Projects
The first step of an analysis is to create a project and import gel images. These can be your own images, or you can use the images of the Non-DIGE Tutorial, the DIGE Tutorial or the Coverage Tutorial.
Projects are managed in the Projects window, where you can create new projects, open existing ones and view and edit the project properties. You can remove projects from your list or delete them from the disk, and you have the option to add them back if needed. Additionally, you can export projects for archiving purposes or to share with colleagues, and later restore them. Finally, you can duplicate projects or move them to different folders.
How to
Create a new project
The first time you open Melanie, the Create Project window will appear automatically. For creating additional projects:
- Click the New button on the Projects screen. If you’re already working on a project, click the Project icon in the workflow and select New project.
- In the Create Project window, enter a short Project name and choose the Project folder for saving.
- Select your desired Project type and click Create.
- Enter additional information if prompted.
- Proceed to add images to your project.
Once you have created your first project, take a moment to explore the elements of the Graphical user interface.
Project folder
You can store new projects in one of the two following folders:
- Local folder – This is the folder where projects are created by default if no Shared folder is defined. Its location, in the user’s Documents folder, cannot be changed.
- Shared folder – This is a user-specified, network accessible folder where projects can be centralized for easy collaboration with colleagues. Please consult the Project options for guidance on selecting and setting up the Shared folder.
Project type
- Single stain – Use this option for differential expression analysis of conventional 2D PAGE experiments where only one sample was run on each gel.
- Pick a stain from the drop down list or type the name of your stain. The stain information is simply for your further reference, and will not be used in the analysis.
- DIGE with internal standard – Use this option for differential expression analysis of 2D DIGE experiments where several samples were run on the same gel, one of them being an internal standard.
- The Internal standard information must be correctly specified and indicates on what image the internal standard can be found.
- Multiple stain without internal standard – Use this option for differential expression analysis of 2D DIGE or other multiplex experiments where several samples were run on the same gel, but where no internal standard was included.
- Coverage – Use this option for coverage analysis of conventional 2D PAGE/WB experiments where HCP antigen and anti-HCP antibody reactivity were detected on different supports (gel and blot, respectively).
- Coverage DIGE/DIBE – Use this option for coverage analysis of 2D DIGE or 2D DIBE experiments where HCP antigen and anti-HCP antibody reactivity were detected on the same support (gel or blot).
- Choose the stain/dye for the primary images (HCP antigen). If your experiment uses different dyes for the primary images (e.g. in the case of dye swap for DIGE), then select the Mixed option. This lets you assign your primary images manually in the Quality control step.
NOTE
If you create a Single stain, DIGE with internal standard or Multiple stain without internal standard project, make sure to read the Expression Analysis Guide for further documentation.
If you are not sure whether differential expression analysis or coverage analysis is most appropriate for your project, you can read this article.
Close a project
Click the Close project icon at the top right of the Melanie window to close the current project and return to the Projects screen.
Open a project
To open a project, double-click on its name in the Project list in the Projects screen, or click the More icon in front of its name and choose Open.
View and edit project properties
The Project list provides an overview of your created or opened projects, displaying their Name, Type, and Reference Stain. You can also see the Folder where each project is stored, with its Location identified as Local, Shared, or Other. Additional details include the Created and last Opened dates, Size on disk, Creator, and the number of Gels and Images within each project. The list also shows at which Step of the analysis you last quit the project. If a Comment is added, you can read its full text by hovering over the Comment field. The Comment will also appear on the cover page of the Project report (PDF).
NOTE
For DIGE experiments, the Reference stain field indicates the dye channel containing the internal standard sample. In Coverage DIGE/DIBE experiments, it specifies the dye used for the primary images.
The More icon next to the project name varies based on the project’s Location. Click the icon to access project-related functionality.
To edit a project’s Name and Comment or to view its file path, click the More icon and choose Properties. You can also edit the project’s Name directly in the list: click on the project’s row, then click once more on the project Name; Melanie will automatically update the name of the project folder and the project file (.prj) on disk to match the new name.
Remove a project
Click the More icon in front of the project name and choose Remove to remove a project only from the Project list, or delete it from your disk as well. This differentiation helps you avoid that unused projects accumulate and waste disk space.
- Remove project from list – This will remove the project from the Project list, but will not delete the project files on your disk. To open the project again later, you can add it again.
- Permanently delete project from disk – In addition to removing the project from the Project list, this will also delete the project files on your disk. The project and associated analysis will be lost permanently. You can export a project for archiving purposes before deleting it.
Add one or several projects
You can reintroduce a previously removed project to your Project list at any time. Additionally, if your colleagues have saved projects in a Shared folder, you can add these to your Project list for collaborative analysis. Simply click the Add button on the Projects screen and browse for a Project (*.prj) file, which can be found in the folder of a particular project.
To add multiple projects from a specific folder, select Add selected projects from folder from the Add button dropdown. Navigate to the desired folder in the Choose project folder window – this could be the Shared folder where your colleagues store their projects. Then, in the Choose projects window, select the projects you want to add to your Project list and click Add to confirm.
Export a project
Click the More icon next to the project name and select Export to save all project-related files into a single compressed file with the .pex extension.
Regularly exporting projects for archiving is a recommended practice, enabling you to restore your work whenever needed. Project exports also make it easy to share your results with colleagues. Thanks to Melanie’s free viewer functionality, any collaborator with Melanie installed can open the Project Export (*.pex) file and view the results of an analysis conducted with the licensed software, even if they don’t have a license.
Restore a project
To restore a project previously exported as a .pex file, click the Add button dropdown in the Projects screen and select Restore projects. Then, browse and select the Project Export (*.pex) file. Click Open, and the project will be added to your Project list.
NOTE
Projects are sorted by their last Opened date, so the restored project may not appear at the top of your list.
Duplicate a project
Click the More icon next to the project name and select Duplicate to create a copy of the project. This is useful for experimenting with various analysis options without modifying the original project, where significant work may already have been completed.
Move a project
You can move a project to either the Local folder or the Shared folder, but not to other folders. To do this, click the More icon next to the project name and select the desired option – Move to Local folder or Move to Shared folder. Note that the availability of these options depends on the current Location of your project and whether a Shared folder has been defined.
Additionally, you have the option to relocate multiple projects to the Shared folder simultaneously.