.. include:: imagerefs.txt

=================
Getting Started
=================

KDXplore comes pre-packaged with a set of plug-ins that contain a wide variety of tools for activities such as data management, curation, and trial design. You can be given access to KDXplore by emailing kdxplore@diversityarrays.com and requesting a copy.

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Requirements
=============

The following will be needed to run KDXplore:

* A computer - KDXplore is cross-platform and will work on Windows, macOS, and Linux operating systems;
* Java 8 installed on your computer; and
* An internet connection for connecting to KDDart (optional).

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KDXplore Plug-ins
==================

KDXplore employs a modular architecture which facilitates plug-ins to extend it's functionality. The **Trial Manager Plug-in** may be thought of as providing the base level tools to manage trial, trait and tag data. Using plug-ins allows for easier configuration and customisation of different tools to suit a variety of user requirements.

Depending on the configuration options, plug-ins that are currently added to KDXplore appear as buttons in the middle of the **Main Window**, as highlighted in the following image.

Select a plug-in to open it. Opening another plug-in will not impact anything in the current plug-in.

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.. only:: html

    |center-start|

    .. thumbnail:: images/KDXplore/KDXplore1.png
        :show_caption: true
        :width: 70%
        :align: center
        :title: KDXplore Main Window

    |center-end|


.. only:: latex

    .. figure:: images/KDXplore/KDXplore1.png
             :scale: 70%
             :alt: KDXplore Main Window

             KDXplore Main Window

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The following table lists the plug-ins available for KDXplore and their release status.


.. list-table:: KDXplore Plug-in Availability - May 2019
   :widths: 20 1 1 70
   :header-rows: 1
   :stub-columns: 1


   * - Plug-in
     - Button
     - Version
     - Description
   * - **Trial Manager**
     - |trial_manager_btn|
     - Production
     - Phenotypic data management (offline/online), curation, QA/QC, data exploration/visualisation, and trait management.
   * - **GenXplore**
     - |gen_explore_btn|
     - Beta
     - Genotype/specimen search and inspection, parentage exploration and visualisation (tree), cross designer.
   * - **Inventory**
     - |inventory_btn|
     - Alpha
     - In depth inventory, genotype and specimen relationship exploration.
   * - **Trial Design**
     - |trial_design_btn|
     - Beta
     - Design of trials, automated or manual.
   * - **DartView**
     - |dartview_btn|
     - Coming soon!
     - Filtering and visualisation of marker and sample data as well as statistics and metadata.


.. note:: More information about each of these plug-ins can be found by navigating to the pages in the menu to the left.

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KDXplore Distributions
=============================

The current beta distribution of KDXPlore has an expiry date so when a new distribution is released, it should be downloaded to continue use. The data from the old version of KDXplore will automatically be present in the new version.

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.. only:: html

   |center-start|

   .. thumbnail:: images/KDXplore/KDXplore4.png
       :show_caption: true
       :width: 60%
       :align: center
       :title: KDXplore Expiry Dialogue

   |center-end|


.. only:: latex

   .. figure:: images/KDXplore/KDXplore4.png
            :scale: 60%
            :alt: KDXplore Expiry Dialogue

            KDXplore Expiry Dialogue

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.. note:: KDXplore cannot be opened following the expiry date and will present the dialogue from the image above. |br| The database **will** persist untouched even if the version of KDXplore expires.

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Updating KDXplore
=================

When a new version of KDXplore has been released, an update dialogue will be displayed on startup of KDXplore. In this dialogue, the update version, update link, help link and update information is displayed.

Any user that has been provided KDXplore from DArT will receive an email notification when a new version of KDXplore is available. This email will also contain a link to download the newest version. If you don't have the link or did not receive the email, you can either contact us at kdxplore@diversityarrays.com or update KDXplore manually. To check for updates manually, select the **File Menu** from the **KDXplore Main Window**, then select the *Check for updates* option.

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.. only:: html

   |center-start|

   .. thumbnail:: images/KDXplore/KDXplore2.png
       :show_caption: true
       :width: 30%
       :align: center
       :title: Check For Updates

   |center-end|


.. only:: latex

   .. figure:: images/KDXplore/KDXplore2.png
            :scale: 30%
            :alt: Check For Updates

            Check For Updates

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.. note:: Updating KDXplore will **not** affect the KDXplore database on the machine in any way; all data on the machine will persist through to the next version.


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.. _connecting_to_kddart:

Connecting to KDDart
====================

KDXplore can be connected to the KDDart platform which will allow you to retrieve and backup data from KDDart.

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.. only:: html

   |center-start|

   .. thumbnail:: images/KDXplore/KDXplore5.png
       :show_caption: true
       :width: 70%
       :align: center
       :title: KDDart Login Window

   |center-end|


.. only:: latex

   .. figure:: images/KDXplore/KDXplore5.png
            :scale: 70%
            :alt: KDDart Login Window

            KDDart Login Window

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To connect to the KDDart Database, navigate to the **File Menu** of the **KDXplore Main Window** and select the |connect_btn| **Connect Button** to open the **KDDart Login Window** as seen above. Enter your credentials and select the |login_btn| **Login Button**.


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