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 (Close the current project to enter the Projects interface).
- In the Create Project window, specify a Project name.
- Click on one of the available project types (see below), specify its options, and click Create.
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 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 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 experiments where several samples were run on the same gel, but where no internal standard was included.
Close a project
To create a new project, or open a different project, you must close the current project first. 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, Dye Type, 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. If a Comment was added, you will be able read its entire text by hovering over the Comment field for the specific project.
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.