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How to install Finnee2016

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Guillaume Erny edited this page Jan 30, 2017 · 26 revisions

Finnee and Finnee2016 are not standalone software; they are Matlab toolboxes, they will only work with an open session of Matlab. However, the toolbox allows processing large files without programming skills. If you do not own Matlab, you can always try to contact [MathWork] (https://www.mathworks.com/programs/trials/) for a product trial. They normally provide software tests that should be sufficient for you to test Finnee and decide whenever this product is of interest for your work.

When you have Matlab installed and running, you will have to copy the functions and classes that compose Finnee2016 to a particular folder. You can either use a particular release or use the Finnee2016 GitHub repository.

From releases

Releases are usually made upon publication of a manuscript. They are a snapshot of the toolbox at a specific date. We assign a DOI to each release using [Zenodo] (https://zenodo.org/features) to facilitate citations.

The following releases have been made:

Finnee

[v3.1] (https://github.com/glerny/finnee/releases/tag/3.1): Final version of the Finnee toolbox.

The original Finnee to obtain the clusters plot.

Linked to the following manuscript(s):
   - Erny, G.L, Acunha, T., Simó, C., Cifuentes, A., Alves, A. Finnee—A Matlab toolbox for separation techniques hyphenated high-resolution mass spectrometry dataset, Chemometrics and Intelligent Laboratory Systems 155 (2016) 138-144; [doi: 10.1016/j.chemolab.2016.04.013] (http://www.sciencedirect.com/science/article/pii/S0169743916300971).
   - Erny, G.L, Acunha, T., Simó, C., Cifuentes, A., Alves, A. Algorithm for comprehensive analysis of datasets from hyphenated high-resolution mass spectrometric techniques using single ion profiles and cluster analysis, Journal of Chromatography A,1429 (2016) 134-141; [doi: 10.1016/j.chroma.2015.12.005] (http://www.sciencedirect.com/science/article/pii/S0021967315017550)

Using GitHub

GitHub is a software repository that allows collaborative work as well as source control. Since Matlab 2014a GitHub can easily be used.

[How to] (http://www.mathworks.com/help/matlab/matlab_prog/retrieve-from-git-repository.html) "Clone a remote Git™ repository to retrieve repository files.

  1. Right-click in the white space (any blank area) in the Current Folder browser, and select Source Control>Manage Files.
  2. In the Manage Files Using Source Control dialogue box, select Git from the Source control integration list.
  3. Click Change to browse for and validate the repository path. (If you know your repository location, you can paste it into the Repository Path box and proceed to step 7.)
  4. In the Select a Repository dialogue box, specify the repository path by entering the path in the box, using the list of new repositories, or by using the Browse to a Git repository on disk button. The Path to Finnee2016 is https://github.com/glerny/Finnee2016.git path2finnee
  5. Click Validate to check the repository path. If the path is invalid, check it against your source control repository browser.
  6. If you see an authentication dialogue box for your repository, enter login information to continue.
  7. When you have finished specifying the path you want to retrieve, click OK.
  8. In the Manage Files Using Source Control dialogue box, select the sandbox folder where you want to put the retrieved files, and click Retrieve."

It is also possible to download all the files from git [here] (https://github.com/glerny/Finnee2016/)

  1. Select Clone or download
  2. Select Download Zip
  3. Extract all in the folder of destination

Add to Matlab path

When using Matlab, specific functions can be called from the command window. This allows using Finnee2016 simply by entering in the command window the right command. However, Matlab will only look for functions that are in its search path, the folder where you download the finnee2016 functions need to be added to this search path. With Matlab running, you can add a folder (and subfolder) on the search path either use

The Set Path dialogue box (permanent until removed)

  1. On the Home tab, in the Environment section, click Set Path. The Set Path dialogue box appears.
  2. Use the Set Path dialogue box to modify the search path.
  3. Apply or cancel the search path changes:

Using the Current Folder panel (Only until the next session)

  1. Click on the browse for folder icon to navigate to the parent folder of the folder you want to add

add2path1

  1. Right click on the target folder
  2. Select add to path|Selected Folders and Subfolders

add2path2

Up            : Where to start?
Next         : [mzML files] (https://github.com/glerny/Finnee2016/wiki/mzML-files)
Previous  : Where to start?

Finnee: The User's manual

1. Where to start?
2. Trace, Dataset and Finnee objects
3. Correcting a Dataset
4. Mining for features, using replicates and peak matching
5. Tutorials

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