Case Study

Genesys PGR

A global informational hub
of the world’s crop diversity
exploration


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Managed by the Global Crop DiversityTrust
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Foreword

Research data is usually boring, unattractive, and not user-friendly. But it doesn’t have to be.

Do you want to know how we helped create a user-friendly online platform where genebanks share information about сrops and trees diversity conserved worldwide? Read below.

Story

Aimprosoft has been working on an online platform called Genesys for the Global Crop Diversity Trust since 2013. The Crop Trust is an international organization dedicated to conserving and making available crop diversity.

“Сrop diversity is essential for life on Earth. It underpins nearly everything we eat and drink. But it’s rapidly disappearing.”

Global Crop DiversityTrust

Genesys is an online platform where you can find information about Plant Genetic Resources for Food and Agriculture (PGRFA) conserved in genebanks worldwide. It is a smart, centralized and exhaustive single entry-point through which users can access accession-level data from genebanks for a variety of purposes.

2010 Genesys is originally implemented as a PHP website
2013 The Crop Trust contracted Aimprosoft to implement
a new version of Genesys in Java
2015 Java version of Genesys goes live
2019 React website replaces JSP
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Project team:
2 Backend developers, 1 Frontend developer, 1 QA, 1 PM

In progress since:
March, 2013

Objectives

Building a global database is a painstaking process that takes many years. During the upgrade process, we were careful to keep the data safe and the website fully functional.

We have been working alongside the Crop Trust team to reach the goals of the platform:

  • enable genebanks to share information about their crop collections
  • allow plant breeders to identify material in genebanks for developing new varieties resistant to pests, diseases and changing climatic conditions.
  • Easy access to genebank data lies at the heart of the platform. Our goal was to make Genesys fit for simple data entry and exploration across the expanding database.
  • Data providers and users from across the world access the platform. It must be fast and secure.
  • The ecosystem of frameworks and libraries continues to evolve. Genesys must keep up to date to stay relevant.
“The team at Aimprosoft is instrumental at keeping Genesys attractive to our users and data providers. Together we have built an open, fast and secure platform that provides researchers and breeders with the data about plant material in genebanks worldwide.”
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“The team at Aimprosoft is instrumental at keeping Genesys attractive to our users and data providers. Together we have built an open, fast and secure platform that provides researchers and breeders with the data about plant material in genebanks worldwide.”
Matija Obreza, Crop Trust
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UI / UX Design

UI/UX development was based on user stories, and user flows thoroughly built on the client’s side.

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Target audience

Genesys connects two distinct groups of stakeholders (1) data providers to the platform: national, regional and international genebanks and (2) breeders, researchers, and policymakers who use Genesys to inform their own work.

It was imperative for us to allow easy access to the database and to keep the data exchange running.

User needs

  • genebanks are able to easily update the database
  • users are able to explore and request samples from genebanks
  • сatchy, mobile-friendly UI
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Development

Backend

Genesys was implemented using Spring MVC and JSP and in 2018 it was ready for an upgrade. In the implementation of the Genesys Catalog project we explored new technologies: React for the frontend and REST APIs at the backend. Since the frontend and backend were strongly coupled in the original project, the task was to migrate to React. Existing entry points had to be migrated from MVC to REST and include the functionality of the Catalog project.

Stack

  • Eclipse Jetty
  • MariaDB
  • mySQL
  • Hibernate
  • Elacticsearch
  • Hazelcast
  • Asciidoctor
  • Amazon S3
  • Liquibase
  • QueryDSL
  • Spring
  • OAuth 2
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    Frontend

    With over 4M entries in the database and increasing in number, it is highly important for users to reach the required info piece as quickly as possible. We needed a fast website.

    React and Angular were considered for implementation of the new website where server-side rendering was a key requirement. On one hand, Angular reduces the amount of JavaScript code required for progressive web applications, but React is more convenient to use with existing Javascript libraries.

    The successful implementation of Genesys catalog project convinced us to move forward with React.

    Stack

  • React
  • Webpack 4
  • i18n
  • Redux
  • SCSS
  • d3.js
  • Material UI
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    Features

    Full-text search

    Finding information about a particular record in a large database can be exhausting for users. We wanted to design the platform so that a user can find an accession in a simpler way. Elasticsearch turned out to be a great solution that allows for full-text search and filtering for specific values.

    Visualization with interactive maps

    Taking into account that the human brain perceives visual content easier than long tables of dry data, we needed a modern Javascript solution for interactive maps that can integrate with Genesys APIs.

    Thus, from an ordinary map, it turned to a visual display channel for users, helping get the information more easily and even help institutions to better plan a logistic.

    Developing the platform on the modern libraries and frameworks, we needed a solution that supports interactive maps based on JavaScript so that we could use it via API. We implemented a map-based search for seekers to explore the provenance of crops based on Leaflet, a JavaScript library for interactive maps.
    The map shows locations of where the samples of crops were originally collected. Users can select a place on the map with an Area selection button and see locations mapped with green spots. After filtering accessions, a map with selected accession indexes associated with a particular area will appear before them accordingly to the required area or across the globe. A user is referred to the accession details page by clicking on the index.
    Users can set a specified location of provenance knowing accession geodata as latitude and longitude and are allowed to select an area to find out which cultivars were originated there. Each accession contains information about its origin, soil, climate, in which weather conditions it was grown, etc.
    Thus, from an ordinary map, it turned to a visual display channel for users, helping get the information more easily and even help institutions to better plan a logistic.
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    Filter by climate

    How plants grow in an area is heavily influenced by the quantity of precipitation, temperature, wind, and water vapor, etc. it is important for breeders to make their choice based on the climate conditions.

    Many cultivars grow in several locations worldwide in a similar climate to that of the place of origin. That’s why we made climate filter functionality that is a starting point in the search for cultivars.

    Users can configure the map, setting the preferred temperature and precipitation values with a slider. We added twelve essential climate layers with current and future climate conditions based on global climate data from WorldClim.org. Users can configure the map layer transparency, putting one layer over another to see their correlation. For example, if users put on the temperature layer and a slightly transparent precipitations layer above it, they can visualize selected climate conditions.

    Map configuration

    By clicking on the Accession list button at the bottom, users are redirected to the list of accessions sourced from the locations of the selected climate conditions. You can see all the details neatly structured in one place by clicking on the accession.

    Now you can look into the complete information and choose a sample for request. Users can sort cultivars by climate conditions and see climate visually at the origin with precipitation on colorful diagrams.

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    Saved filters and maps

    Everybody knows it’s tedious having to check off filter settings again and again. We tried to provide users with a shortcut to finding what they are looking for.

    The ability to save filtered content in the browser reduces the search time of users. That’s why we made it possible to save accession filter settings in order not to set up again when the browser is reopened. The same feature is available for climate maps.

    My list

    Researchers and breeders can request samples of cultivars from select genebank. Two fields are required for a successful search: accession numbers and code of holding institute. You can request multiple accessions from different genebanks at the same time.

    Another appropriate way to make a list of accessions for the request is finding them on the map. The map-first way of search allows starting with geo conditions, which is a decisive factor for many breeders.

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    Image handling

    Unoptimized image quality and size result in high bandwidth usage while browsing the website. We introduced gradual image resampling from high to low resolutions for thumbnails served by the website.

    The visibility sensor helps determine when a user is ready to see more images of samples and calls algorithms to action. This prevents fetching images that are not visible on screen.We made it work smoothly without long loading times for users.

    Genesys API

    Gathering data about all crops is a labor-intensive and noble cause at the same time.

    How do we engage institutes in data sharing? By providing them with simple solutions that simplify the process.

    The Genesys platform offers APIs and allows using a Java-based Anno upload tool for quick data contribution. We made the Anno app downloadable to convert users’ Excel and CSV files and database SQL queries to Multi-Crop Passport Descriptor format (MCPD). After that, saved data goes to the Genesys platform for publication.

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    Results

    • As the result of cooperation with the Crop Trust, Aimprosoft significantly contributed to a platform of global importance.
    • Due to the tireless efforts of Crop Trust’s team and Aimprosoft’s technical implementers, users are now able to explore data of over 4M plant samples.
    • The project experiences a permanent improvement. We are going to move forward.
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    Millions of records structured in a complicated manner, but you want to search fast. Is that about you?

    Contact us to discuss how we can help you.




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