Tutorial: Tour of a Gene Inspector Notebook

One of the central components of the Gene Inspector is the GI Notebook. The notebook is a file created by the Gene Inspector that serves as a place for you to take notes about experiments, design posters or slides for presentations, and as a receptacle for output from sequence analyses performed by Gene Inspector. This tutorial will take you through some of the features of a GI notebook and together with Tutorial 2: Editing Sequences and Tutorial 3: Using Analysis Setups will serve as an introduction to the program.

  1. Double-click on the Gene Inspector® to start the program. You will see a new empty notebook window called Untitled. This empty notebook can be used to hold any new analyses you do. We will not use it right now but will use a previously created notebook. Choose File Open… which will allow you to open a Gene Inspector file. The checkboxes and other details of the dialog box will be discussed in other tutorials. For now, choose the notebook file in the Gene Inspector® folder which is named “GI Notebook Tour” and press the Open button to open the document. It might take a bit of time for the notebook to open as it sets up all the bookmarks and other navigation tools used in this particular notebook. You will see Figure 2.
    Figure 2: The “Tour” Notebook

  2. This special notebook is designed to demonstrate the kinds of uses you might have for the GI Notebook in your own research. The GI Notebook is basically a word processor with many special features designed to facilitate its use in research. Background text (starting with the word “Objectives” in this case) can be entered and edited just as in a standard word processing program. Using the Format menu in combination with the items in the GI Notebook’s ruler allows you to do many of the standard manipulations you expect in a word processor. The Notebook menu has many special features unique to the Gene Inspector. Since this tutorial is meant to be an overview, it will illustrate some of these features but will not go into details of how to create them – see elsewhere in the manual for that.
  3. The title with the colorful border across the top of the notebook is a text object, into which the title text was typed. Text objects (sometimes called sidebar text) are extra blocks of text you can create in addition to what is in the background (body) text of your notebook. Text objects can be located any place on a notebook sheet and can be any size, from tall and skinny to short and wide, like the text object containing the title here. We have placed a red, blue, and green frame around the text object to make it stand out.
  4. The small elliptical object to the left of the word “Objectives” is a graphic object that was created in another program and pasted into the notebook to serve as a recognizable marker – in this case as a graphic that can easily identify the location of a bookmark. Graphic objects like this one can be stored within the notebook for easy access. Choose Notebook Tool Extensions dot marker. The mouse cursor will change to an (tool extension pointer). Click the mouse button on the notebook sheet to the right of the background text. A new “dot marker” appears. You can add tool extensions of your own creation easily as a means of storing graphics (and other objects) you might want to use repeatedly.
  5. Bookmarks can be used to navigate to different locations in the notebook. Choose Notebook Bookmarks Analyzing the Peptide. This bookmark will take you to a location in the notebook which contains peptide analysis results. These analyses were generated by the Gene Inspector and represent the results of analyses of a peptide coded for by the DNA being cloned in the cloning project that is the subject of this notebook. Performing analyses is discussed in Tutorial 3: Using Analysis Setups. For this tutorial we are focusing just on the GI Notebook.
  6. Let’s return to the top of the notebook again by choosing Notebook Bookmarks Objectives. Since bookmarks can be given meaningful names and attached to any object in the notebook, they can be used as a very convenient way to navigate through a great deal of information. You might even choose to create a bookmark called “current” and place it where you are currently entering notes. This bookmark can then be moved at the end of each day and still be accessible through the bookmark menu where it will transport you to the last location you were working.
  7. In addition to the standard styles you find in most word processors (like Bold, Italic, etc.), the Gene Inspector has additional styles, including one called Conditional Text (see the Format Style menu). This text can be shown or hidden. Choose Notebook Display Show Conditional Text. Previously hidden text is now displayed. In this particular notebook, we set the conditional text to have green, bold, and strikethru attributes. Conditional text can be hidden or shown whenever you want to do so by choosing the appropriate menu items. Leave the conditional text showing for the remainder of this tutorial.
  8. The Gene Inspector also allows you to define your own styles and add them to the Format menu. Style Sheets can be used to define the appearance of text as well as the appearance of analysis objects in the GI Notebook. Note that the word “Objectives” at the start of the background text has its own unique style, which suggests that it is a section title. You can duplicate this style for any other text in the notebook because a “Section Title” style has previously been defined. Choose a different word in the background text and then select Format Style Sheets Section Title to convert the selected text into the new style. Once you have created a style sheet it can be used from within any notebook you open – it becomes part of the application’s menus. Creating style sheets is described in Tutorial 10: Creating and Using Style Sheets.
  9. Use the vertical scrollbar on the right side of the notebook window to scroll down to the next notebook sheet that says Sequencing Subcloned Segment of pBG123. The descriptive text on the left side of the notebook page discusses the current set of experiments, while the CodonPreference data analysis on the right indicates a possible problem in the sequencing project (see the January 28th notes). The ability to mix your notes with analysis results and other notebook objects provides a convenient way to keep a running commentary on your experiments – just as in a paper lab notebook, but with added flexibility and convenience.
  10. Scroll down the page further and you will see a scanned image of a restriction digest gel. Note also that lane 11 in the legend has conditional text which is actually part of this text object. This is another use of a text object (the notebook title was the first example). Also note that the figure legends for the figures in this notebook are actually text objects. Text that is in a text object will not flow with the background text when the background text is edited.
  11. Scroll down to Figure 3 (or use the Notebook Bookmark menu to go to the Figure 3 bookmark). Notice how specific parts of a figure can be indicated and referred to from within the background text.
  12. Scroll down to notebook sheet 4a (or use the “Subcloning the Coding Sequence” bookmark) to see how restriction digests were used to identify an appropriate region of the DNA for subcloning.
  13. Looking further down on sheet 4 of the notebook will show you Figure 3. These are aliases. Just like the Finder’s aliases, they point to another location. In this case the aliases point to appendix objects, which can contain large amounts of data that you might not want directly in your notebook, but do not want to discard either. Double-click on the icon in the left part of the alias which says “Features of pBG123-2”. It will open up a new window containing the appendix to which the alias points. This appendix contains a “features view” of the sequence being cloned. A features view is a kind of notebook object the Gene Inspector uses to display formatted sequence information. Scroll down the sequence to see how different features can be labelled and highlighted in different ways. Close the appendix by clicking in the close box at the top left corner of the appendix window.
    Figure 3: Notebook Aliases

  14. Appendices, like bookmarks, are also available through a menu. Choose Notebook Appendices Assaying CAT Activity. This appendix is really just a text object (yes! another use for a text object) that has been moved to the appendices for this notebook. The advantage of placing a protocol like this in the appendices instead of just leaving it in the notebook is that it can now be accessed from anywhere in the notebook by choosing it from the menu. You might also choose to store buffer recipes in the same way. Putting commonly used information in appendices makes the information available from anyplace in the notebook. Look at some of the other appendices to get an idea of how you might be able to use appendices. Close this appendix window when you are done looking at it.
  15. Choose Notebook Bookmarks Define Promoter Behavior. This section of the notebook contains a table that was created using the notebook’s table tool to create the table. Tables present a useful way to organize experimental information. In this case the table is displaying the data from a particular experiment.
  16. You might create a table for repeated use (e.g. for identifying lanes in gels) and add it as a tool extension, as explained elsewhere in the manual. To see how this works, choose Notebook Tool Extensions gel table and click the mouse in the notebook to place a new gel table. The table will be placed with its top left corner at the location of the mouse click. Tool extensions provide an easy way to keep frequently used objects, whether they be graphic objects, tables, or even analyses.
  17. Feel free to explore other aspects of this notebook to see how they might be useful to you in your work. Notice how the Gene Inspector sequence analyses are integrated with the discussion and experimental results. This provides an easy way to keep track of all your work in one place, rather than having to run multiple applications, each with its own purpose.

When you are finished exploring the notebook, close it by choosing File Close or by clicking the close box in the top left corner of the window. When asked if you want to save changes, just say Don’t Save, so that others can go through this tutorial in the future.

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