Store/Expose RNAseq pipeline processing parameters

[stripathy]

RNAseq datasets in gemma should have some basic information about parameters used for aligning and quantification, including: which genome version? which reference transcriptome version? which quantifier? etc. If Manuel's pipeline also gets info about read length, single vs paired end reads, etc, that'd be useful info too.

[tesar-stepan]

Current proposition is to either store this information in a <key, value> array, or in case we want to keep old values when adding new ones, a <key, <date, value> tree.

[tesar-stepan]

Added a simple string 'metadata' property to datasets and bioAssays, removed processing dates from bioAssay description.

[tesar-stepan]

Quick update: We sat down with Manuel and agreed to load first batch if metadata in, manually for now. They will be stored as a plain text. This will be immediately available through the API since the model, including the VOs, is ready. Once I have the data I'll edit the EE UI to show the data after some small pre-parsing for easier readability.

After this 'first stage', we will work on automatizing the process.

[tesar-stepan]

Progress update: In the first stage we will be displaying file content of files generated from the RNASeq pipeline directly. There will be several files linked to each experiment.
The second stage will mean parsing out some batch information and storing this in a formalized format within the Gemma model. How exactly this will be done is still up for debate.

[tesar-stepan]

Basic UI done in 99e8dff - gemma will detect any metadata for each experiment when the ee details page is loaded and display download links for each file it finds. This can be changed to display the file content directly in the future if downloading the file proves inconvenient.