Version 7 (modified by e.vansomeren@…, 3 years ago)

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Scenario 'Eugene'

Import study-level information of toxocologic studies from NTC into GSCF using the simple import wizard.

Background

The Netherlands Toxicogenomics Centre (NTC) will perform toxicological experiments for different toxicological endpoints (liver, carcino, repro, immuno etc.) using different model systems (different organisms, different cell systems, in vitro-in vivo-ex vivo) using different omics approaches (transcriptomics, miRNA, (phospho-)proteomics, metabolomics, imaging). NTC wants to use GSCF for full metadata capture and use it in combination with Array Track for data storage/visualization/analysis. Currently, NTC uses a website, called NTC Sharing, to collect information at study-level of all NTC experiments and store it in a simple Excel sheet. For GSCF, it should be possible to import this study-level information from NTC Sharing using the simple import wizard and a dedicated NTC Study template.

Description of Scenario

We want to test the scenario of importing study-level information for NTC. To this end, we have created three mock NTC experiment descriptions in an Excel sheet which has the exact same columns as used for NTC (see attachment "NTC_Experiment_test3.xls"):

  • [NTC_Experiment_test3.xls]

This scenario should be implemented with the following milestones:

  • gscf 0.6
  • sam 0.1.1

NTC Experiment_test3.xls

This Excel sheet contains the study-only information of three mock NTC experiments. For NTC there exists a website called NTC Sharing which collects this study-level information of all NTC experiments. If these three mock NTC experiment descriptions can be imported into GSCF as study info using a dedicated NTC Study TemplateNTC experiments are described using an exactly similar Excel sheet. These results are directly Screenshot van de Excel file bijvoegen is handig Screenshot of NTC Experiment test3 (part1, only left-most columns) Screenshot of NTC Experiment test3 (part2, only mid columns) Screenshot of NTC Experiment test3 (part3, only right-most columns)

Scenario execution

Explain all the steps to execute the scenario (optionally with screenshots)

Step 1:

Etc.

Attachments