xQTL workbench application user stories

As a user I want to have an overview of available data per investigation

Short name: StudyBook?

Acceptance criteria:

• I want one page overview of all annotations, observedvalues and data sets available
• This screen must be very prominent, maybe even starting point of the app
• This overview must function as a portal for browsing and adding data to the database (see ImportWizard?), plus downloading of sections or a complete set (see DownloadWizard?)
• ...

As a user I want to be able to import any data type as quickly and easily as possible

Short name: ImportWizard?

Acceptance criteria:

• The import must be a (semi) guided process where it is clear what I must do (next), and what I have done wrong or right
• I would like import in Excel and CSV file formats (with the tool automatically choosing the right import procedure based on type)
• I would like to keep other files in existing well-defined formats (eg. BAM, CEL, FASTA files)
• As a developer I would like the ability to 'plug-in' importers for other types
• I would also like to attach miscellanious files, such as images, videos, docs, machine output etc.
• There must be help available on how to succesfully import, and examples of datasets I can edit and reuse
• I would not want to loose progress during the import process so that partial imports must be logged (tech note: this info is kept between sessions)

As a biologist I want to choose and run pre-defined compute protocols

Short name: ApplyCompution?

Acceptance criteria:

• I would like a clear overview of compute protocols I can run, and what their purpose is
• I do not want to be bothered with technical details on how they are implemented unless I choose to
• I would like to see help on the analyses I can run and their input and output parameters
• The application should make clear to me if my data is not complete for running a certain tool, and suggest how/where to fix it
• If anything goes wrong, I want a clear error message with suggestions how to proceed, or who to contact
• When a computation protocol is running I want to monitor progress and choose to get an email if it is completed
• When a tool is finished running, I would like to go directly to my results
• I want to be able to get a report of all the settings and software I used to produce the data so I can report my provenance to others (note: so also get this information when browsing data)
• ...

Technical notes:

• This has a huge overlap with ApplyProtocol? where we also want to allow provide users with a dialog to parameterize a protocol
• Implementation can use Measurement.dataType and molgenis.framework.ui to autogenerate these dialogs

As a biologist I want to view results

Discussion: incomplete, needs concrete examples of what should be possible and may be multiple stories

• The place to view data (including results) should be reachable from multiple places so I never get lost
• The viewer should provide a clear menu of things I can do with the data
• I want useful viewers (plugins) that add meaning to my data and save me from using my own tools to e.g. make a graph
• I would like to see help and instructions on how to use the more complicated viewers
• ...

As a biologist I want to download all data, investigation data, or a selection thereof

Short name: DownloadWizard?

• I would like to retrieve the data in multiple formats, both 'generic' (Excel, CSV..) as 'specific' (FASTA, PDF) if the data allows it
• I would like to make aggregated views on the data (ie. include annotation) and them download them
• Downloading 'archives' is handy, where data is exported into a single file for backup/reuse in similar databases
• ...

As a bioinformatician I want to add new computational protocols/tools

Short name: AddTools?

• I want a clear screen to add and configure new tools including parameters, help and test cases to validate they function properly
• I want to be able to testdrive the tools privately before other people can use them
• I want to be able to configure technical details such as compute resource, batching, default parameters so the user does not have to deal with this
• I would like information on who to contact if the application or computation server needs additional configuring or installing
• ...

As a bioinformatician I want to add and configure workflows

Short name: ComputeWorkflows?

Acceptance criteria:

• I want to be able to build workflows using existing compute protocols as elements using a helpful screen (may or may not be graphical)
• I would like help connecting analyses in a meaningful way, ie. be sure the outcome is not nonsense, by having good documentation, ontologies, strict typing, etc
• The screen not have to be extensive, a simple concatenation of a few steps is already very helpful (ie. normalization -> correction -> scan QTL -> make network -> visualize)
• I want to be able to import workflows from tool such as Taverna or Galaxy, from files
• I would like to be able to browse a catalog of workflows or services and incorporate those as well
• I want to be able to export workflows in various formats
• I would like to share workflows with others within the system, but also share them with the outside world (ie. MyExperiment?)
• ...

TODO: add specific workflows that we want to have demonstrated succesfully such as R/qtl, impute, NGS.

Technical note:

• Strong overlap with ProtocolWorkflows? for the wet lab

As a biologist I want to link my data to public databases

Discussion: we need specific examples here so we know what we need to be able to do at least.

• I want to have automatically rendered linkouts to popular databases based in data types (e.g. by recognizing ENS identifiers)
• I want to manually add linkouts if they are not automatically present
• I want to link genomic information to other genome browsers using a DAS service that I can plug in elsewhere

[Discussion: be more precise on what tools and what data below; the generic story is that we want to enable them]

• I want to able to export XGAP data immediatly into popular online tools
• It would be great if XGAP already featured integration or enrichment functions ???? with popular database, for example map genes to KEGG and them visualize them
• ...

As an molgenis administrator I want to configure the application

Discussion: this is probably too big for one story. Should also include automated deployment etc.

• I want a configuration screen for all kinds of application settings, such as:
• View the status of the database, is it set up correctly, move it to other backend, how much space am I using, how much is available, how fast are the queries, etc
• View status of file storage, does the application have read/write rights, are backups being made, what kind of files do people store, how often are they retrieved, etc
• I want the ability to restore backups of the database, additional files, other settings such as this panel, and view a history of changes/additions/deletions of these aspects
• I would like to view user activity and registration, and be able to communicate with users by either email, messages inside the application, or otherwise
• ...

As an administrator I want user management and security

See all stories of ​auth.