SEEK & JERM Progress

Stuart OwenDecember 2009

Alphabetical pagination

• Requested by several users.• Will also be applied to Sops, Models & Data– (needs some enhancements to allow for

authorization filtering).

Define culture growth with organism

• Feedback suggested it didn’t make sense to have it within the technology type

• Either Chemostat or Batch (or not specified)

Improvements to tagging

• Fixed some bugs with Chrome and Safari that prevented tags being removed.

• Caching of the tag-clouds to give a noticeable performance improvement.

• Admin maintenance of tags, to tidy some of them up.

Consolidated Organism definitions

• Removed tagging of Organisms.• Organisms are now only stored as a CV.• Will be enhancing this to provide a hierarchy

for Organisms.

Clarified when you can delete an Assay, Study or Investigation

• Only possible if you are a project member and the ISA has no items associated with it.

Easier selection of SOPs & Datafiles

• Now only lists those of your projects, with the option to show those from other projects.

• Plans to add a simple search facility.

Allowing PALS to add/edit Model type and format

• Likely to extend to other administration tasks.• Still need to add ability to delete!

Versioning

Versioning (cont…)

• New versions are only created for new files – not for changes to descriptions etc.

• Assays are linked directly to the version of the SOP or DataFile at the time the link was made.

• Experimental conditions or Factors studied are linked to a specific version, but default to the same as the previous version.

Providing feedback & bug reports

• Providing feedback within SEEK.• Feedback & bug reports via mailing list.

Next steps

• JERM integration and extraction takes top priority.– E.g. Support for multiple authors, adding remotely held

assets by URI

• Minor user interface improvements.• Supporting multiple Model files.• Enhancements to Model metadata extraction (e.g.

SBML).• Improving access control to ISA• Linking in models within ISA

Tracking progress

• How we use JIRA– http://www.mygrid.org.uk/dev/issues/browse/SYSMO

• Testing at http://testing.sysmo-db.org– Has private data stripped out.– Content will NEVER be merged with live site – so

feel free to add nonsense.– Generally will be in sync with progress in JIRA– Can’t always guarantee it will be working.

JERM Integration

• 2 pass approach– Prevents projects being left behind.– Get all the Harvesters working for all projects• Integrate with Project DM system, and fetch Assets and

associated metadata such as time, author.• Registers Assets to SEEK, along with available metadata

– Next get the Extractors working• Processes the DataFiles and SOPs and extracts the

Data.• Needs to handle individual classes of Data, Templates

and SOP formats.

JERM Harvesters progress

• Designed, and implementation in progress.• Now largely working for systems that use

Wiki’s or provide WebDav access• SUMO, Cosmic, BaCell, SysmoLab, Scarab, Translucent

• Currently working on registering within SEEK, checking for duplicates and handling deletions.

Some UML