Welcome to Germinate

The generic plant genetic resources database

MCPD compatible

The Multi-Crop Passport Descriptors (MCPD) is a widely used international standard to facilitate germplasm passport information exchange defined by the FAO. Germinate is fully MCPD V.2.1 compatible. The MCPD standard is used by many genebanks and genetic resources tools and utilities.

Visualization driven

We love visualizations. When done right, they can uncover new patterns in your data that would otherwise remain undetected. This is why we try to offer intuative visualizations in Germinate where appropriate. Both the data visualizations and the underlying experimental data can be exported for further analysis in a variety of other tools including Helium, Flapjack, CurlyWhirly and R.

Customizable

We all have projects that involve different data types. No two projects are exactly the same! This is why we designed Germinate to cater for the varying needs and circumstances of our users. From user interface template styling to full localisation and internationalization support - Germinate has it covered.

Export Formats

Germinate can export data in a number of formats. Depending on the types of data you are storing we provide a variety of ways that you can get your data out of the database. These range from plain text format, that can be used to import your data into Excel or R, to more advanced formats for tools like Google Earth, Helium, Mapchart, Strudel and Flapjack.

We are always looking to increase the functionality of Germinate and would welcome any suggestion on how we can improve our export features to better meet the requirements of the community.

Publications

We have recently published a paper on the Germinate 3 platform.

Shaw, P.D., Raubach, S., Hearne, S., Dreher, K., Bryan, G., McKenzie, G., Milne, I., Stephen, G. and Marshall, D.F. Accepted. Germinate 3: Development of a Common Platform to Support the Distribution of Experimental Data on Crop Wild Relatives. Crop Science. doi: 10.2135/cropsci2016.09.0814.

You can get advance access to this from here.

Future Work

We are continually trying to improve Germinate by adding new features requested by our users.

We are currently developing tools to make the upload of data into Germinate a little bit easier with automated data import and validation tools for MCPD terms. We are also looking at ways that we can use Germinate to track germplasm through breeding programmes and experiments and generate visualizations to explore the relationships between germplasm and the experimental work which has been carried out on it.

We are also now working to implement Data Object Identifiers (DOI) across appropriate germplasm within our platform.

Why Germinate?

Germinate is an open source plant database infrastructure and application programming platform on which complex data from genetic resource collections can be stored, queried and visualized using common, reusable, programming components. Germinate utilises modern web and database standards to provide a common architecture and high performance web-based user interface and analytics functionality across a wide variety of data types including: passport, phenotypic, field trial, pedigree, genetic, climatic, geographic location data as well as user-submitted annotations. In addition, it provides links to an expanding variety of external visualization and analysis tools such as Helium for pedigree visualization, Flapjack for graphical genotyping and CurlyWhirly for 3D coordinate data.

The single point of access for all background data on genetic resources collections that Germinate implements, provides a valuable digital curation resource as well as offering essential continuity on how new data is recorded and presented to researchers and breeders which brings focus and facilitates community building into research communities.

Want to know more? Browse this page and have a play about with our demo database or drop us an email on germinate@hutton.ac.uk.

GERMINATE INSTANCES

There are a number of Germinate instances that have been set up by our team here at the James Hutton Institute in Dundee. We have worked with collaborators worldwide to get their data into Germinate. Some of these are open access whereas others require registration before you can access the data. While we like open data we realise there are times where keeping things private or ensuring that users agree to conditions are a requirement.

So go on give it a try! Our demo database below showcases all of the Germinate features. You can browse the data and have a play about with the features that Germinate offers.

If you are using Germinate and would like us to add your instance to this list, send us an email to us at germinate@hutton.ac.uk - ask for Paul or Sebastian, both are helpful chaps!.

All JHI CIMMYT Crop Trust Other

Germinate Barley Database

Germinate Berrybase

Germinate Demo Database

Commonwealth Potato Collection

Germinate Grasses Database

SeeD Maize Germinate

Crop Wild Relatives Rice Database

Crop Wild Relatives Sunflower Database

SeeD Wheat Germinate

DOWNLOAD

Source Code

Configuring and compiling Germinate from source gives you the most flexibility. The installation section in our documentation will guide you through the process and make this as simple as possible.


More Info

Docker Image

If you just want to give Germinate a try without having to configure and compile it, our Germinate Docker Image might be for you. Docker images are available for all Germinate versions starting with 3.3.1.


More Info

Linux Install Script

Since version 3.3.2 we offer an installation script for Germinate. This script is meant to be used when you are using Germinate for the first time. It will make the setup process a lot easier and will automate most of the steps.


More Info

ADDITIONAL MATERIAL

Official Documentation


Download

Changelog Documentation


Download

Poster


Download

DEVELOPERS

These handsome chaps are responsible for the development of Germinate.

Paul Shaw

Paul developed the Germinate data warehouse backend and manages the Germinate project.

Sebastian Raubach

Sebastian develops the snazzy Germinate interface and spends his time implementing cool new features.

Iain Milne

Iain has provided code that allows us to convert extracted data from Germinate in to Flapjack format.

Gordon Stephen

Gordon has recently become involved with Germinate and focuses on Germinate integration with BrAPI.

David Marshall

David provides scientific advice and promotes the project and its benefits on his travels.

More about Germinate

If you want to learn more about the development and history of Germinate, please visit Germinate on the James Hutton Institute's Information & Computational Sciences website.


More Info

Germinate allows the distribution of complex plant data in a common, easy to use format. Its tools and visualizations allow you to get more from your data.


Why not try our demo database and see for yourself?

FUNDERS

Germinate 3 has been developed in close collaboration with the following funders.

Contact

If you have any questions about Germinate, are having problems (Just Germinate related ones - no neighbour disputes or crosswords), want to let us know about bugs (yes they sometimes happen) or have ideas on how we can improve the platform we would love to hear from you! germinate@hutton.ac.uk

Useful Links

Address

Germinate
Information & Computational Sciences
AF Block
The James Hutton Institute
Invergowrie
Dundee
DD2 5DA
Scotland