-
We should have a prototype of an SDRF definition for metabolomics data. EPMA will work with SDRF for the standard metadata for samples for proteomics and metabolomics, and in principle, the file forma…
-
### Description of the bug
Hi all, I keep encountering the following error on diverse datasets that I am trying to use with quantms. I have tried it multiple times on the same HPC cluster but with di…
-
Hey,
I noticed the SDRF validator is a bit difficult to maintain and to understand in it's current state, as it is one long python script.
To make it more maintainable and extendable for future c…
-
It would be nice to have links to the most relevant repositories and resources related to `sdrf-pipelines` in the `README.md`. e.g. to the https://github.com/bigbio/proteomics-metadata-standard repo.
…
-
@ypriverol Do you have a set of SDRF files for experiments of all different kinds of expected flavors?
If not we should systematically generate SDRF example files with all the different labelling t…
-
technology type is mandatory in SDRF but no section in the SDRF mentions it, and even when it is added to the templates, we have confusion about where should be. The validator says after the assay nam…
-
In the following issue #671 we discussed the major changes for SDRF specification during the next release 1.1. One of them, is the extension of SDRF for metabolomics.
> **GOAL**: The aim of adapti…
-
Hi all,
I made a pull request with three exemplary annotations for MSI data to start a discussion: https://github.com/bigbio/proteomics-metadata-standard/pull/450
Here are some thoughts about t…
-
@jpfeuffer sometimes the pipeline fails in the id part because of the peak-peaking step by the ThermoRawFileParser. Would be great to "restart" the pipeline, same parameters but with the openms peak p…
-
In the PXD014525 project, the steps in the following figure are used. A raw file contains a mixed protein of Yeast and HELA. And in different raw files, there are different dilution ratios. How shoul…