currently contains over 80,000 accessions and 2.5 billion phenotypic observations. CASSAVABASE allows users to search, manage, analyze and visualize diverse data types to support cassava breeding. Ongoing work involves developing new analysis tools, improving existing tools, and establishing mirror sites for African users.
Cassavabase SolGS presentation PAG 2016
The document describes solGS, a web-based tool for genomic selection in plant and animal breeding. solGS allows users to store genotype and phenotype data, compose training populations, build prediction models using RR-BLUP or GBLUP, predict breeding values for selection candidates, and perform additional analyses like estimating genetic correlations and calculating selection indices. The tool addresses challenges of large genomic data volumes and enables data cleaning, imputation, statistical modeling, and interactive visualization. Models are fitted using 10-fold cross-validation, and solGS provides options for composing training populations by trait, trial, or custom individual lists.
Cassavabase SolGS poster PAG 2016
solGS is a web-based tool that addresses challenges in genomic selection including data management, analysis, and sharing results. It stores phenotype and genotype data in a database and provides an intuitive interface for statistical modeling, visualization, and estimating genomic breeding values. Breeders can build prediction models from training populations, validate models, and estimate genomic estimated breeding values for selection candidates to select best individuals. The open-source code can be adapted to any breeding program.
3a Cassavabase worksop: manage breeding-program ands locations
This tutorial teaches how to manage breeding programs and locations in CASSAVABASE by allowing the user to create new breeding programs and locations from the "Manage" menu. It covers setting up breeding programs under the "Manage breeding programs" section and setting up locations under the "Manage locations" section to organize data.
3e Cassavabase workshop: manage genotyping-trials
This document provides instructions for managing genotyping trials, including creating a genotyping experiment, generating a submission spreadsheet for the Cornell sequencing facility, and adding a trial page linking to the genotyping trial submission. It outlines the process for setting up and submitting samples for genotyping through the Cornell sequencing facility.
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- 1. • In this tutorial you can find how to: -> Manage trials - 1a- export from Cassavabase an existing trial file - 1b- Import to Cassavabase an existing trial file - 2- Create in Cassavabase a new trial using accession list - 3- Access and edit existing trials & informations: - field map - field design - available accessions and plots - available phenotypic traits - 4- Upload/Download features for Phenotypic traits assayed in the trial using Field Book Manage Field Trials
- 2. CASSAVABASE workshop “Manage Field trials”
- 4. 1a- Export from Cassavabase an existing trial file
- 5. 1a- Export from Cassavabase an existing trial file
- 6. 1a- Export from Cassavabase an existing trial file
- 7. 1a- Export from Cassavabase an existing trial file
- 8. 1b- Import to Cassavabase an existing trial file
- 9. Upload trial file format 1b- Import to Cassavabase an existing trial file
- 10. 1b- Import to Cassavabase an existing trial file Upload trial file format
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- 12. Upload trial file format 1b- Import to Cassavabase an existing trial file
- 13. 1b- Import to Cassavabase an existing trial file
- 14. 2- Create in Cassavabase a new trial using accession list
- 15. 2- Create in Cassavabase a new trial using accession list Add a trial infos
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- 25. Upload field trial coordinates file
- 27. field trial coordinates format Field design informations
- 33. List of phenotypic traits assayed in the trial
- 37. 4- Upload/Download feature for Phenotypic traits assayed in the trial using Field Book