Germinate

We have a new page describing Germinate and what it can do!

Please visit https://ics.hutton.ac.uk/get-germinate for more information.

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 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 based server.

Germinate is free and we envisage that the use of these technologies will enable us and other groups to develop a range of standard interfaces and analytical tools to interact with the underlying database that are free to distribute to interested parties.

For further information on the Germinate project you can contact us at germinate@hutton.ac.uk

We also have a Germinate demo site available!

Why we need Germinate

There has been a growing need for the ability to organise germplasm collections and associate these with additional data types, such as phenotypic or genotypic information and allow users to export this data in logical groupings. Germinate 2 introduced the concept of groups whereby any common entity (germplasm entries, markers and so on) can be defined as groups. A group is a sub selection of the larger total database and allows users to logically break down larger datasets into more discrete entities. Groups can be combined at export stage to provide a powerful selection mechanism for the Germinate database.

The ability to merge germplasm background information and passport data with genotypes and phenotypic scores provides researchers a powerful tool in the analysis of quantitative traits. Germinate 2 provides the ability to export data into commonly used file formats such as plain text or into Flapjack format files which can then be imported into Flapjack for visual genotype analysis (http://ics.hutton.ac.uk/flapjack). This seamless integration with our other analysis tools reduces the complexity of information interchange between applications and removes the overhead and burden of users needing to manipulate text files before loading into other applications. We are happy to discuss including other file formats into our core distribution.

The Germinate Ethos

While Germinate may be seen as a platform it is also true to say that it combines more than just an architectural framework, but is also about the ethos behind the development of simple tools to perform complex tasks. Germinate is about breaking tasks down into their common components and releasing these so that they can be reused as required. We focus on delivering solutions to current problems instead of devoting large amounts of time to developing complex solutions which are infrequently used. Because of this Germinate has historically been malleable and we have been able to quickly adapt to new challenges and quickly offer robust solutions to different challenges. This has led to a diverse set of databases that have been developed using this platform.

Keeping Out Prying Eyes

While we firmly believe in collaborative science we appreciate there are times when data is private and needs to be kept that way.

Because of this we have implemented Germinate Gatekeeper. Gatekeeper acts as an authentication mechanism for the Germinate 3 system and allows restricted access to a Germinate database. Trusted users are provided with usernames and they can log in as required. Users can also change their passwords without manual intervention as was the case with Germinate 2. Germinate Gatekeeper is freely available as a standalone add on for Germinate 3 and we have rolled this out with some of the collaborative work we have undertaken with the James Hutton Institutes commercial arm MRS.

Germinate on the go

The development of Germinate 3 has also coincided with us looking at ways to allow users to easily access their data on mobile devices. This has led to the development of Germinate Mobile. We have dedicated pages for Germinate Mobile where you can get more information on this application.

Installations

There are a number of Germinate installations that we have been working on covering a diverse range of crop plants. Because these are all implemented in a common platform the creation of new tools and visualization components can benefit all installations if required. We see this as one of the main benefits to our common platform and it has worked well for us over the past few years.

These installations should give you an idea of what can be achieved using the Germinate platform.

Freely Available Germinate 3 Installations

Seeds of Discovery Germinate Wheat Catalogue http://ics.hutton.ac.uk/germinate-wheat

Seeds of Discovery Germinate Maize Catalogue http://ics.hutton.ac.uk/germinate-maize

Freely Available Germinate 2 Installations

Germinate CPC Database http://bioinf.hutton.ac.uk/germinate_cpc

Germinate Grasses (Lolium and Festuca) http://bioinf.hutton.ac.uk/germinate_grasses

Germinate Pea (Pisum) http://bioinf.hutton.ac.uk/germinate_pea

Password Protected Germinate 2 Installations

Germinate Barley (AGOUEB) http://www.agoueub.org

Credits

Germinate is being developed by Paul Shaw and Sebastian Raubach with the aid from other members of the Information and Computational Sciences Group in Dundee and members of Cell and Molecular Sciences in Dundee. In no particular order the following people have been instrumental in getting Germinate up and running and have been invaluable in giving us feedback throughout the development: David Marshall, Andy Flavell, Iain Milne, Linda Milne, Gordon Stephen, Robbie Waugh, Bill Thomas, Joanne Russell, Jordi Comadran and Luke Ramsay.

Germinate 3 was developed with CIMMYT as part of the MasAgro Seeds of Discovery project.

As with all of the tools we produce we are happy to get feedback on how well they are working for you and if there are features that you think would be beneficial to add. We are also more than happy to talk to prospective users about using Germinate or answering any questions they may have. If you want to develop components for our system that’s even better! Just contact us and let us know!

If you have any questions or comments we can be contacted at germinate@hutton.ac.uk.

Open source sponsors

The following companies have very kindly provided open source licences for their products to assist in the development of Germinate.

IntelliJ IDEA by JetBrains

Crowdin