DIAMONDS project

1
DIAMONDS project

• WORKPACKAGE 5
• Cell Cycle Portal
• MARSEILLE MEETING
• 2006, June 15th

2
GENERAL INDEX

• WORKPACKAGE PROGRESS
• FIRST PROGRAMMING STAGE
• FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
  IMPLEMENTATION
• NEXT STAGE PLANNING FUTURE DELIVERABLE

3
WORKPACKAGE PROGRESS
JAN 05
1. REQUIREMENTS ANALYSIS
JUN 05
Deliverable 5.2
2. PLATFORM PREPARING
DEC 05
3. PROGRAMMING 1st PHASE
JUN 06
4. PROGRAMMING 2nd PHASE
DEC 06
Beta version
5. DEPURATION AND TRAINING
DEC 07
Final version
4
WORKPACKAGE PROGRESS
JAN 05
1. REQUIREMENTS ANALYSIS
JUN 05
Deliverable 5.2
2. PLATFORM PREPARING
DEC 05
3. PROGRAMMING 1st PHASE
JUN 06
4. PROGRAMMING 2nd PHASE
DEC 06
Beta version
5. DEPURATION AND TRAINING
DEC 07
Final version
5
WORKPACKAGE PROGRESS
JAN 05
1. REQUIREMENTS ANALYSIS
JUN 05
Deliverable 5.2
2. PLATFORM PREPARING
DEC 05
3. PROGRAMMING 1st PHASE
JUN 06
4. PROGRAMMING 2nd PHASE
DEC 06
Beta version
5. DEPURATION AND TRAINING
DEC 07
Final version
6
WORKPACKAGE PROGRESS
JAN 05
1. REQUIREMENTS ANALYSIS
JUN 05
Deliverable 5.2
2. PLATFORM PREPARING
DEC 05
3. PROGRAMMING 1st PHASE
JUN 06
4. PROGRAMMING 2nd PHASE
DEC 06
Beta version
5. DEPURATION AND TRAINING
DEC 07
Final version
7
WORKPACKAGE PROGRESS
JAN 05
1. REQUIREMENTS ANALYSIS
JUN 05
Deliverable 5.2
2. PLATFORM PREPARING
DEC 05
3. PROGRAMMING 1st PHASE
JUN 06
4. PROGRAMMING 2nd PHASE
DEC 06
Beta version
5. DEPURATION AND TRAINING
DEC 07
Final version
8
WORKPACKAGE PROGRESS
JAN 05
1. REQUIREMENTS ANALYSIS
JUN 05
Deliverable 5.2
2. PLATFORM PREPARING
DEC 05
3. PROGRAMMING 1st PHASE
JUN 06
4. PROGRAMMING 2nd PHASE
DEC 06
Beta version
5. DEPURATION AND TRAINING
DEC 07
Final version
9
FIRST PROGRAMMING STAGE
1. Add new functionalities to EXPRESSION
PROFILER, as well as GIN-DB interface and
DIAMONDS resources.
EXPRESSION PROFILER

• Microarray data analysis and transformations
• Clustering
• Gene Ontology annotation

GIN-DB

• and more

• Protein classification
• Gene homologies
• Periodic profiles detection
• Public databases annotation
• Modeling and simulation

DIAMONDS RESOURCES
Links to partners tools and web sites

• and more

10
FIRST PROGRAMMING STAGE
1. Add new functionalities to EXPRESSION
PROFILER, as well as GIN-DB interface and
DIAMONDS resources.
2. We can understand the set as new entity called
DIAMONDS tool. To give DIAMONDS tool its own
identity we change the appearance

• Microarray data analysis and transformations
• Clustering
• Gene Ontology annotation

• and more

• Protein classification
• Gene homologies
• Periodic profiles detection
• Public databases annotation
• Modeling and simulation

11
FIRST PROGRAMMING STAGE
1. Add new functionalities to EXPRESSION
PROFILER, as well as GIN-DB interface and
DIAMONDS resources.
2. We can understand the set as new entity called
DIAMONDS tool. To give DIAMONDS tool its own
identity we change the appearance
3. Finally, the DIAMONDS tool is included into a
web portal with extra features.

• Microarray data analysis and transformations
• Clustering
• Gene Ontology annotation

GIN-DB

• and more

• Protein classification
• Gene homologies
• Periodic profiles detection
• Public databases annotation
• Modeling and simulation

DIAMONDS RESOURCES
Links to partners tools and web sites

• and more

12
FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS

EXPROF Web service developed by CBS
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FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS

EXPROF Web service developed by CBS
WU-Blast, implemented using web service available
in EBI web site
16
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FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS

EXPROF Web service developed by CBS
WU-Blast, implemented using web service available
in EBI web site
Completely developed in NorayBio for Kegg,
Reactome, GeneBank, SwissProt, Homologene and OMIM
19
(No Transcript)
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(No Transcript)
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FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS

EXPROF Web service developed by CBS
WU-Blast, implemented using web service available
in EBI web site
Completely developed in NorayBio for Kegg,
Reactome, GeneBank, SwissProt, Homologene and OMIM
Developed in NorayBio with Umed collaboration
23
(No Transcript)
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(No Transcript)
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(No Transcript)
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FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS

EXPROF Web service developed by CBS
WU-Blast, implemented using web service available
in EBI web site
Completely developed in NorayBio for Kegg,
Reactome, GeneBank, SwissProt, Homologene and OMIM
Developed in NorayBio with Umed collaboration
Web service developed by HUJI
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(No Transcript)
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(No Transcript)
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FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS

EXPROF Web service developed by CBS
WU-Blast, implemented using web service available
in EBI web site
Completely developed in NorayBio for Kegg,
Reactome, GeneBank, SwissProt, Homologene and OMIM
Developed in NorayBio, using the DB provided by
UMed
Web service developed by HUJI
Interface for local downloads
30
(No Transcript)
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(No Transcript)
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FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS
• TEXT MINING

EXPROF Web service developed by CBS
WU-Blast, implemented using web service available
in EBI web site
Completely developed in NorayBio for Kegg,
Reactome, GeneBank, SwissProt, Homologene and OMIM
Developed in NorayBio, using the DB provided by
UMed
Web service developed by HUJI
Interface for local downloads
iHOP web service from CSIC
33
(No Transcript)
34
(No Transcript)
35
(No Transcript)
36
FUNCTIONALITIES IMPLEMENTED AND WAITING FOR NEXT
IMPLEMENTATION

• EXPRESSION DATA
• Analysis, transformations and normalization
• Clustering
• t-test
• PERIODIC EXPRESSION PROFILES DETECTION
• GENE HOMOLOGIES
• PHYLOGENETIC TREES
• PROMOTER ANALYSIS
• PUBLIC DATABASES ANNOTATION
• Gene Ontology
• Other databases
• GIN-DB INTERFACE
• PROTEIN CLASSIFICATION
• MODELING AND SIMULATION
• RESIDUE SUBSTITUTIONS
• TEXT MINING

EXPROF Web service developed by CBS
WU-Blast, implemented using web service available
in EBI web site
Completely developed in NorayBio for Kegg,
Reactome, GeneBank, SwissProt, Homologene and OMIM
Developed in NorayBio, using the DB provided by
UMed
Web service developed by HUJI
Interface for local downloads
iHOP web service from CSIC
37
NEXT STAGE PLANNING FUTURE DELIVERABLE
Deliverable 5.3 GUI Beta version, in Month 24
(December 2006)
For the platform beta version we will
Improve and finish the actual functionalities
Include new tools not available in previous
stages, as long as the tool responsible provide
some integration facilities
Add some important features for tool operation
Complete manual
Drag and drop functionalities Mouse over
assistance Workspaces management user workspace,
common workspace and intercommunication Tool
profiles and permissions GIN-DB profiles and
permissions
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QUESTIONS AND COMMENTS
?
WORKPACKAGE 5. Cell Cycle Portal