Welcome to the web site for the Information & Computational Sciences (ICS) group. The creation of the group at the James Hutton Institute was in response to the increasingly central role that computational approaches are playing in contemporary Plant and Environmental Sciences.
What is Germinate 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 […]
Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, allowing for rapid navigation and comparisons between lines, markers and chromosomes. Visit the download page to get the latest version of Flapjack (1.15.08.31; 31st August 2015). You can get a full list of recent new additions, changes or bug fixes by reading through the […]
Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. Visit the download page to get the latest version of Tablet (1.15.09.01; 1st September 2015). Please cite: Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, Cardle L, Shaw PD and Marshall D. 2013. Using Tablet for visual exploration of second-generation […]
Germinate Mobile is an Android application that acts as a mobile interface for the Germinate system. The goal of this app is to enable researchers to get detailed information about plants on their smartphone or tablet while they are out and about in the fields. Images as well as passport and pedigree information are accessible […]
CurlyWhirly is an application for viewing multi-dimensional data, with a particular focus on the outputs of Principle Coordinate Analysis and Principal Components Analysis. Visit the download page to get the latest version of CurlyWhirly 1.15.09.01 (1st September 2015). CurlyWhirly features: 3D display of multi-dimensional data. Rotate the graph by dragging on the display. Zoom in […]
Helium Pedigree Visualization Framework The ability to predict and visualize the inheritance of genes that facilitate resistance to pathogens or any other commercially important characteristic is crucially important to experimental plant genetics and commercial plant breeding programmes. Derivation of this information by traditional molecular techniques is expensive and time consuming, even with developments in high-throughput […]
“Currently we have some 50 staff and research student members of the group based at our sites in Dundee and Aberdeen. The skill base of the group encompasses computational geography, bio- and geo-informaticians and computer scientists; as well as a range of modelling disciplines (including risk and uncertainty analysis, climate change and scenario modelling, crop modelling, whole systems modelling). The common aspect of our work is the utilisation of computational and integrative approaches to our science. In partnership with members of the other four Science Groups, we work across all seven of the Institute’s Research Themes, and across a broad range of scales from the molecular to the landscape.
Our quantitative skills are in great demand and currently that demand frequently outstrips existing capacity. In consequence, we are always actively recruiting in several areas and we welcome approaches from either potential research students or staff members from other organisations who would like to spend a training period with us.” Rupert Hough, ICS Group Leader