====== Creating a Construct ======
  * Open GeneDesigner.  
      * Double clicking on the program icon will create a new project, containing a single (empty) new construct.  
      * Double clicking on an existing project will open that project.


===== The Project Window =====
{{:guide:screenshot_a.jpg}} 
  * An open project has two windows
     * [[ui:library_explorer | Library Explorer]].
     * [[ui:construct_editor | Construct Editor]].
 
  * The [[ui:construct_editor | Construct Editor]] is divided into two sections: 
     * On the left, elements are displayed in the [[ui:navigation_pane | Navigation Pane]] in a hierarchical tree.
     * On the right, elements are displayed in the [[ui:workspace_pane | Workspace Pane]] in a linear arrangement.

===== Adding a New Construct to a Project ===== 
  * Select "add a new construct" from the "Add" button on the bottom left corner of the Construct Editor.  You will be prompted to  choose 
     * a construct name
     * whether your construct is circular or linear
     * a codon table
     * add notes, if any
{{:guide:screenshot_b.jpg}}
===== Adding Elements to a Construct =====
 
=== Adding new elements ===
  * New sequence elements can be added to a construct by dragging an element out of the New Elements Tab in the [[ui:library_explorer | Library Explorer]] and into the desired position within the construct.
       * When dragging in a new DNA element you will be prompted to type / paste a name and DNA sequence for the new element. 
       * When dragging in a new amino acid (AA) element you will be prompted to type / paste a name and amino acid sequence for the new element. 
       * When dragging in a new open reading frame (ORF) element you will be prompted to type / paste a name and DNA sequence for the new element. You will also be prompted to select a reading frame and the DNA sequence will be automatically translated. 
  * New sequence elements can also be added to a construct using the "Add" button at the bottom of the Construct Editor.  Elements will be created within the "Elements Not in a Construct" section of the Navigation Pane, and may then be dragged into the desired position within the construct.

=== Adding existing elements from the Library Explorer ===
  * Sequence elements can be added to a construct from the [[ui:library_explorer | Library Explorer]] by dragging existing elements out of the [[ui:Design_toolbox | Design Toolbox]] and into the desired position within the construct.
    * Dragging a folder from the [[ui:Design_toolbox | Design Toolbox]] will add all of the elements within that folder as a [[ui:groups | group]] within the construct.
{{:guide:screenshot_c.jpg}}

=== Adding sequences from other files on your computer ===

     * Dragging a fasta file from elsewhere on your computer into the desired position within the construct.
       * If the fasta file contains more than one sequence, the sequences will be added as a [[ui:groups | Group]]
     * Dragging a genebank file from elsewhere on your computer into the desired position within the construct.
       * If the genbank file contains more than one sequence, the sequences will be added as a [[ui:groups | Group]]
  * Sequence elements can be dragged into either the [[ui:navigation_pane | Navigation Pane]] or the [[ui:workspace_pane | Workspace Pane]].

===== Manipulating Elements within a Construct =====
  * This can be done within the [[ui:icon_view | Icon View]]  

===== Saving a Construct into your Library =====
  * A construct or sequence element can be saved for use in other projects by dragging its icon from the [[ui:navigation_pane | Navigation Pane]] to the [[ui:library_explorer | Library Explorer]].
    * A construct or sequence element can be added to an existing folder in the [[ui:Design Toolbox]] or [[ui:Vectors]] window.
    * A new folder may be created in the [[ui:Design Toolbox]] or [[ui:Vectors]] window by selecting the green "Add" button at the bottom of the Library Explorer
  * A construct or sequence element that has been saved into the [[ui:library_explorer | Library Explorer]] will be available for use in any new construct.