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Web-Interface to browse, filter and visualize plant genotyping data

Basterrechea, Martin (2017) BINP30 20171
Degree Projects in Bioinformatics
Abstract
The BRIDGE project is an initiative by the German Federal ex situ Genebank of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben which aims to make the information stored in the genebank available in a one stop shop fashion for plant breeders and researchers. IPK hosts the biggest genebank in EU-27 and is undertaking a proof-of-concept study based on genotyping-by-sequencing its entire barley collection of more than 20 000 accessions. The barley genome has 7 chromosomes and it is diploid. This Master's Degree Project is embedded in the context of the BRIDGE project. Our goal is to design and develop a web application to visualize and filter plant genotyping data stored in the BRIDGE database. This application... (More)
The BRIDGE project is an initiative by the German Federal ex situ Genebank of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben which aims to make the information stored in the genebank available in a one stop shop fashion for plant breeders and researchers. IPK hosts the biggest genebank in EU-27 and is undertaking a proof-of-concept study based on genotyping-by-sequencing its entire barley collection of more than 20 000 accessions. The barley genome has 7 chromosomes and it is diploid. This Master's Degree Project is embedded in the context of the BRIDGE project. Our goal is to design and develop a web application to visualize and filter plant genotyping data stored in the BRIDGE database. This application will work with other applications to make genotype information available to the public in a visual and user-friendly way. We developed a web application that allows the user to access the barley genotypic data stored in the BRIDGE project database. The user can explore the genotypes, filter the samples and export the data shown on the display. We also developed a server that runs an API (Application Programming Interface) application, connecting the web application with the database. This server also processes the information before being sent to the client to increase performance and reduce the amount of data to be sent. Due to the size of the database, we used Oracle's In-Memory Database technology to reduce the time needed to access the database. (Less)
Popular Abstract
Our goal is to design and develop a web application to visualize and filter plant genotyping data stored in the BRIDGE database. The BRIDGE database con-tains information about more than 20.000 barley samples stored in the German Federal ex situ Genebank of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. This application will work with other applications to make genotype information available to the public in a visual and user-friendly way.

Given current and future food demand, caused by population increase and change in global weather, solutions are needed to increase food availability. One of such solutions is increasing food production. Plant research and breeding is considered a solution for these... (More)
Our goal is to design and develop a web application to visualize and filter plant genotyping data stored in the BRIDGE database. The BRIDGE database con-tains information about more than 20.000 barley samples stored in the German Federal ex situ Genebank of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. This application will work with other applications to make genotype information available to the public in a visual and user-friendly way.

Given current and future food demand, caused by population increase and change in global weather, solutions are needed to increase food availability. One of such solutions is increasing food production. Plant research and breeding is considered a solution for these concerns. Gene banks exist in order to conserve genetic diversity and aid plant breeding. The German Federal ex situ Genebank of Agricultural and Horticultural Crop Species is located in Gatersleben, Germany, stores 151,002 accessions from 3212 spe-cies. The IPK-Gatersleben research institute is undertaking the BRIDGE project, a proof-of-concept project whose aim is to genotype the barley samples stored in the Genebank. Genotyping the samples gives the researchers access to the genetic infor-mation of each sample. This allows plant breeders to learn about the processes that the plant undergoes during its life cycle, providing tools to create better breeds.
The project
For this Master’s Degree Project our aim is to design and develop a web interface to access the information stored in the database in a visual way. The tool’s specifications include analytical and filtering tools to help the user gather information about the sam-ples of interest and discover new samples using their genotype. The purpose of this masters thesis is to assess if it is possible to create an application that is technically able to fulfil certain requirements and to build the application to a basic alpha state, which can be used to build upon later.

This application includes server running an API (Application Programming Interface) to access the information stored in the server. The API connects to the BRIDGE data-base containing the most recent genotype information. The database currently has gen-otype information of more than 8500 samples across all 7 chromosomes, so our imple-mentation must use advanced database technologies to reduce the time needed to ac-cess the data.

The application has proved to be successful in displaying the information to the user and providing an interactive interface with the data. However, due to the size of the database, some technical challenges remain to reduce the time needed to retrieve the information.

Master’s Degree Project in Bioinformatics 30 credits 2017
Department of Biology, Lund University

Advisor: Matthias Lange and Uwe Scholz
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) (Less)
Please use this url to cite or link to this publication:
author
Basterrechea, Martin
supervisor
organization
course
BINP30 20171
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8910613
date added to LUP
2017-06-02 14:47:09
date last changed
2017-06-02 14:47:09
@misc{8910613,
  abstract     = {The BRIDGE project is an initiative by the German Federal ex situ Genebank of Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben which aims to make the information stored in the genebank available in a one stop shop fashion for plant breeders and researchers. IPK hosts the biggest genebank in EU-27 and is undertaking a proof-of-concept study based on genotyping-by-sequencing its entire barley collection of more than 20 000 accessions. The barley genome has 7 chromosomes and it is diploid. This Master's Degree Project is embedded in the context of the BRIDGE project. Our goal is to design and develop a web application to visualize and filter plant genotyping data stored in the BRIDGE database. This application will work with other applications to make genotype information available to the public in a visual and user-friendly way. We developed a web application that allows the user to access the barley genotypic data stored in the BRIDGE project database. The user can explore the genotypes, filter the samples and export the data shown on the display. We also developed a server that runs an API (Application Programming Interface) application, connecting the web application with the database. This server also processes the information before being sent to the client to increase performance and reduce the amount of data to be sent. Due to the size of the database, we used Oracle's In-Memory Database technology to reduce the time needed to access the database.},
  author       = {Basterrechea, Martin},
  language     = {eng},
  note         = {Student Paper},
  title        = {Web-Interface to browse, filter and visualize plant genotyping data},
  year         = {2017},
}