4.1. Step-by-step instructions for creating datasets (dose-response)

4.1. Create new experiment description

The following steps show how to create Investigation, Study and Assay and a dose-response example data file. This tutorial was prepared using the “Advanced” version of the ISAcreator, so we suggest that you make use of that (the differences are anyway slight).

  First login (or “create a profile” if you are using ISAcreator for the first time). The profile is specific to the local installation and does not communicate e.g. with the ToxBank data warehouse. No data is sent anywhere at this point. If you forget the password you can just create a new log-in without losing anything.

 Create new experiment in ISAcreator

Select a configuration (use the “ToxBank config”– see requirements above) and “load selection”.

Create new experiment in ISAcreator

 ii.)  Create a new study
   The next screen “Create new study” appears, click on “create manually”.

Create new study in ISAcreator

The next step is to create the study itself, by using the “+” button shown at the figure below.

Create new study in ISAcreator

iii.) Add study metadata
  An experiment in ISA-TAB is known as Investigation (top left). An investigation may have multiple studies. There is one study in this case. A study may have one or more assays. The next step will be to add an assay (click “add new assays(s)”).

Add study metadata - ISA creator


Select the assay


An assay in ISA-TAB is described by the measurement, technology and platform. There are about 30 predefined assay templates. New templates are defined by ISAConfgurator (a different application from the ISA-TAB suite). In this example, select “cell viability” as measurement, “Neutral red uptake” as technology, “other” as platform. Click “add assay”. The assay will appear in the bottom panel.  Multiple assays could be added for a single study. Once ready, click “Done”.

If you need support developing a new assay template, you can contact ToxBank support (support@lists.toxbank.net) for assistance.

Select the assay, ISAcreator

v.) Study and assays
  The newly added assays appear under Study Assays section, and also in the tree at the left panel. Clicking on the “View” button within Study Assay section will open the Assay screen (next screenshot). To browse assays: Click on the assay file at the left panel (assay files names follow the template “a_*.txt” , e.g. “a_study_Cell viability.txt”).

Study and assays

An example based on the BII-S-1 investigation, which is included in the ISAcreator. SEURAT distribution is shown below.

Example based on the BII-S-1 investigation

Link to the Creating an Investigation video Tutorial.

Proceed to:

4.2. Step-by-step instructions for creating datasets (dose-response):

4.2. The Study metadata