Further questions on info management

[mgrauer]

• should we use a circular diagram to encode the various people in the research and the flow of data between them, as a conceptual diagram for showing how the research group works? see screenshot
• should we have a templated SVG diagram to allow individual experiments to build up a diagram that allows their data to be linked
• how can we alter the table on the model page to express the flow of multiple experiments per agent?
• how can we alter the individual agent pages to best capture multiple experiments per agent?
• how can we alter Girder and GitHub to best capture and organize multiple experiments per agent?
• what tooling can we put into place on Girder that provides better guardrails for organizing multiple experiments per agent and links that in with the website?

[mgrauer]

This diagram could be changed to more fully capture the below content:

An experimentalist might perform a co-cultured experiment of an immune cell type with A. fumigatus. Various experiments including transcriptomics and ELISA are used to measure transcriptional and protein-level changes. After sequencing, the data is preprocessed and analyzed by a computational biologist. Such analysis (such as differential expression analysis, pathway analysis, etc.),together with the protein-level data, is then used to enrich a preliminary intracellular mathematical model built from literature knowledge. The implementation of this individual-cell model is then incorporated into the tissue-level 3D model. From this example alone, we see the various data and artifacts that were required and/or generated:

Experimental notebooks describing the protocol of the experiment. Raw data (e.g. RNA seq fastq files). Computational scripts analyzing the generated data. Versions of different software dependencies used in the analysis. Literature results. Implementation of mathematical model.