User Guides

Uploading Workflow Steps From Excel

Last updated on 29-Aug-2018 by Thomas P. Boesen
Thomas P. Boesen


The core of a workflow is the steps that make up the experiment, so we will start by defining these. However, getting Scifeon to recognise an Excel file for upload has a few requirements to the naming and layout of the worksheet. Let us quickly run through these before starting on the workflows:

1. Defining a Scifeon Worksheet

For Scifeon to recognize the uploaded worksheet, the name of the sheet has to be Scifeon:

You can have as many sheets as you want in the same workbook and Scifeon will still only parse the sheet named Scifeon.

2. Defining the Workflow Format

The top left corner of the worksheet (cell A1*) defines what kind of upload you wish to do: Whether you want to add an entirely new experiment to the database with *Experiment, or add stuff to experiments already in the database with Upload.
Let us start by creating a new experiment:

3. A Basic Experiment

Different parts of an experiment are defined by different tags in the cell comments. For our simple experiment we use a [section] tag. This tells the parser that everything following the tagged cell belongs together.
Thus, our basic experiment has a name property and a type property. Other properties such as Date Started or Scientist could also be written as Key-Value pairs of the experiment section and would be added to the experiment data in the database. To see the full list of Key-Value pairs, see the datamodel page in Scifeon.

In section tagged regions the parser only reads the columns A and B so you are free to use the rest of the worksheet for notes or data storage.
The parser also does not care about vertical whitespace, you can have as many empty cells between your Key-Value pairs as you desire.

4. Taking Your First Step

Now to add some steps to our experiment:

Like previously, we use the [section] tag in the comments to define a new step in our experiment workflow. The steps are automatically added to the experiment and can be individually linked using the Parent keyword.
Here we have simply made a linear experiment of three steps, but the steps can branch out in whatever way we want.
Uploading this workflow to Scifeon results in the following:

This is the experiment display in Scifeon. We can see all relevant data concerning the experiment and its steps and a graphic representation of the step branching is displayed.

5. Sampling the Goodies..

If you want to play around with the demo file, you can download it here.
Or if you would like to continue with the tutorial, head over to *uploading samples and results*.