Bioinformatics, biometrics and data management

Inventory

Inventory is an open-source application that lets users collect inventory and weight data simultaneously. The app can perform as a standalone sample collection platform but is also compatible with Elane USB scales. These scales can be plugged directly into Android devices with USB OTG functionality. A USB hub can be used to allow both a scale and barcode scanner to run at the same time.

Linear selection indices in modern plant breeding

This book represents a compilation of work done in the area of “selection indices” in animal and plant breeding.

Selection indices were originally developed by Smith (1936) in plant breeding and by Hazel (1943) in animal breeding to address the selection of plants or animals scored for multiple traits.

In agriculture, the breeding worth (or net genetic merit) of a candidate for selection depends on several traits. For example, grain yield, disease resistance, and flowering time.

Highly Interactive Data Analysis Platform (HIDAP)

The Highly Interactive Data Analysis Platform (HIDAP) was developed for clonal crop breeders at the International Potato Center (CIP)

It is part of on-going efforts to unify best practices which practices include data collection, data quality and data analysis in clonal crop breeding. HIDAP builds on the former in-house tools DataCollector (DC) and CloneSelector (CS). These tools supported potato and sweetpotato breeding, respectively.

Breeding API (BrAPI)

The Breeding API (BrAPI) specifies a standard interface for plant phenotype/genotype databases to serve their data to crop breeding applications.

It is a shared, community-developed and open API, to be used by all data providers and data consumers who wish to participate.

BrAPI is a very powerful API that caters for a variety of possible use-cases. Development has focused on the following:

EiB Galaxy instance

Galaxy is an open-source application to enable researchers without informatics expertise to perform computational analyses through the web. A user interacts with Galaxy through the web by uploading and analyzing the data. Galaxy interacts with underlying computational infrastructure (servers that run the analyses and disks that store the data) without exposing it to the user.

Sample Tracker

Sample Tracker is a web-based application developed by the International Maize and Wheat Improvement Center (CIMMYT) to facilitate the workflow and sample identity assignation and tracing around DNA sampling.

Sample tracker provides interfaces to load, generate and query scientist and project information, sample information, genotyping provider requisite plate layouts, plate layouts for lab implementation of DNA extraction, QC metric capture, DNA storage locations, sample file generation and shipping management.

SNPviewer

SNPviewer is a tool that enables genotyping data to be viewed as a cluster plot, but that does not include data analysis or reporting functionality.

Opening genotyping service project results in SNPviewer will allow you to view the genotyping clusters plate by plate. Genotyping calls cannot be changed within SNPviewer; if you need to be able to edit the calls then you will require our KlusterCaller software.

 

Coordinate

Coordinate replaces our previous DNA Plate App and Seed Tray App with a unified data collection app. Coordinate is based on defining templates and then collecting data in grids created from those templates. Two templates are included by default: Seed Tray and DNA Plate.

Verify

Verify is a simple app for importing and managing a list of entries. Utilizing an internal or external barcode scanner, Verify can identify individuals in the list, keep track of how many times they've been scanned, and order in which the items are scanned are correct.

In its simplest form, Verify is integral for viewing data associated with a given entry, making it very useful for sample tracking and management. Sample files are provided with the installation to demonstrate the utility of Verify in research programs.

CassavaBase

CassavaBase offers access to data and tools for breeders and researchers, including genomic selection algorithms and analysis capacity, a cassava genome browser, cassava ontology tools, phenotyping tools, and social networking.

Examples of activities supported by CassavaBase: