The Drafting Board is the main window for viewing pre-existing MAPPs or creating new MAPPs. It is the main window of the GenMAPP Program. When you start the GenMAPP program, the Drafting Board appears in this window. Closing the Drafting Board by choosing Exit from the File menu or by left-clicking on the close button in the title bar closes the program. All of the main functions of GenMAPP can be accessed through the Drafting Board itself and through the GenMAPP menus found at the top of the window.
A MAPP is a special file format produced by GenMAPP that contains a graphical representation of a biological relationship between genes or gene products. Examples of the types of MAPPs that can be represented in GenMAPP are metabolic pathways (e.g., glycolysis), signal transduction cascades (e.g., protein kinase cascades), subcellular locations (e.g., mitochondrial genes), gene families (e.g., G protein-coupled receptors) or lists of genes associated with a Gene Ontology category. MAPPs may be complex, using many lines and arrows to indicate direct and indirect interactions of genes, or they may be as simple as a list. The decision of how best to indicate relationships between genes or gene products is left up to the individual user.
MAPP files are saved with the extension .mapp (e.g., glycolysis.mapp). The files save the graphical elements of a MAPP and the gene identifiers required to view expression data and other information about the genes. MAPP files are relatively small (< 300 k) and can be easily traded among researchers.
To view a pre-existing MAPP on the Drafting Board, select Open from the File menu, choose a file from among those listed in the window, and click OK. The first time you run the GenMAPP program, the Open window displays files in the MAPPs folder installed with the program. (The installation default is C:\GenMAPP 2 Data\MAPPs.) Subsequently, the Open window will return you to the last folder used. To view a different MAPP, choose Open again. GenMAPP will ask you if you want to Save the current MAPP if you have made any changes to it. Alternatively, double-left-clicking on a MAPP file from within the Windows Explorer launches the GenMAPP program and opens that particular MAPP file. Note: A MAPP that has been made "read-only" through the Windows operating system may be opened and manipulated in GenMAPP but not saved under the same name. It may, however, be saved under a different name.
The size of a MAPP may be larger than the window in which it is contained because it was created on a large-sized Drafting Board. The Drafting Board window has scroll bars that allow you to navigate the window to see all parts of a large MAPP. To view an entire large MAPP you can zoom out using the zoom drop down box on the right side of the drafting board toolbar. Alternatively, you can go to View > Zoom and select the percent zoom you would like. You can automatically fit the MAPP to your screen by going to View > Zoom to Screen.
You can close the MAPP on the Drafting Board by clicking on the close button in the title bar of the Drafting Board window or by clicking on File > Exit. Either will close both the Drafting Board window and the program.
You may view more than one MAPP at a time by opening another instance of the GenMAPP program from the Windows Start menu. When two or more instances of the GenMAPP program are running, you may switch between different instances, and thus view different MAPPs, by clicking on the GenMAPP buttons in the Windows Task Bar. Although you can view different MAPPs in this manner, the multiple instances of the GenMAPP program do not interact. This means that you cannot move or copy objects between different MAPPs in the current version of the program, although you may duplicate objects in the same Drafting Board window. If the same MAPP has been opened in two separate instances of the GenMAPP program, changes to the MAPP will only be saved in the last instance closed.
To create a new MAPP, you may start from an existing MAPP that is displayed on the Drafting Board by selecting Save As from the File menu. By typing in a new filename and clicking the save button, you will now be working with a copy of the existing MAPP with a new name. Additions, deletions, and changes to the new MAPP can be made without affecting the old one.
Alternatively, you can create a new MAPP from scratch on a blank Drafting Board. When you first launch GenMAPP, it will open a blank Drafting Board on which you can begin to create your MAPP. If you already have a MAPP open, you can clear the Drafting Board by selecting New from the File menu. GenMAPP will ask you if you want to Save the current MAPP if you have made any changes to it.
To fill in the graphical elements of a new MAPP, you must place objects from the Drafting Board Toolbar or Object Toolbox onto the Drafting Board and manipulate the location and orientation of those tools and objects. The Drafting Toolbar contains the gene object and the drawing tools. The Object Toolbox contains pre-assembled MAPP elements. Drafting Board Toolbar and objects from the Object Toolbox are manipulated in similar fashion, so we will refer to all of them as objects. Functions that involve the placement and manipulation of objects on the Drafting Board can be accessed from the Tools and Format menus at the top of the Drafting Board window.
In addition to objects like rectangles and arrows that you may typically find in other graphics programs, GenMAPP has a specialized object called the gene. The gene object represents a biological gene or gene product and is the link between the graphic on the MAPP and information about that gene contained in the Gene Database, and your Expression Dataset. When you first place a gene on the Drafting Board, you must establish the link between the object and the Gene Database through the Gene Finder. Open the Gene Finder window by right-clicking on a gene on the Drafting Board. In the Gene Finder enter the identifier for the gene, as well as other information. For more details, see the section on the Gene Finder.
Once a gene has been given a gene identifier in the Gene Finder window, information contained in the Gene Database about that gene may be displayed by double-clicking on the gene on the Drafting Board. This opens the Backpage for that gene as an Internet Explorer browser window. Information for the gene on the Backpage may include information you entered in the Gene Finder window, annotation in the Gene Database from any tables containing the particular identifier, and data for that gene from an Expression Dataset. There will be hyperlinks to the gene's entry in the public databases that are represented in the Gene Database. Gene expression data will be displayed on the Backpage if an Expression Dataset has been chosen.
The size of the actual Drafting Board may be larger than the Drafting Board window in which it is contained. The window has scroll bars that allow you to navigate the window to see all parts of a large board. You may change the area of the Drafting Board window viewed on your screen by dragging the bottom or right edge or lower-right corner of the window. This only changes your viewable area and does not affect the dimensions of the actual Drafting Board or of your MAPP.
You may also maximize the viewing area of the Drafting Board window by left-clicking on the maximize button in the GenMAPP title bar. Again, this does not change the dimensions of the actual Drafting Board, only the viewable area of the window. If the actual Drafting Board is larger than the screen, the Drafting Board window will expand to fill the entire screen. However, if the actual Drafting Board size is smaller than your screen, the Drafting Board window will not increase beyond the size of the actual Drafting Board when you click on the maximize button.
You may minimize the Drafting Board window by left-clicking on the minimize button in the GenMAPP title bar. You can then restore the Drafting Board window to its original size and location by clicking on the GenMAPP button in the Windows Task Bar.
You may use the zoom function to change the viewable portion of you MAPP within the Drafting Board Window. Go to View > Zoom and enter the percent zoom you would like. You can automatically fit the MAPP to your screen by going to View > Zoom to Screen. You can also access the zoom function from a drop-down menu in the Drafting Board Toolbar.
The maximum allowable zoom factor for any MAPP is 250% and the miminum allowable zoom factor is 10%. The actual maximum and minimum zoom factors for a particular MAPP may be less than 250% and greater than 10%, respectively, depending on the size of the Drafting Board.
The zoom factor does not affect the size of the MAPP when printed. However, when a MAPP is exported, it will be sized according to the zoom factor showing on the screen.
You may change the size of the actual Drafting Board (as opposed to the Drafting Board window) in the Drafting Board Size window. This window can be opened by left-clicking on the View > Drafting Board Size menu or by pressing Ctrl+B. Change the numerical values for the width and height in the input boxes that appear and click OK. If you close this window by left-clicking the cancel button or the close button in the title bar, the Drafting Board size will remain unchanged.
If you are making the Drafting Board smaller than the current Drafting Board window, GenMAPP will shrink the window to the new dimensions of the Drafting Board. If you are making the Drafting Board larger than the current Drafting Board window, scroll bars will be activated so that you can scroll to the new area of the Drafting Board.
The Drafting Board size is given in centimeters. However, because screen sizes and resolutions vary, this is an approximation. The Drafting Board's initial size is 40 cm wide by 30 cm high (approximately 16 by 12 inches). Its minimum size is 8 by 6 cm (approximately 3 by 2 inches), and its maximum size is 57 by 57 cm (approximately 22 by 22 inches).
You may reduce the size of the Drafting Board to accommodate only the objects present by checking the Size to fit objects box in the Drafting Board Size window. You may want to do this before printing or exporting your MAPP because the entire Drafting Board will be printed or exported, including any unused white space. Thus, the MAPP on the screen will most likely appear to be at a different scale than the printed MAPP. The zoom factor does not affect the size of the Drafting Board and does not affect the size of the printed MAPP. However, the MAPP will be exported at the zoom factor shown on the screen.
You may also force a change in the Drafting Board size by moving objects. If you move an object so that part of it falls outside the Drafting Board (not the window) to the right or to the bottom of the board, GenMAPP automatically resizes the Drafting Board to accommodate the object up to the maximum size of the board (57 by 57 cm). Deleting an object or moving an object inward will not change the size of the Drafting Board. You cannot force a change in the size of the Drafting Board by moving an object off the top or left side of the Board at any time, or by moving an object off the right or bottom edge when the Drafting Board has reached its maximum size. In these cases, GenMAPP will just move the object back to within the confines of the Drafting Board.
The MAPP title entered in the MAPP Information window is always automatically centered at the top of the Drafting Board. If you change the width of the Drafting Board, the title will move to the new center point.
To place new objects on a MAPP, left-click on the desired object from Drafting Board Toolbar or the Object Toolbox. For line tools and ligand/receptor pairs, click the down arrow next to the icon to choose the tool. Position the crosshair at the desired location for the object and click the left mouse button again. For most objects, the center of the object will appear where the crosshair was. For line tools, this first click sets one end of the line, in all cases the plain end. A second left-click sets the other end of the line, which may contain a graphic element such as an arrowhead or receptor.
If you place an object (or move it later) so that part of an object lies outside the top or left edge of the Drafting Board, GenMAPP relocates your object to fit on the Drafting Board. You will probably have to make adjustments after this.
If you place an object (or move it later) so that part of an object lies outside the bottom or right edge of the Drafting Board (not the window), GenMAPP resets the size of the Drafting Board to accommodate the object. If the Drafting Board has reached its maximum size, the object will be relocated to a position within the confines of the Drafting Board.
To select a single object,
left-click on the object. One or more red
target boxes
will appear when the object has been successfully selected. This
deselects any other objects that have already been selected,
including any multiple selections.
An object selected singly can be moved, duplicated, or deleted. It may also be sized or rotated, depending on the object. (See the individual object under Drafting Board Toolbar or Object Toolbox for instructions on these functions.) In most cases, selecting the object puts it on top. If two objects overlap, the one placed last will be topmost.
To deselect an object, left-click on a blank area of the Drafting Board or select another object.
Multiply selected objects may be moved, duplicated, or deleted. To select multiple objects, there are two options:
The selected objects are highlighted in red and a green dotted rectangle is displayed around the farthest edges of the objects you have selected. The mouse pointer changes to an icon with arrows facing in four directions if you move the mouse anywhere over this box. Deselect all selected objects by left-clicking anywhere on the Drafting Board outside of the green rectangle. Multiply selecting objects deselects any singly selected object.
Most objects are selected when the selection box surrounds the center point of the object. Line tools are selected when either or both of the end points are surrounded. The MAPP Information Area and the Legend cannot be part of a multiple selection.
Although you can select a group of objects by either of these techniques, you cannot permanently "group" the objects together so that they are always selected together. Thus, if you wish to move a group of objects together, be careful that you have selected them all each time.
To move an object or objects, you must first select it either singly or multiply. The behavior is slightly different depending on the type of selection.
Singly Selected Objects: Most objects show one or more red target boxes when they are selected. The one at the center is the movement target. On line tools, targets appear at both ends of the line. To move the object or end of a line, hold down the left mouse button while the pointer is within the target, drag it to the new location, and release the button. The object remains selected (and hence movable) until you select something else, choose a new object from the Drafting Board Toolbar window or Object Toolbox, or click on the Drafting Board where there is no object.
Multiply Selected Objects: The mouse pointer changes to an icon with arrows facing in four directions when you move the mouse over the green selection rectangle. Holding down the left mouse button and dragging this arrow moves the green selection rectangle. When you release the mouse button, the moved objects are redrawn in their new location. Be careful! Since you may have selections all over the Drafting Board, dragging anywhere within the green selection rectangle moves all of the multiply selected objects. Multiply selected objects can be moved with the arrow keys. Each time you press the key, the object will advance a short distance in the appropriate direction.
After you move an object, you may need to have GenMAPP redraw the MAPP by selecting View > Redraw if the graphics seem corrupted or missing.
To duplicate objects that are selected (either singly or multiply), press the Insert key. The new object or objects will always appear in a selected state on top of the originals, slightly below and to the right. You now may move or change them as you would any other object.
You cannot use this function to copy and paste objects between different MAPPs. Multiple MAPPs can only be manipulated at the same time through separate instances of the GenMAPP program that are completely separate from each other. The ability to cut, copy, and paste objects between different MAPPs is a feature that is being developed for a future version of the GenMAPP program.
Many objects such as genes, labels, rectangles, ovals, line tools, curves, braces, and protein complexes can be resized. However, only singly selected objects can be resized. Generally, an object is resized by dragging one of the red target boxes that appear when the object is singly selected. For more specific instructions, see the individual object.
Some objects, such as
rectangles,
ovals,
curves, and
braces, may
be rotated.
Rectangles, ovals, and curves can be rotated through 360º; braces
may be rotated
only in 90º increments. However, only singly
selected objects can be rotated.
Generally, an object is rotated by single-clicking the object and then dragging
one of the circular target boxes
.
The rotation of rectangles, ovals and curves can be restricted to
45º increments by holding down the
shift key while dragging the circular target box. For specific instructions, see the individual object.
Objects from the Drafting Board Toolbar, such as rectangles, ovals, line tools, curves and braces, may be colored. To change the color of rectangles, ovals, and braces, right-click on the object on the Drafting Board. A Color window will open. To change the color of line tools and curves, right click on the object to open the Line Data window. Click on the Color button to open the Color window. Choose a color from the palette displayed and click OK. If you cancel out of this window by left-clicking the cancel button or the close button in the title bar of the window, you will return to the Drafting Board, and the object will remain its previous color.
More color choices can be created by left-clicking on the Define Custom Colors button. Create a new color by changing the values in the hue, saturation, and luminosity, or red, green, and blue fields. Alternatively, drag the sliders in the color gradients to a new color. To add the new color to the palette on the left side of the window, click the Add to Custom Colors button. The new color may then be chosen for the object.
For line tools, curves, and braces, the entire object will become the color you choose. For rectangles and ovals, the black outline will remain, and the object will be filled with the color you choose. Once a rectangle or oval has been colored, it cannot become transparent again (even white is a solid fill); to change it back, you would have to delete the rectangle or oval and draw another one without filling it.
The color of a label can also be changed. Right-click on a label on the Drafting Board. In the Label Data window that appears, left-click on the Font button. Choose a color from the Color pull-down menu and click OK. If you cancel from the Font window by left-clicking on the cancel button or close button in the Font title bar, or cancel from the Label data window by clicking the cancel button or close button in Label data title bar, the label will remain its previous color.
Genes change color only when data from an Expression Dataset has been applied to the MAPP. Criteria for coloring genes may be determined in the Expression Dataset Manager. You can color genes on a MAPP with different Expression Datasets by choosing Data > Choose Expression Dataset, from the menu at the top of the Drafting Board window. You may switch between different Color Sets for the same Expression Dataset by selecting a different Color Set from the pull-down menu in the Drafting Board Toolbar. Left click on the name of the Color Set you want to display on the MAPP. Each time you choose a Color Set, GenMAPP automatically applies the expression data to the genes on the Drafting Board according to the Criteria you have set in the Expression Dataset Manager. You may return the genes on a MAPP to white by selecting No expression data in the Color Set pull-down menu. If you add a new gene to a MAPP that has already been colored with an Expression Dataset, you may color the new gene by selecting Data > Apply Expression Data. If the gene remains white after you have applied the data, it means that the particular gene does not exist in the Expression Dataset chosen for display.
The MAPP Information Area is designed to display general information about the MAPP itself, independent of any Expression Datasets that may be applied to the MAPP. The Information specific to a particular Expression Dataset is displayed in the Legend.
To enter content into the Information Area, use the MAPP Information tool under Tools > MAPP Information (Ctrl+I). Information entered through the MAPP Information tool appears either as the title of the MAPP or in this Information Area. After you have entered information in the MAPP Information window for the first time and clicked OK, this area appears in the upper-left corner of the Drafting Board. It is sized automatically to accommodate the information provided. Thus, a later change in the MAPP Information may change the size of the Information Area, which means that you may have to adjust its location.
To move the Information Area, left-click
on it to select it. A movement target
appears in the upper-left corner. Drag
the target to where you want the Information Area to move. When you drop the
target, the Information Area moves to its new location. The Information Area cannot be
multiply selected, duplicated, or deleted
(with the Delete key). To
delete the Information Area, open the MAPP Information window and delete the
content from each field. The MAPP Information always appears on
top of all objects except the Legend.
You can hide the display of the Information Area in the
Options
menu. Choose Tools > Options. . ., uncheck the box next to Show
Information Area and click OK. You can restore the display of the Information
Area by returning to the Options menu and rechecking the box.
Once the Information Area is on the Drafting Board, you may access the MAPP Information window through the menu or by right-clicking on the Information Area.
Open the MAPP Information window by left-clicking on Tools > MAPP Information or by pressing Ctrl+I. You may fill in information in any or all of the following fields:
Titles for your MAPP must be 50 characters or fewer. The MAPP title can be different from the filename. The title will appear centered at the top of the Drafting Board. If the width of the Drafting Board is changed, the title will be automatically recentered on the Drafting Board.
Enter the name(s) of the individuals that created the MAPP using 50 characters or fewer.
Enter the name(s) of the individuals that are currently responsible for the content of the MAPP, if different than the Author. This field must be 50 characters or fewer.
Enter the e-mail address for the person who is willing to be contacted about the MAPP, the "corresponding author." This is usually the e-mail address of a person listed in the Author or Maintained by fields. This field must be 50 characters or fewer.
Enter the date that the MAPP was last modified. You may use whichever format you choose for the date as long as it is 50 characters or fewer.
Enter any remarks or explanations for this particular MAPP. For example, you may wish to list a reference for the MAPP or information about nomenclature or symbols used in the MAPP here. This field must be 50 characters or fewer.
If you wish to copyright your MAPP, GenMAPP will display on the MAPP the Copyright and © next to the year and entity you supply in this field. For example, if you fill in 2003, Whizbang Labs, the Information Area on the MAPP will display Copyright © 2003, Whizbang Labs. This field must be 50 characters or fewer.
Text entered in the Notes field will not appear on the MAPP, but will be available through this window. The amount of text this field can hold is unlimited. If you run out of room in any of the other fields, this is a good place to put the full information.
To save the information and return to the Drafting Board, click OK. To return to the Drafting Board without saving the information, left-click on the cancel button or the close button in the title bar of the MAPP Information window.
In contrast to the MAPP Information Area, which contains general information about the MAPP, the Legend displays information specific to the particular Gene Database and Expression Dataset being applied to the MAPP.
The Legend exists on the Drafting Board when you choose an Expression Dataset and one or more Color Sets. The information in the Legend changes automatically when you change your selections of Expression Dataset and Color Set, and sizes automatically to accommodate all the information. Thus, changing Expression Datasets or Color Sets may change the size of the Legend, which means you may have to adjust its location.
To move the Legend, left-click
on it to select it. A movement target
appears in the upper-left corner. Drag
the target to where you want the Legend to move. When you drop the target, the
Legend moves to its new location. The Legend cannot be
multiply selected, duplicated, or deleted
(with the Delete key).
The Legend always exists if a MAPP is colored but you can control whether and how it is displayed. To change its display characteristics, click on the Tools > Options. . . menu or right-click on the Legend if it is visible. To hide the Legend, uncheck the box next to Show Legend. To hide individual items in the Legend, uncheck the appropriate box. You can change the size of the font for the Legend by using the Font size pull-down menu. You can make changes to the display properties at any time by returning to the Options menu.
The Legend always appears on top of other objects.
When a single color set is selected, the Legend displays information about this Color Set, along with information about the Gene Database and Expression Dataset.
When multiple Color Sets are selected, the Legend also explains the partitioning of the gene box into multiple Color Sets, in addition to the information on Gene Database and Expression Dataset. If multiple Color Sets are selected, the Legend can display information for either all Color Sets selected, or the first Color Set. If you choose to display information for all selected Color Sets, information for the individual Color Sets will be stacked vertically in the Legend.
If multiple Color Sets are configured similarly in terms of the fold regulation and coloring, it may be redundant to view information for all Color Sets in the Legend. In these cases it may be more convenient to include only information for the first Color Set selected. This option is user-defined and can be changed in the Options menu. The information on how the gene box is partitioned will appear in the Legend anytime multiple Color Sets are selected.