Using This Template This protein interaction diagram template is designed for biology and biotechnology researchers who need to document the interactions of proteins and cellular pathways. The purpose of this help document is to describe the features of the template and its contents. What is it? In biochemistry, a metabolic pathway is a series of chemical reactions within a cell, catalyzed by enzymes, which either results in the formation of a product to be used or stored by the cell, or the initiation of another metabolic. When to use it: The shapes in this template support a diagramming methodology promoted by the Alliance for Cellular Signaling (AfCS). If you wish to document your research using this method, the template provides the appropriate proteins, molecules, and interaction connectors. Contents of the Template This sample template does not open any standard Visio stencils. However, the template’s Document Stencil is open and contains the shapes used to construct the sample diagrams. You may save these shapes to your own stencil to use with other drawings. The template contains the following pages: CD40 Pathway Map (a sample drawing) G Protein Coupled Receptor (a sample drawing) Symbols Background The document stencil contains the following shape types: Molecules Proteins Interaction connectors Groupings Legends Border This document contains shapes that do not ship with Visio 2003 Standard. These shapes exist on one or more of the pages in the drawing, but they also exist on the template's Document Stencil. If you have closed the Document Stencil you may reopen it to view these master shapes. From the File menu, select Shapes, and then select Show Document Stencil. From here, the shapes can be added to your drawing. You can also copy these shapes from the Document Stencil, and add them to your own new stencil. For more information on creating Visio stencils, please see Visio Help. How to create a diagram Drag protein and molecule shapes from the stencil to the drawing and then connect them with interaction shapes. The protein and interaction shapes contain Custom Properties that you may fill in with appropriate data. After the diagram is complete, these properties may be exported to a report in various formats by selecting Tools then Reports from the Visio menu or to XML by selecting File then Save As file type .vdx. To access Custom Properties, select Shape then Custom Properties on the Visio menu. The text you enter into the Protein Name field will display in the shape. Note that you cannot type directly into the shape. This is done to ensure that the shape text remains synchronized with the Properties data. You can color code the symbols to represent cell localization by selecting the shape, then Format and Fill to edit the color. Interaction connectors will glue to the perimeters or vertices of the various shapes so that when the symbols are moved on the page the interactions will remain connected. Some of the connectors contain yellow control handles that enable you to alter the configuration of the line. For example, the Negative Control (Inhibition) connector has a control handle at the center symbol that will curve the connector if moved and another that will alter the angle of the short line at one end of the connector. You can set a symbol to display Greek letters by selecting the shape and changing its font to Symbol through the Visio menu or the Formatting tool bar. In the Custom Properties Protein Name field, type “a” for , “b” for , and so on. When you drop a shape into a Grouping shape it is automatically added to a group that will move as a unit. The border is contained on the Background page. The date and page number will appear automatically at the lower right. At the top of the page border, the title box will show the name of the page tab, so if you wish to change the text in that box, rename the page as required.
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