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 projects, add existing projects or project exports from disk, duplicate, remove and export projects, as well as view and edit the project properties.
The first time you open Melanie, the Create Project window will directly show up. For the creation of subsequent projects:
- Click the New button in Projects. If you have been working on a project, you can also click the Project icon in the workflow and choose New project.
- In the Create Project window, specify a Project name.
- Click on one of the available project types (see below) and click Create.
- Specify additional information, if requested.
- Add images to your project.
Once you have created your first project, take a moment to explore the elements of the Graphical user interface.
- 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.
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 interface.
To open a project, double-click on its name in the Project list, or click the More icon in front of its name and choose Open.
The Project list gives you an overview of the projects you have created or opened, and lists their Name, Type, Staining, Created and Opened dates, Size on disk, Creator as well as the number of Gels and Images in the project. It also mentions at which Step of the analysis you last quit the project. Note that for DIGE experiments, the dye in the Staining field represents the internal standard or reference dye. If a Comment was added, you will be able to read its entire text by hovering over the Comment field for the specific project. The comment will also be included on the cover page of the Project report (PDF).
To edit the Name and Comment of a project, and view its file path, click the More icon in front of the project name and choose Properties. When renaming a project, Melanie will automatically change the name of the project folder and project file (.prj) on disk as well.
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 use Add to browse for it.
- 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 with be lost permanently. You can export a project for archiving purposes before deleting it.
Click the More icon in front of the project name and choose Duplicate to create a copy of the project. This is useful when you want to experiment with some of the analysis options without touching the original project on which you may already have worked a lot.
Click the More icon in front of the project name and choose Export to save all project-related files into a single compressed file with the extension .pex.
Project exports are useful for regular archiving so you can recover your work at any time. They are also convenient to make a project available to colleagues so you can share the results.
Previously removed projects or exported projects can be re-inserted at any time. Just click the Add button in Projects and browse for a Project (*.prj) or Project Export (*.pex).
If a project is saved in a shared network folder, colleagues having access to the folder can add the project to their Project list and thus collaborate on the project.