myExperiment Team F2F Manchester

November Team Face to Face Meeting (Manchester) Thursday, 26th November myExperiment meeting. University of Manchester, Room 2.33, Kilburn building. Start time: 10am start, finishing at working meetings in afternoon Confirmed attendees: DDeR, Carole (from 10.30), Jits, Don, Danius (remotely), Paul, Sean, Franck, Paolo, Shoaib (from 10.30), Matt, Mannie, David Newman (remotely from 11.30), Rory Apologies: Katy, Stuart

1. Developer report (10am) Codebase (Don) Taverna plugin (Jits) Demo (Mannie) 2. User report (10.30) Opportunities (Carole) 3. Collaborating projects (10.45) 4. Project planning (11.30) Struct metadata &curation planning Biocatalogue integration (Jits) Revised JISC workplan (DDeR) 5. Repositories (12.15) EPrints (DDeR) e-Scholar 6. Papers (12.20) Chapters CCPE status e.g. Nucleic Acids Reserch Bioinformatics appnote Future ops 7. Diary NeISS (Sean & Rory) Apace (Danius) Biocatalogue (Jits) DataONE (Paolo) e-Lico, RapidMiner (Jits & Carole) eStat (Danius) Microsoft (Jits) MOLGENIS, BioExtract (Jits) NEMA and SALAMI (DDeR) Obesity e-Lab (Shoaib) Sysmo (Carole?) neurohub (DRN)

Developer Report (Don) 30% supporting service (users and developers) Bulk uploads (for content admin / power user) SPAM detection assist T2 support (metadata extract) Support for new licenses API support (e.g. versioning API) OAI Static repository for export Zotero and OpenSearch support Test branch almost Rails 2 (hence OpenSocial) Structured metadata mockups and design Linked data discussions with EPrints team Forthcoming updates include OAI export and Sergej’s event logging code Releasing virtual machine image as trial

Taverna plugin (Jits)

User report

Sharing innovation across e-labs Every project that builds on the myExperiment codebase is innovating How does this feed back to myExperiment and the other e-Labs projects? Short term – the Monday meetings are working well – pragmatic benefit from all using RoR! Long term – e-Labs is a “long game” – Matt doing great job with ROs (but needs to get on with PhD) Suggestion: specific exercises – Jits doing Biocat-myExp integration is very high-value

NeISS (Sean)

Apace (Danius)

Biocatalogue (Jits)

Sysmo (Stuart sent apols)

DataONE (Paolo)

e-Lico, RapidMiner (Jits & Carole) One such setting for collaboration between users will be provided by a customised version of the myExperiment system, supporting both the laissez faire, free-range, exploratory and 'brainstorming' activities that are required in the early stages of collaborative work, as well as the more structured and principled forms of interaction needed as scientific work reaches maturity. myExperiment will be both a social exchange forum for workflows, models, algorithms and codes; and a portal for launching Taverna workflows; accessing visualisation tools and accessing shared repositories. The collaboration models supported are both largely decoupled and asynchronous, though we will be on the alert for genuine opportunities for synchronised collaboration. Closely integrated with the myExperiment system, and sharing ontologies with it and myGrid will be the UTOPIA semantic core, providing real-time mechanisms for data-sharing between desktop visualisation and interactive analysis tools.

e-LICO's e-science infrastructure

WP1: E-lab Infrastructure and integration the creation and deployment of a customised version of the myExperiment collaboration environment to support all workpackages (WP1.3); integration of collaborative ontology engineering support into myExperiment. This would include both social as well as technical support and for synchronous and asynchronous building of ontology (WP1.4);

eStat (Danius)

Microsoft (Jits)

MOLGENIS, BioExtract (Jits)

NEMA NEMA and SALAMI (DDeR) Meandre myExperiment 1. Native Meandre support 2. Support for music repositories 3. NEMA flow support

NEMA Meeting 27 th November in London

SALAMI Structural Analysis of Large Amounts of Music “applies new computational approaches to the huge and growing volume of digital recorded music now available in such large scale resources like the Internet Archive, to deliver a new and very substantive web-accessible corpus of musical analyses in a common framework for use by music scholars, students, and beyond". 8 projects funded out of 87

Obesity e-Lab (Shoaib)

neurohub (DRN)

Other e-Labs projects Ondex

Curation and Structured Metadata 1.Support for contribution quality categories – Spam gets removed – Repository content admin e.g. tutorial submissions “will be removed on date” – New T&C 2.Support for workflow categories – This can be run, this is an example,... – Pertinent to Biocat 3.Structured metadata – Tabs for inputs, outputs, examples – Have done mockup 4.Curated descriptions Barometer/accolades Curator comments in text a la wikipedia 5.Support for workflow functional classification e.g. “text mining” Controlled vocabulary in addition to tags 6.Conducting the content sweep Paul and The Curators Fest, month or ongoing 7.Navigation by category 8.Assisted metadata

Papers Chapters CCPE status Need pub in e.g. Nucleic Acids Research (George/Carole/Marco) Bioinformatics appnote Future ops