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Sebastian Raubach

Staff picture: Sebastian Raubach
Information and Computational Sciences
Information and Computational Sciences
Bioinformatics Software Developer
sebastian.raubach@hutton.ac.uk
+44 (0)344 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

 

I am a Bioinformatics Software Developer in the Information and Computational Sciences group. Before starting work at the James Hutton Institute in 2012, I studied Computer Science at the RWTH Aachen University in Germany and received my Master of Science with distinction.

Since joining the institute in late 2012 I have been working on software tools for data management, data processing and data visualization.

Current research interests

  • Design and development of the Germinate 3 plant database platform.
  • Development of mobile and web applications to simplify the access to data stored in Germinate.
  • Data visualization using d3.js.
  • Maintenance of the Seeds of Discovery website.

Current Software Applications

Germinate 3

Germinate is a generic plant genetic resources database and offers facilities to store both standard collection information and passport data along with more advanced data types such as phenotypic, genotypic and field trial data. Germinate was originally implemented in MySQL and Perl but is moving with version 3 to MySQL and Google Web Toolkit (GWT). Germinate is not a standalone desktop application and requires MySQL, Apache Tomcat and GWT to run. The usual use case would be installation on a Linux or Windows based server.

Germinate Daim

Germinate Daim is a Java based desktop application to aid in the upload of experimental datasets into Germinate. The aim of this tool is to simplify the process of entering data into the system. Germinate Daim allows permitted MySQL system users to upload data in text file format into a specified Germinate installation.

Germinate Scan

Germinate Scan is designed to make scanning and storing barcodes easy! Just connect the external barcode scanner to your Android device and start scanning or use your device’sinbuilt camera. Germinate Scan will scan barcodes as a key-value pair, i.e. the first code represents the key while the second code is the value. All scanned pairs are tagged with the time and date of the scan event as well as the geographic location of the device if GPS is enabled. As long as the attached barcode scanner is connected as an input device, Germinate Scan can handle all types of bar codes the scanner is able to read. All scanned bar codes are saved in an internal database to make sure that you can continue exactly where you left off. The database can be exported to a text file at any time.

Humbug

Humbug is a multi-platform barcode generator which can be used alongside our Germinate Scan application to generate sheets of user-defined barcodes to aid in the recording of data in the field or glasshouse. Humbug and Germinate Scan are primarily suited for the recording of categorical data categories which could include traits such as flowering time.

Buntata

Buntata is an Android based mobile application which aids in the identification of plant disease and pathogens and offers information to farmers where they can go to get more details about any pests. It provides downloadable datasets allowing users to use the application in the field without the need of a mobile signal.

Recent publications

Printed from /staff/sebastian-raubach on 15/08/18 11:55:31 PM

The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.