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# GRIN-Global Community Edition Overview
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# GG-CE Overview
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**GG-CE** assists in the internal data management of genebank collections. The primary objective is to capture and make use of data across routine genebank operations: acqusition, management and monitoring, and distribution of material in the collection.
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###### *What is GRIN-Global Community Edition?*
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Only select aspects of the data in GG-CE are shared with external users (e.g. via Genesys).
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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.
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## Inventory management
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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.
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Genebank collection management primarily deals with what, in what form, how much, and where plant genetic resources **are physically** in the bank. 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.
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**GRIN-Global Community Edition** (GG-CE) is a freely accessible, open-source software solution, designed for genebanks to store and manage all aspects of information 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.
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The GG-CE database 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.
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![GG-CE](images/GG-CE.png)
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GG-CE provides tools for technicians to update the database as they go about their daily work in the genebank: from acquisiton of new material, viability testing, to distribution of material to users.
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**GG-CE** is an evolution of the original GRIN-Global system, which was based on the classic Germplasm Resource Information Network (GRIN) software. GG-CE features a **fully developed database model** that addresses most genebanks’ data requirements. It provides a complete genebank inventory management solution. Our primary objective is to enable technicians to **capture and make use of data across all genebank operations**, from acquisition, management and monitoring of material in the collection, and its distribution to clients.
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## Monitoring the collection
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## Inventory management
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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.
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Genebank collection management primarily deals with what, in what form, how much, and where plant genetic resources **are physically** in the bank. 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.
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Planning and prioritizing of monitoring activities relies on having access to the most recent and current information about collection state.
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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.
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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.
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## Monitoring the collection
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Therefore, GG-CE provides tools that guide and support technicians during their routine oprations, 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.
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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.
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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.
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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.
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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.
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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.
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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.
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## Barcoding the collection
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New material is added through acquisition, rejuvenation or regeneration of material, 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 bank.
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More material is added to the collection through acquisition, rejuvenation or regeneration of material, 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 bank.
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Use of barcoding for every physical lot in the bank 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.
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Barcoding is absolutely essential and GG-CE comes with best-practice **label templates including barcodes** ready for use. GG-CE supports barcode scanning on mobiles, tablets and desktops.
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## Passport and trait data
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## Passport, trait and marker data
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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 bank, since material is often given a new identifier.
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GG-CE support for the acquisition process ensures that key identifiers are captured as soon as the material arrives at the genebank and passport data can more reliably be linked to the correct inventories. This enables genebanks to proceed with introduction processes while the data itself may not yet be available.
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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 low level of detail of documentation of material in the bank, since material is often given a new identifier. GG-CE support for the acquisition process ensures that key **indentifiers** are captured as soon as the material arrives at the genebank and passport data can more reliably be linked to the correct inventories.
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Curation and updating of passport data continues long after the acquisition itself, as the provider of material makes updated and curated information available.
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Curation and updating of passport data continues long after the acquisition itself, as the provider of material makes updated and curated information available (e.g. in [Genesys](https://www.genesys-pgr.org/)). GG-CE enables genebanks to proceed with introduction processes while the data itself may not yet be available.
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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.
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## Material requests
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GG-CE provides the **MCPD view** of accession data and also allows for direct publishing of accession data to Genesys.
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GG-CE communicates with other systems, such as Genesys, the latter can be used as a public portal to enable users to order gene bank material electronically. GG-CE will take care of recording the requests and publishing to Genesys the updated passport data inventory.
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## Requests for material
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## The application
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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 for both external clients (distribution) and internal use (for regeneration, monitoring) and supports technicians in fulfilling the requests.
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**GG-CE** is deployed as a web application comprised as two main components: a *server* and a *client*. The server implements the main business logic and takes care of storing the application's data. The client provides the user interface to the user's browsers and communicates with the server to persist state.
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Maintaining a full 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.
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The main interface is the GC-Client which is accessed through a web browser. The server does implement a user interface, but it is dedicated to administrative tasks performed by gene bank technicians and managers.
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Genesys is commonly used to provide public access to accession data and enable 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.
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The GG-CE-Client user interface is divided into two distinct areas: a left *navigation pane* which contains a hierarchical list of commands and a right detail pane that displays the page corresponding to the selection in the left pane.
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## GG-CE Web application
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![application](../documenting/images/application.png)
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GG-CE is accessed through a web browser on desktop workstations, tablets and mobiles.
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The left navigation pane represents the main gene bank areas that the application documents.
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The web application is subdivided along the different areas of gene bank operations and provides specialized tools for each section.
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*Passport data* deals with accession level data. It is possible to consult the list of all accessions documented in the gene bank, including information regading their backup, core collection and web published status. It is also possible to consult the Multicrop Passport Descriptors (MCPD) associated with each accession. There is an option to display a summary of accessions grouped by a number of characteristics. Finally, one can check in progress, pending and completed actions related to accessions.
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### Passport data
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*Passport data* deals with accession level data. It is possible to consult the list of all accessions documented in the gene bank, including information regarding their backup, core collection and web published status. It is also possible to consult the Multicrop Passport Descriptors (MCPD) associated with each accession. There is an option to display a summary of accessions grouped by a number of characteristics. Finally, one can check in progress, pending and completed actions related to accessions.
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### Inventory
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*Inventory* deals with the management of packets, cryo tubes or plants in the field, it allows gene bank staff to track where germplasm is currently stored, deployed, for what purpose and to which accession it belongs. This application section provides the key functionality for managing resources in the gene bank. It is possible to have a summary of inventories subdivided by a number of variables. One can consult actions associated with germplasm which are in progress, pending or completed. It is possible to check available amounts and availability status on germplasm, also by scanning barcode labels. Finally, it is possible to create new germplasm records by importing data from spreadsheets or creating new acquisitions.
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*Distribution* deals with material requests, either internal to the gene bank or for external requestors. One can see the current list of pending requests, verify request items via barcode scanning, print retrieval lists by scanning the order barcode, or consult material requests recieved via the Genesys website.
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### Distribution
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*Distribution* deals with material requests, either internal to the gene bank or for external requestors. One can see the current list of pending requests, verify request items via barcode scanning, print retrieval lists by scanning the order barcode, or consult material requests received via the Genesys website.
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### Seed viability
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*Seed viability* deals with the scheduling and data capture of seed viability checking. It will select gerplasm which is due to be tested, prepare the material order, associate a viability rule and record observations. The actions associated with the testing activities can also be managed by this option. This set of features can be used to ensure the gene bank keeps a sufficient germplasm quantity before germination levels fall below safe rates.
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*Seed viability* deals with the scheduling and data capture of seed viability checking. It will select germplasm which is due to be tested, prepare the material order, associate a viability rule and record observations. The actions associated with the testing activities can also be managed by this option. This set of features can be used to ensure the gene bank keeps a sufficient germplasm quantity before germination levels fall below safe rates.
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*Taxonomy* deals with the scientific classification of material stored in the gene bank.
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### Other data
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*Crops* and *Trait data* deal with the evaluation of material stored in the gene bank.
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*Taxonomy* deals with the scientific classification of material stored in the gene bank.*Crops* and *Trait data* deal with the evaluation of material stored in the gene bank.
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*Geography* provides a common geographic administrative level information standard which can be used in the other application areas when referencing locations.
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*Methods* is an entity that groups together a set of characteristics and contexts under a single definition which can be associated with actions applied to germplasm. It includes reasons for performing actions, plant anatomical part definitions and geographic administrative information and coordinates.
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*Cooperators* is an address book and information resource on all staff which contributes to data handled by the application. It is particularly important since all information records in the application come with a time stamp and the reference to the staff that created it.
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*Cooperators* is an address book and information resource on all staff which contributes to data handled by the application. It is particularly important since all information records in the application come with a timestamp and the reference to the staff that created it.
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*Admin tools* collects all functionality needed for application configuration and ancillary data management. This set of tools is only available to GG-CE Administrators.
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## GRIN-Global Curator Tool
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The GRIN-Global Curator Tool allows for convenient importing of bulk data and updating of large numbers of records. These are common tasks for the genebank data manager, the only person to install and use the Curator Tool (CT) with GG-CE. All other genebank staff will use the GG-CE Web application on their mobiles and desktops.
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## Deployment
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GRIN-Global is divided into two main software components: the *server* and the *client*.
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![server-client](images/server-client.png)
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The server, **GG-CE-Server**, manages the application business logic, interacts with the **database** which stores the application data, and with a **file volume** to store user-uploaded files and documents.
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Clients, like the **GG-CE-Web** client that provides a web user interface to the application, communicate with the server. The 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 any other software that uses the GG SOAP protocol.
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GG-CE components are packaged as Docker images and designed for container deployment on Windows, Linux and macOS hosts. This makes it easy for IT departments to deploy, manage, backup and upgrade individual components automatically.
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## Trying out GG-CE
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**GG-CE Test Environment** is available at[ https://demo.ggce.genebanks.org](https://demo.ggce.genebanks.org/). Please contact us at [helpdesk@grin-global.org](mailto:helpdesk@grin-global.org) to request access to the Demo GG-CE!
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Please explore https://gitlab.croptrust.org/grin-global/support for documentation and assistance.
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## How is GG-CE different from GG?
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Genebank staff interact with the original GRIN-Global using the **Curator Tool** (CT). CT requires that every user installs MSSQL Express engine and the correct version of the .Net Framework. IT departments in most organizations do not grant Administrator permissions to users and do not allow installation of any “additional” software on their computers. In larger organizations, updating the CT across the network is not a trivial task.
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GG-CE is a web application and can be accessed without installation of additional software, but can still be accessed with the Curator Tool. Usually only the genebank data manager will install and use the CT.
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The original GRIN-Global Server is an ASP.Net web application that requires a Windows Server and IIS. GG-CE components are packaged as **Docker images** and designed for container deployment on Windows, Linux and macOS hosts. There is no “installer”, no Windows registry entries, and no pollution of the host system with software dependencies.
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See [Installation Guide](installation/Installation.md) for more information.
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*Admin tools* collects all functionality needed fo application configuration and ancillary data management. This set of commands is only available to users which have the specific role of application administrators.
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## Leftovers
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The user interface behaves in a consistent way featuring essentially three user interface component classes:
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