This is a sandbox where DigiSal members can learn to use the SEEK.
Tutorial document: http://tinyurl.com/seek-ds17
The SEEK is a web interface to a database of research "assets" organised in a hierarchical "ISA structure" (investigation-study-assay) . These are further organised into projects and programmes.
- Programme = Overarching research theme (The Digital Salmon)
- Project = Research grant (DigiSal, GenoSysFat)
- Investigation = a particular biological process, phenomenon or thing (typically corresponds to [plans for] one or more closely related papers)
- Study = experiment whose design reflects a specific biological research question
- Assay = standardized measurement or diagnostic experiment using a specific protocol (applied to material from a study)
The main Asset types are
- Data file
- Model file
- Standard operating procedure (SOP)
A key benefit of the SEEK is that it provides context for research assets. Each asset's webpage has an interactive graph linking to related assets. Thus, simply sharing a link to an experiment (a Study) makes clear its purpose and broader motivation, shows the resulting data, and links to SOPs for method details.
Learning objectives for the SEEK tutorial at the DigiSal 2017 workshop:
Know your way around the SEEK web page for an asset:
- Navigate the ISA graph to obtain context for the asset.
- Copy a hyperlink to this and a related asset, pasting it into an email so your recipient know exactly what experiment or data you are referring to.
- Navigate to attached files or hyperlinks.
Edit an existing SEEK asset:
- Flesh out an asset Description that your coworker has begun.
- Upload a new version of an attached file.
- Share an asset with another colleague.
Create new SEEK assets:
- Create an Investigation, a Study, and an Assay, and share them with your Project.
- Upload a Data file linked to an Assay.