NMC DSP short term requirements

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September 1 2010

The following steps shoud be implemented by September 1st 2010

  • Enter Study in GSCF
  • Retrieve all samples from the study
  • Assign new names for internal use to each samples
  • Assign order to samples and create QCs, blanks
  • Export these information as an excel sheet
  • Upload the excel sheet with measurement design and peak information
  • Display the uploaded information in a table editor
  • Store the displayed information in a database
  • Retrieve peak table information for selected samples within a study
  • Retrieve all study data, including measurement design and peak data in the form of an excel sheet.

Enter Study in GSCF

We assume a study has been created in the Study Capturing Framework and contains a number of samples. The GSCF provides access to studies and their samples by means of a few REST calls. The user first logs into the system and selects the study of interest. Retrieve all samples from the study

Next the user should be able to view the list of all samples in that study. The list of studies that the user will be able to see will later be limited to those studies which the user is authorized to view.

In fact, this listing of samples is part of creating a measurement. It comes with a description of the measurement platform and possibly compounds of interest and other metadata. This can be implemented as an optional textfield.

Adding names

The list of samples is displayed to the user. Laboratories like the DCL in Leiden assign internal names to samples. This assignment is one-to-one. This is currently done in Excel because it offers the possibility of automatically number consecutive elements in a column. This functionality should be implemented! Here we try to replace excel. Assign order to samples and create QCs, blanks

Samples are then put into batches. They are given an order. Subsamples are created, QC’s and blanks are introduced. This is the measurement design. note that in order to create subsamples, the original sample names hsould be duplicated. Export these information as an excel sheet

The measurement design information is stored and can be downloaded in an Excel like format. This file is then fed into the vendor specific software and the measurements are performed. The result is an Excel file including peak information for the samples. We take the lipodomics files as leading. Upload the excel sheet with measurement design and peak information

The excel file with peak information (lipodomics example file) is uploaded by the user. No new sample names are introduced. When the excel data does not match the measurement design stored in the system a warning should be issued.


Display the uploaded information in a table editor

The measurement design and peak information should be viewable for inspection by sample. The user should be able to make corrections.


Store the displayed information in a database

The displayed information should be stored. Peak information should be related to the sample.


Retrieve peak table information for selected samples within a study

Peak information should be retrievable for each selected sample. Retrieve all study data, including measurement design and peak data in the form of an excel sheet.

All data regarding a study, including the GSCF and measurement design, should be downloadable in a single excel file.