Work Package Deliverables

All work packages specify targets to be reached. The results for these targets are reported in the Deliverables you will find below.

From the numbering it may seem some documents are missing. This is not the case, the numbering reflects the candidate proposals, and simply not all proposals made it into reality. Gaps in the numbering therefore reveal rejected proposals, not missing documents.

Work Package 1
Deliverable Description
De1.1.1_1.1.2.doc doc 1.1.1) Prototype EMBL-Bank nucleotide sequence database services
1.1.2) Prototype Swiss-Prot, TrEMBL, UniProt protein sequence database services
De1.1.3.doc doc Prototype ELM database services
D1.1.4_1.1.5.doc doc 1.1.4) Prototype macromolecular structure data services
1.1.5) Prototype ArrayExpress microarray database services
De1.1.6.doc doc Public standard interface to services for EMBL-Bank nucleotide sequence database data resources
De1.1.7.doc doc Public standard interface to services for SWISS-PROT, TrEMBL, UniProt data resources
De1.1.8.doc doc Public standard interface to services for ENSEMBL genome annotation data resources
De1.1.9.doc doc Public standard interface to services for InterPro protein motif database resources
De1.1.10.doc doc Public standard interface to services for ELM Eukaryote Linear Motif database
De1.1.11.doc doc Public standard interface to services for SMART protein domain annotation resources
D1.1.12.doc doc Public standard interface to services for Macromolecular Structure Data
D1.1.13.doc doc Public standard interface to services for ArrayExpress
D1.1.15.doc doc Standard Literature Content Services
D1.1.17.doc doc Public standard interface to services for untranslated regions
D1.1.18.doc doc Standard interface to 3D Electron Microscopy Data services
D1.1.19.doc doc Public standard interface to services for ProDom
D1.1.20.doc doc Public standard interface to services for GenomeMatrix
D1.1.21.doc doc Public standard interface to services for PairsDB
D1.1.22-23.doc doc D1.1.22: Standard CATH Database Services
D1.1.23: Standard Gene3D Database Services
D1.1.24.doc doc Standard interface to Visual Omics services
D1.1.25.doc doc Standard services for transcriptional regulators of mammalian genes
D1.1.26.doc doc Public standard interface to services for transcription factors
D1.1.27.doc doc Public standard interface to Topology Classification of Membrane Proteins (TCOMP) Database Services
Work Package 2
Deliverable Description
De2.1.1.doc doc Prototype EMBOSS sequence analysis suite tools services
De2.1.2.doc doc Prototype PatSearch tools services
De2.1.3.doc doc Public standard interface to launching EMBOSS sequence analysis tool services
De2.1.4_v2.doc doc Public standard interface to launching SMART protein domain annotation EBI services
De2.1.5_v2.doc doc Public standard interface to launching ELM Eukaryote Linear Motif database analysis services
D2.1.6.doc doc Public standard interface to PatSearch services
D2.1.7.doc doc Public standard interface to PatSearch services
D2.1.8.doc doc Public standard interface to PatSearch services
D2.1.9.doc doc Public standard interface to UTOPIA
D2.1.11.doc doc Public standard interface to NPS@ services
De2.1.12.doc doc Public standard interface to launching Prodiv-TMHMM (formerly modHMM) analysis services
De2.1.13.doc doc Public standard interface to launching Palign profile alignment services
D2.1.14.doc doc Prototype interface to PDB modules services
D2.1.15.doc doc Prototype interface to Homology Modelling services
D2.1.17.doc doc Public standard interface to FunCUT services
D2.1.19new.doc doc Prototype interface to BioConductor scripts services
D2.1.20.doc doc Prototype interface to Binding Site Prediction services
D2.1.21.doc doc Public standard interface to SignalP services
D2.1.22.doc doc Public standard interface to GlobPlot services
D2.1.23.doc doc Public standard interface to HitKeeper services
D2.1.24.doc doc Public Soaplab2 interface to EMBOSS services
D2.1.25.doc doc Prototype CMC tools services
D2.1.27.doc doc Public production interface to HitKeeper
D2.1.28.doc doc Public standard interface to TOPCONS
D2.1.29.doc doc Public standard interface to SHRIMP
D2.1.30.doc doc Public standard interface to ProQ
D2.1.31.doc doc Public standard interface to Pcons.net
D2.1.32.doc doc Description of a web system for the prediction of protein binding sites
D2.1.33.doc doc Prototype Interface to Chipster
D2.1.34.doc doc Public Interface to Chipster
D2.1.35.doc doc Public standard interface to Spoctopus
D2.1.36.doc doc Public standard interface to MPRAP
D2.1.37.doc doc Public Interface to ChipsterIllumina
D2.1.38.doc doc Public Interface to ChipsterAnnotator
De2.2.1.doc doc Prototype EMBOSS structure analysis tools services
De2.2.2.doc doc
D2.2.2-public1.0.pdf pdf
Public standard interface to launching EMBOSS structure analysis tool services
De2.2.3.doc doc Public standard interface to launching SAMOSA Protein domain services
De2.2.4.doc doc Public standard interface to launching Cathedral (formerly ZZtop) microarray normalization services
D2.2.7.doc doc Public standard interface to 3D-EM tools via 3DEM-DAS
D2.2.8.doc doc Prototype interface to WHAT IF web-services
D2.2.9.doc doc PeppeR: an implementation of the Public standard interface to 3D-EM tools.
D2.2.10.doc doc Public standard interface for the FLORA method for predicting functional subgroups in the CATH database
D2.2.11.doc doc Public standard interface for scoring Linear Motifs in 3D structures
D2.2.12.doc doc Public interface for scoring Linear Motifs in interaction networks
D2.2.13.doc doc aGEM: an implementation of the public standard interface to Visual Omics tools
D2.3.1.doc doc Public standard interface to PyBioS services
D2.3.4.doc doc Public standard interface to ConsensusPathDB
Work Package 3
Deliverable Description
D3.1.1_v2.0.doc doc Report on technology survey
D3.1.1_3.3.1_final.doc doc Report on technology and network infrastructure surveys
D3.1.2-1.0.doc doc Revision of the technology recommendation
D3.1.3.doc doc Workshop on data integration at OGF25
D3.1.4.pdf pdf Recommendations of the web service annotation task force: Web Services Annotation Guide
D3.2.1v2.0.doc doc Initial technological analysis of test problems
De3.2.2-v2.0.doc doc Second technological analysis of test problems
D3.2.3_final.doc doc First evaluation of test case implementations
D3.2.4.doc doc First evaluation of WP4 test problem implementations
D3.2.5.doc doc Second evaluation of WP4 test problem implementations
D3.3.2.doc doc Report on EMBRACE grid deployment
Work Package 4
Deliverable Description
D4.1.1.doc doc Integrated tools to address Test Case 4.1.4, Build Hepatitis C Virus Sequence Alignment on GRID
D4.1.2.pdf pdf Integrated tools prototype to address Test Case 4.1.1
De4.1.3.doc doc first PROSITE-filter server
D4.1.4.pdf pdf
D4.1.4-addendum.pdf pdf
Second PROSITE filter
D4.1.8.pdf pdf Integrated tools to address test problem 4.1.3
D4.1.9A.doc doc Evaluation of EMBRACE integrated tools solution to address test case 4.1.1 by the user community
D4.1.9B.doc doc Final report on the initial test cases work
D4.1.10.doc doc Final report on the PROSITE-filter server generation process
De4.2.1.doc doc Detailed specification of new test problems
De4.2.2.doc doc Workshops related to issues presented by new test cases
De4.2.3.doc doc Detailed specification of new test problems
D4.2.4.doc doc Detailed specification of new test problems
De4.2.5_AC.doc doc Detailed specification of new test problems
D4.2.6A.doc doc Integrating promoter motif analysis and gene expression
D4.2.6B.doc doc Detailed specification and prototype solutions of the new test problems
D4.2.7A.doc doc Prototype to address test case: 4.2.11 "Workflow for association mapping in dogs and for evaluating candidate mutations by comparative genomics"
D4.2.7B.doc doc Web pages and workshops through the WP5 outreach work packages
De4.3.1.doc doc Web service presenting test case statistics
De4.3.2v2.doc doc Detailed analysis of currently active test problems
D4.3.3.doc doc Test problems FAQ list
D4.3.4.doc doc List of test problems considered solved by the network
De4.3.5.doc doc
De4.3.5_programme.pdf pdf
De4.3.5_Participants.doc doc
Workshop jointly with biologists to track progress of solutions created
D4.3.6.doc doc Workshop together with biologists to track progress of solutions created by partners
D4.3.7.doc doc EMBRACE User Forum together with biologists to publish and track progress of solutions created by partners
D4.3.8.doc doc User generated experiences are presented on a special page on the EMBRACE portal
Work Package 5
Deliverable Description
De5.1.1.doc doc Grid installation guide for EMBRACE
5.1.2
(No associated document)
Installation of grid technology at all partners
D5.1.3.doc doc Permanent grid workshop
De5.2.1.doc doc Grid technology workshop - meeting page
De5.2.2.doc doc Workshop 2: Data, data modelling and interoperability - meeting page
De5.2.3_complete.doc doc Grid Portal integration workshop - meeting page
De5.2.4complete.doc doc Workflows over Grid-based Web services - meeting page
De5.2.5.doc doc
De5.2.5APPENDIX.xls
Grid and Web Services technology for bioinformaticians - meeting page
D5.2.6.doc doc EMBRACE Workshop on Bioinformatics of Immunology
De5.2.7.doc doc EMBRACE RSMD Workshop - meeting page
De5.2.8.doc doc Exploring Modular Protein Architecture - meeting page
D5.2.9.doc doc Applied Gene Ontology - meeting page
De5.2.10.doc doc Deploying Web Services for Biological Sequence Annotation - meeting page
D5.2.12complete.doc doc EMBRACE Workshop in membrane bioinformatics - meeting page
D5.2.13.doc doc EMBRACE Workshop on protein domain analysis
D5.2.14.doc doc EMBRACE Workshop on Web services in Systems Biology
D5.2.16.doc doc
D5.2.16_ABSTRACTS.pdf pdf
EMBRACE Workshop on Systems Biology: Expression, interactions and system level modeling
D5.2.17_publication.pdf pfd WIWS: a protein structure bioinformatics Web service collection
D5.2.18.doc doc EMBRACE Workshop on the BioCreative II.5 challenge
De5.2.20.doc doc EGEE EMBRACE tutorial - meeting page
De5.2.X1_EMBL.doc doc Exploring Modular Protein Architecture – An EMBRACE outreach bioinformatics training workshop
D5.2.X2_DTU.doc doc EMBRACE Workshop: Client Side Scripting for Web Services
D5.2.X3_Rome_Workshop.pdf pdf EMBRACE Workshop: Next Generation Sequencing
D5.2.X4_EMPA2010.doc doc EMBRACE Workshop: Exploring Modular Protein Architecture
D5.2.X5.doc doc EMBRACE Workshop: Next Generation Sequencing data analysis
D5.2.X6.doc doc EMBRACE Workshop: Perl, SQL and Web Services
D5.2.X7_report.pdf pdf
D5.2.X7_participants.pdf pdf
EMBRACE Workshop: Next Generation Sequencing II
D5.2.X8.doc doc EMBRACE Workshop for Web Service providers in bioinformatics: syntax, semantics and publishing
De5.3.1.doc doc Public website and portal
De5.3.2_5.3.3_5.3.4.doc doc Project Managment system on portal
5.3.5A
(No associated document)
Technical reports available on portal
D5.3.5B.doc doc Software tools service information continued
D5.3.6-9A.doc doc D5.3.6A) Info for potential external participants
D5.3.7A) Data service information on portal
D5.3.8A) Software tools service information on portal
D5.3.9A) Single point of access on portal
D5.3.6B.doc doc Demonstration of integrated products
D5.3.7B.doc doc Reports continued
D5.3.8B.doc doc Single point of access continued
D5.3.9B.doc doc Portal revamped for eternity
D5.3.10A.doc doc Demonstration of integrated products
D5.3.10B.doc doc EMBRACE registry long-term implementation
5.3.11A
(No associated document)
Portal up-to-date
D5.3.11B.doc doc The EMBRACE Data Types and Methods Ontology (EDAM) available on the portal