SEEK and JERM Demo Scenario

Functionality in the SysMO-HUB for exchanging and sharing will be incremental. SysMO consortium members will get access to tools and resources as and when they are available. The first release will be made available at the SysMO evaluation conference in May 2009. This release will contain the SEEK Yellow Pages and Assets Catalogue as well as a prototype demonstration of the JERM and data exchange across a few projects.

1. Discover that project X works on the same organism as you by searching by organism/strain
   • We can use the Organism Saccharomyces cerevisiae and discover that Moses is working on this.
2. Navigate to a type of data shared by that project (e.g.microarray) – see what different data files/types there are available
   • Here we see that MOSES has 2 data files.
3. Select a data file and look at the metadata and data
   • We select the first data file, Metabolites Intracellular
   • We explain the factors studied that is related to this file, and how it relates to the JERM/SEEK overlap (in Caroles talk).
4. Download the data and open it.
   • Explain here that data would reside within MOSES's repository, and SEEK is merely acting as a gateway to it.
5. Show the Assays associated with this Data, and select the metabolomics Assay type.
6. Navigate to another metabolomics Data file from another project, via this assay type.
7. Discover the SOPs associated with that data through SEEK
   • From the sop related to the Assay of the current Data item (so need to make sure that Assay has a SOP).
8. Show the experimental conditions that would have been extracted from that SOP (or provided manually).
9. Upload a new and related SOP.
   • Here we show the sharing and authorisation, and add the attribution back to the previous SOP. We explain that we intend to allow a new SOP to be created based on a previous one without uploading a new file, but by simply defining the differences in Experimental Conditions.
10. Search for other assets belonging to that project and find a model relating to the data generated.
    • I will add Models to the Assay, and they can be linked through this.
    • Alternatively we search by Organism to get to the Model.
11. Run a model simulation in JWS online using some of the new experimental data
12. Upload the results of running the model, and associate with the same Assay.

We are currently building towards this prototype, which will allow us to demonstrate the following:

1. Discover that project X works on the same organism as you by searching by organism/strain

2. Navigate to a type of data shared by that project (e.g.microarray) – see what different data files/types there are available.

3. Select a data file and look at the metadata and data

4. Discover the SOPs associated with that data through SEEK

5. Upload a new and related SOP. Perhaps this is after the researcher has gone off and done a similar experiment based on the one they found and changed some of the parameters

6. Share new data from the related experiment to compare the original data and the new data – this could be sharing with everyone in the other project, or only the individual researcher that carried out the original experiment

7. Search for other assets belonging to that project and find a model relating to the data generated

8. Run a model simulation in JWS online using some of the new experimental data

9. Search for people in the project with modelling expertise to provide help and advice with the model and the interpretation of the results

10. Upload the results of the simulation to SEEK

11. Find workflows that enable further analysis of the data and either run them through myExperiment, or download them for local use