Sys MO-DB 2 progress update and future activities

Sys. MO-DB 2: progress update and future activities Prof Carole Goble FREng BCS CITP University of Manchester, UK carole. goble@manchester. ac. uk Sys. MO conference May 2011 Oxford, UK

SEEK Platform and Service Find experts, colleagues and peers Find, exchange and interlink, preserve, publish data, models, publications, SOPs& analyses. Launch and validate models and analyses: JWS Online Gateway to Access restrictions. public tools and resources Mix local and central stores. Post-project Standards archiving & publication. compliant.

Metadata Catalogue. Results Repository.

SEEK Facts and Figures Registered Users: 325 (202) l l 21, 600 page views, 520 unique visitors, 110 unique users log ins. User visits: >30% at least once per week, > 50% at least once per month Registered Content: l l l Investigations 24 (19) | Studies 64 (46) | Assays 127 (99) Data files 862 (590) Models 33 (23) SOPs 119 (116) Publications 109 (37) > 15 JERMs

Trends within Sys. MO Current & new project trends l Majority direct uploads l Local SEEK adoption l Mixed adoption of JERM templates l More assays End-project trends l Deadline flurry – preservation and review l Export data from SEEK l You can use the funders group Cross-project trends l Membership movement permissions

One Stop to model standards SBML model format, SBGN schema, MIRIAM annotation SEEK integrated tool to: • construct, or modify, models, save in SBML format • get automated generation of SBGN schema • to annotate model (MIRIAM), implementing web services from semantic. SBML.

: JERM Annotation with Standards http: //www. rightfield. org. uk Bio. Portal Controlled vocabulary restrictions

Community this year l l Model curation “service” Meetings l l l l 3 full PALs meetings Experienced active past PALs New PALs ramping up “The Old PALs club” Training l l l All 7 Sys. MO-2 projects 2 Era. Sys. Bio+ 2 Sys. MO-1 Projects 21 PALs l l Bacell, Sys. MO-LAB, COSMIC, Sys. MO-DB First cross projects in May 2011 In Rostock Preez Franco Du Result of local PALs activity Presenting each others data, analytics, SOPs 1 workshop (3 total) 2 summer schools (4 total) Supporting end project data curation and project migrations Discussions on opening up SEEK

Outreach l l Website: 10, 590 hits, 1, 850 unique visitors. Publications l l l 25 invited talks Presentations l l l l 1 accepted, 1 in review, 1 book chapter Intell Sys Molecular Bio Integrative Bioinformatics Intl Conf Sys Bio Microsoft e-Science ESFRI ISBE Era. Sys. Bio+ CISBIC, Xperiment. R

Sys. MO is a-changing Transition 1 2 l l l Projects leave Projects stay Projects come PALs changing Opening up l Projects l Content l Development Core of ecosystem l l Development team Related projects Requirements l nt e nm o vir n E Project structure

2 1 Sys. MO 2 Sys. MO 1 MOSES COSMIC KOSMOB AC Silico Tryp SUMO PSYSMO Ba. Cell Sulfo. SYS Sys. MOLAB SCa. RAB TRANSLUCENT Noisy-Strep STREAM ~100 institutes TB-HOST-NET SHIPREC 325 scientists

CISBIC SSFH (pending)

Evolution I want to find people and skills I want to use I want to share excel SOPs Can I open data to the Can I share in a hidden world? area? Can I let in some collaboration partners as Don‘t do flexible "almost“ members? data integration Can I search data in and comparison other SEEKs from my Link publications & SEEK? data Don‘t do My data from 2 distributed projects, is I want my search interesting for 3 project‘s brand I want to (other) projects visible compare published and I need to track unpublished slices of mouse data liver

Opening Up l Open up content l l Open up project boundaries l l Other sites and systems Open up adoptions l l Associate members in related projects Open up SEEK integration l l Publication platform More user communities, different content Open up development l Re-contributed features

Opening up Content l l Consultation with community portal forum Public interface l l l l Community portal Hiding ISA structure Projects l Defaults & reports Permissions feedback One click publishing ISA-Infrastructure Data sharing policy

Open up project boundaries l l Associate members in related projects Ad hoc groupings External members Simplifying sharing interface Permissions arrangements over ISA structure

Opening up to other Systems l l l l Cross system authentication Log in with Open. ID Pub. Med Bio. Portal ISA-Infrastructure Bio. Models Ch. EBI ids

Opening up adoption l Virtual Machine & packaging l l Easy Configuration Branding SEEK ecosystem l l So that other projects can set up their own SEEK Cross SEEK exchange SEEK export New data types New features

Opening up development Large data file sending / uploading „email-style“ Buddy-to-buddy mailing Feels like buddy-buddy,

Opening up development Large data file sending / uploading „email-style“ Buddy-to-buddy mailing Feels like buddy-buddy, can share later

Bigger team, More collaborations, More users New processes

Searching and Linking Prioritising! Long Feature lists! l SEEK as a community site l l l Searching and processing data l l Permissions and visibility tweaking Information portal Universal tagging Extracting data from Spreadsheets Spreadsheet tooling Viewing data Project centric folder view and assay builder l In Browser spreadsheet viewing l l Linking & comparing data with models l l l Data Fuse: Running models with parameter values from spreadsheets. Linking and searching across other systems Automated analysis (encouraged by SUMO)

Search and Analysis Workflow Management System l l across data sets, models and stuff Analysis pool Analysis As A Cloud Service Analysis using Cloud Computing Services Run analysis tools and knowledge bases Automated Model Generation MCISB Centre (Li) Annotation pipeline SUMO Sys. MO project (Maleki-Dizaji) Next Gen Seq annotation pipelines using Amazon Cloud Services (Noyes, Li ) Li et al, BMC Bioinformatics 2010, 11: 582, doi: 10. 1186/1471 -2105 -11 -582, high Hucka and Le Novère, BMC Biology 2010, 8: 140, doi: 10. 1186/1741 -7007 -8 -14

New challenges summary People Projects Processes Software Cross-Sys. MO contacts Beyond-Sys. MO contacts New models New data New metadata New Structure Adapt PALs process Curation Propagate best practices Maintainability Usability Evolution Extensibility Feature lists Coordination

“Annotation Standards by Stealth” http: //www. rightfield. org. uk