Thank you for trying Utopia Documents. This guide is not a complete user manual, but a quick overview of the main functionality to get you started.
When you first run Utopia Documents, it will start up with an 'empty' document window, showing just the Utopia logo as shown above. Of course, it will look a little different depending on whether you're running the software on a PC or a Mac, but the interface is essentially the same whichever platform you're using.
You can use Utopia Documents in the same way as any other PDF reader, such as Adobe Acrobat Reader or the Preview application on a Mac. You can open a file in one of three ways: 1) click on the folder icon on the far left of the toolbar, 2) select 'Open' from the File menu, or 3) drag and drop a file from somewhere in your file system on to the Utopia Documents window. The other controls in the toolbar allow you to tailor the display of the document to fit your screen size and viewing preference. You can also find these options by right-clicking or looking in the View menu.
Although you can use Utopia Documents to look at any PDF file, the software really comes into its own as a reader for scholarly papers in the field of biochemistry. In order for the software to function properly, you'll need to have a working network connection: you'll be warned when you open a file if it's not possible to connect to the online services that make the software interesting. The rest of this guide assumes you're reading one of the articles from the Semantic Biochemical Journal by Portland Press.
The application's workspace is split into three main panes: the PDF file itself is displayed on the left, a 'pager' is displayed at the bottom, and a light-blue sidebar to the right. The pager allows you to scan back and forth through the document and to move rapidly from one page to another. The arrow keys move you page by page, and clicking on one of the thumbnails in the pager takes you directly to wherever you've selected. The sidebar allows you to explore whatever material you're currently reading in more depth, by displaying additional information about the biochemical objects and concepts contained in the paper.
Utopia Documents provides two easy ways to find additional information about biological and chemical terms in your document. The first is to select a term of interest in the paper itself; either by double-clicking on a single word or highlighting a word or phrase with the mouse. in the sidebar to the right, you'll see the term (or terms) appear, and Utopia Documents will begin to search for definitions and related database records. These will appear as 'sticky notes' as and when they are found. (The speed at which these appear will depend on the speed of your network connection, and also on the speed of the external databases providing the information; an indicator in the upper right of the window shows the progress of the current search). Alternatively, if you'd like to search for something that isn't explicitly mentioned in the paper itself, simply type the phrase into the 'Look Up' box at the bottom of the sidebar. To stop a search, press the 'Cancel' button at any time, or make a new selection in the document.
As well as looking up terms as you read through a paper, Utopia Documents allows you to see extra information and auxiliary data that have been added to a paper by the Biochemical Journal's editorial team. These are not stored in the PDF document itself, but are instead are fetched from Portland Press' servers whenever you read a paper from the Semantic Biochemical Journal. This means that this extra information and data is always up to date, and may change from reading to reading. To see these annotations, simply open a paper from the Semantic Biochemical Journal with Utopia Documents - if it has been annotated (all papers published after 10th December 2009 will be) then the software will retrieve the latest annotations and apply them to the paper you're reading.
These annotations added to the document by Portland Press are indicated in two ways: in the pager, you'll see a small red flag on the corner of each page containing extra information, and on the page itself the annotation will be marked with small red glyphs in the left and right margins. The darker the glyph, the more annotations are present in that region of the page. Pointing at a marker or on the same line as a marker with the mouse causes the annotated regions of that line to be highlighted, and selecting one of these regions with the mouse will display the additional information associated with that region in the sidebar.
In some cases, an annotation may not just provide additional information in the sidebar, but may indicate that additional interaction with document is possible. These regions are marked by a much longer glyph in the margins surrounding the annotation. When you point at one of these regions with the mouse, additional controls will be shown, enabling you to interact with that area. The 'play' button fetches the data and starts the visualisation, and the 'expand' button pops the visualisation out into a new window. The next sections briefly describe each of the visualisation styles.
If the region annotated represents a molecule, click and drag with the mouse to rotate the view, or hold the control key (or command key on a Mac) to zoom in and out.
If the region annotated represents a protein sequence or set of sequences, use the mouse to scroll through the sequence, or click and drag to insert and remove gaps within the sequences.
If the region annotated represents a set of numerical data, it wil be shown as a table of the information. Use the mouse to select which data you would like to plot, and click the 'plot' button to see the data as a 2D scatter-plot. Individual data items can also be edited - click the 'plot' button again to toggle between the two views of the data.