Genebanks safeguard and make available the genetic diversity of our food crops. This is a critically important endeavor, but maintaining and sharing plant materials – seeds, tissues in test tubes etc. – alone is not enough. Beyond the cold rooms and the laboratories, the greenhouses and the regeneration fields, there is a wealth of information that accompanies each sample. Only accurate and current information enables genebank staff to do their work effectively and efficiently.
This information includes everything from where and when a seed was collected to who requested and received samples, when and where the material was regenerated, and what is its current health status. But keeping track of this breadth of information is no easy feat. The cost and technical challenges of developing and maintaining a genebank management and information system can be daunting.
GRIN-Global Community Edition
GRIN-Global Community Edition (GG-CE) is a freely accessible, open-source software solution, designed for genebanks to store and manage data associated with plant genetic resources in their collections. GG-CE provides the genebank with current information about each sample in the collection, allowing for better allocation of their limited resources, and prioritization of activities.
GG-CE is an evolution of the original GRIN-Global system, which is based on the classic Germplasm Resource Information Network (GRIN) software. GG-CE builds on decades of experience in genebank database design of GRIN-Global and therefore features a suitably designed and fully developed database that addresses most genebanks’ data requirements.
GG-CE aims to provide a complete genebank inventory management solution.
GG-CE enables genebank staff to capture and make use of data across all genebank operations, from acquisition, to management, monitoring, and evaluation of material in the collection, and its eventual distribution to clients. It provides tools that enable genebank technicians to capture data as early as possible, usually alongside routine genebank operations.
Genebank collection management primarily deals with what, in what form, how much, and where plant genetic resources are physically in the genebank. We refer to this as Inventory management. The documentation about the material origin, performance and characteristics is crucial for effective utilization of PGR, and for the purposes of explaining GG-CE that is described below in the Passport and trait data section.
GG-CE always maintains the current, up-to-date information about physical material that is stored as seed, in vitro, in the field, etc. This database mirrors the actual status of each individual seed packet, cryo tube or plant in the field. GG-CE provides tools for technicians to update the database as they go about their daily work in the genebank: from acquisition of new material, viability testing, to distribution of material to users.
Monitoring the collection
The biological material in genebank collections ages with time and therefore requires routine monitoring so that appropriate actions are taken to keep sufficient amounts of material alive and healthy. Planning and prioritizing of monitoring activities relies on having access to the most recent and current information about collection state.
Very commonly, there exists a large time-gap between data generation and capture on paper, transcription to an electronic spreadsheet (Excel), and transfer to the central genebank database where the data is made accessible to all genebank staff. This gap makes it very difficult for data managers to verify and correct the data, and in turn effective planning of monitoring activities becomes impossible.
GG-CE provides tools that guide and support technicians during their routine operations, like seed viability testing. Data capture is aligned with the process, which ensures data is correctly recorded, time-stamped and linked to the person who recorded the data.
By reducing the time between data generation and its recording in the database, data validation and curation is simplified and improved. GG-CE enhances the validity and correctness of viability data. The availability of current, valid and correct data in GG-CE allows genebanks to prioritize and plan the activities required to keep the collection healthy, available and, most importantly, alive.
Barcoding the collection
Material is added to the collection through acquisition, rejuvenation or regeneration, while distribution will reduce the quantity on hand when samples are sent to users. GG-CE relies on barcoding to uniquely identify each lot/batch/packet of material stored in the genebank.
Use of barcoding for every physical lot (inventory in GG parlance) in the genebank enables technicians to make accurate reference to the material they are handling, and the acquired data is always linked to the correct record in the database. Barcoding is not limited to inventory lots, GG-CE utilizes barcoding across all operations.
Barcoding is essential for modern-day data management and GG-CE comes with best-practice label templates, including barcodes ready for use. GG-CE supports barcode scanning on mobiles, tablets and desktops.
Passport, trait and marker data
Accession passport data is critical for any collection. The time gap between receiving the material and recording the passport data in the database is the primary reason for the low level of detail of documentation of material in the genebank, since material is often given a new identifier.
GG-CE supports the acquisition process ensuring that key identifiers are captured as soon as the material arrives at the genebank and passport data can be linked more reliably to the correct inventories. This enables genebanks to proceed with introduction processes while the data itself may not yet be available.
Curation and updating of passport data continues long after the acquisition itself, as the provider of material makes updated and curated information available.
GRIN-Global and GG-CE both support recording of trait and marker definitions and their observations allowing to choose accessions that feature the selected traits.
GG-CE provides the MCPD view of accession data and also allows for direct publishing of accession data to Genesys.
Distribution of material
Making healthy and viable plant material available to clients is a key objective of any genebank. GG-CE allows for recording incoming requests for material from both external clients (for distribution) and internal use (for regeneration, monitoring, etc.) and supports technicians in fulfilling these requests. Maintaining a database of request records allows for tracking past distributions, understanding your clients and monitoring trends of which types of materials are requested, when, and by whom.
Genesys is commonly used to provide public access to accession data and enables users to request genebank material online. GG-CE seamlessly integrates with Genesys. It retrieves and displays request information and allows the genebank to queue requests from Genesys into the pipeline.
How is GG-CE different from GRIN-Global
GG-CE uses the GRIN-Global database model and MSSQL Server remains the preferred database engine. The data model is updated with community extensions. GG-CE is backwards compatible with existing GRIN-Global databases.
GG-CE provides a web interface and genebank staff can access and interact with GG-CE without installation of additional software on desktops, tablets and mobiles across different operating systems.
The Curator Tool allows for convenient importing of bulk data and updating of large numbers of records, which are common tasks for any genebank data manager, only the data manager may want to install and use the Curator Tool with GG-CE. All other genebank staff should use the GG-CE Web application on their mobiles and desktops.
GG-CE provides tailored user interfaces (replacing Wizards) for different areas of genebank operations and provides specialized tools for each activity area in a genebank: from updating passport data, inventory management, seed viability, to managing the distribution of material to clients. GG-CE provides integrated printing of barcode labels directly from the web interface.
The GG-CE Server implements JSON and SOAP API endpoints that provide the business logic in support of genebank operations.
The JSON API is preferred and is used in all new client applications. The SOAP API is provided for backward compatibility with the original GRIN-Global, allowing for use of the Curator Tool and other software that uses the GG SOAP protocol.
GG-CE is intended for internal management of genebank data. It is commonly hosted and managed by IT departments on the internal protected network and not directly accessible from the Internet. A Public Website is not bundled with GG-CE.
A public website may be developed using GG-CE APIs. Embedded Genesys offers a convenient alternative.
The original GG server is an .Net web application that requires a Windows Server and IIS. GG-CE components, on the other hand, are packaged as Docker images and designed for container deployment on Windows, Linux and macOS hosts.
See Installation Guide for more information.