... | ... | @@ -6,23 +6,27 @@ Genebanks safeguard and make available the genetic diversity of our food crops. |
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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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**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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**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.
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![GG-CE](images/GG-CE.png)
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![GG-CE](images/collage1.png)
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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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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. It provides a complete genebank inventory management solution.
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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.
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![collage2](images/collage2.png)
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## Inventory management
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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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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.
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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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## Monitoring the collection
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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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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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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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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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... | ... | @@ -30,17 +34,17 @@ By reducing the time between data generation and its recording in the database, |
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## Barcoding the collection
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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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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.
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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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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.
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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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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.
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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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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.
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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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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.
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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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... | ... | @@ -48,93 +52,30 @@ GRIN-Global and GG-CE both support recording of trait and marker definitions and |
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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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## Requests for material
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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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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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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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## GG-CE Web application
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GG-CE is accessed through a web browser on desktop workstations, tablets and mobiles.
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![image-2](images/image-2.png)
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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
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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
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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 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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### Other data
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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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## Distribution of material
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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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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.
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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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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.
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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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## How is GG-CE different from GRIN-Global
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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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Unlike the original GRIN-Global (GG), 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. The GG Curator Tool requires a Windows operating system, making it difficult to use GG on macOS or Linux, and impossible on mobiles and tablets without custom app development.
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## GRIN-Global Curator Tool
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GG-CE provides specialized user interfaces 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. With GG, most of such functionality requires development of “wizards”.
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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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Because 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 (CT) with GG-CE. All other genebank staff should use the GG-CE Web application on their mobiles and desktops.
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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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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 any other software that uses the GG SOAP protocol.
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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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The original GG server is an ASP.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. There is no “installer”, no Windows registry entries, and no pollution of the host system with software dependencies.
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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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See [Installation Guide](installation/Installation.md) for more information.
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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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## Leftovers
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The user interface behaves in a consistent way featuring essentially three user interface component classes:
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1. *Menus* which are comprised of the left navigation pane, which is always visible and holds first end second level commands, and optional menus above the right detail pane which feature third level commands associated to the current detail page.
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2. *Detail pages*, which are displayed in the right pane. These pages are divided into *tables*, which are used to browse information organised in a list and *forms* which are used to capture information provided by users.
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Table rows can be selected to create groups. When a list element refers to a specific entity the cell contains a link to that entity, such as an accession number in an inventory list. The list header allows hiding and sorting columns, this selection is stored as a preference associated to the specific user. When relevant, lists feature a plus sign button to enable users to create a new entry.
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Forms are implemented as pages, when available as a first level choice, or overlays, when the form references an entry in a table. Some forms feature an expanded area under the control which includes the label and input area which can display documentation regarding the control; this feature is not yet globally implemented, but could be key in providing reference documentation in-app. |