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LargeScale Metabolic Network Alignment: MetaCyc and KEGG PowerPoint PPT Presentation
LargeScale Metabolic Network Alignment: MetaCyc and KEGG - There are an increasing number of encyclopedic' metabolic ... Dan Davison. Anamika Kothari. Joseph Dale. MetaCyc.org. 13. SRI International Bioinformatics ...
There are an increasing number of encyclopedic' metabolic ... Dan Davison. Anamika Kothari. Joseph Dale. MetaCyc.org. 13. SRI International Bioinformatics ...
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The EcoCyc and MetaCyc Pathway/Genome Databases PowerPoint PPT Presentation
The EcoCyc and MetaCyc Pathway/Genome Databases - Ocelot Storage System Architecture. Persistent storage via disk files, Oracle DBMS ... DBMS is submerged within Ocelot, invisible to users ...
Ocelot Storage System Architecture. Persistent storage via disk files, Oracle DBMS ... DBMS is submerged within Ocelot, invisible to users ...
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Pathway Tools / BioCyc Fundamentals PowerPoint PPT Presentation
Pathway Tools / BioCyc Fundamentals - Pathway Tools / BioCyc Fundamentals Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International pkarp@ai.sri.com BioCyc.org EcoCyc.org, MetaCyc.org, HumanCyc.org
Pathway Tools / BioCyc Fundamentals Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International pkarp@ai.sri.com BioCyc.org EcoCyc.org, MetaCyc.org, HumanCyc.org
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Pathways and Molecules: Noodles and Meatballs in the Metabolite Soup PowerPoint PPT Presentation
Pathways and Molecules: Noodles and Meatballs in the Metabolite Soup - EMP enzymology and metabolism data. MetaCyc metabolic pathways. EcoCyc E. coli genome and metabolism. PathDB biological pathways and networks ...
EMP enzymology and metabolism data. MetaCyc metabolic pathways. EcoCyc E. coli genome and metabolism. PathDB biological pathways and networks ...
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Recent Developments in Pathway Tools GMOD Workshop November 07 PowerPoint PPT Presentation
Recent Developments in Pathway Tools GMOD Workshop November 07 - Taxonomic pruning reduces false positive pathway predictions ... variants in MetaCyc mean potentially many false positive pathway predictions ...
Taxonomic pruning reduces false positive pathway predictions ... variants in MetaCyc mean potentially many false positive pathway predictions ...
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Pathways PowerPoint PPT Presentation
Pathways - http://www.genome.ad.jp/kegg/ http://www.brenda.uni-koeln.de ... EMP enzymology and metabolism data. MetaCyc metabolic pathways ...
http://www.genome.ad.jp/kegg/ http://www.brenda.uni-koeln.de ... EMP enzymology and metabolism data. MetaCyc metabolic pathways ...
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Challenges in Creating and Curating Plant PGDBs: Lessons Learned from AraCyc and PoplarCyc PowerPoint PPT Presentation
Challenges in Creating and Curating Plant PGDBs: Lessons Learned from AraCyc and PoplarCyc - Challenges in Creating and Curating Plant PGDBs: Lessons Learned from AraCyc and PoplarCyc Peifen Zhang Carnegie Institution For Science Department of Plant Biology
Challenges in Creating and Curating Plant PGDBs: Lessons Learned from AraCyc and PoplarCyc Peifen Zhang Carnegie Institution For Science Department of Plant Biology
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BioWarehouse: A Bioinformatics Database Warehouse PowerPoint PPT Presentation
BioWarehouse: A Bioinformatics Database Warehouse - A Bioinformatics Database Warehouse Peter D. Karp, Thomas J. Lee, Valerie Wagner BioCyc BioPAX BioCyc ENZYME CMR Genbank BioWarehouse Eco2DBase Oracle (10g) or
A Bioinformatics Database Warehouse Peter D. Karp, Thomas J. Lee, Valerie Wagner BioCyc BioPAX BioCyc ENZYME CMR Genbank BioWarehouse Eco2DBase Oracle (10g) or
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Pathway%20Tools%20User%20Group%20Meeting%20Introduction PowerPoint PPT Presentation
Pathway%20Tools%20User%20Group%20Meeting%20Introduction - Read the release notes! SRI International. Bioinformatics. Behind the Scenes. 330,000 lines of code, mostly Common Lisp. 4.5 programmers ...
Read the release notes! SRI International. Bioinformatics. Behind the Scenes. 330,000 lines of code, mostly Common Lisp. 4.5 programmers ...
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Selected PathoLogic Refining Tasks PowerPoint PPT Presentation
Selected PathoLogic Refining Tasks - Selected PathoLogic Refining Tasks Creation of Protein Complexes Assignment of Modified Proteins Operon Prediction Creating Protein Complexes Refine - Create Protein ...
Selected PathoLogic Refining Tasks Creation of Protein Complexes Assignment of Modified Proteins Operon Prediction Creating Protein Complexes Refine - Create Protein ...
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Submitting%20pathway%20to%20MetaCyc PowerPoint PPT Presentation
Submitting%20pathway%20to%20MetaCyc - Why Curate a PGDB? A well curated PGDB can serve as a central online resource that integrates many ... Curate full information for enzymes and genes. ...
Why Curate a PGDB? A well curated PGDB can serve as a central online resource that integrates many ... Curate full information for enzymes and genes. ...
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Combining Computational Prediction and Manual Curation to Create Plant Metabolic Pathway Databases PowerPoint PPT Presentation
Combining Computational Prediction and Manual Curation to Create Plant Metabolic Pathway Databases - Combining Computational Prediction and Manual Curation to Create Plant Metabolic Pathway Databases Peifen Zhang Carnegie Institution For Science
Combining Computational Prediction and Manual Curation to Create Plant Metabolic Pathway Databases Peifen Zhang Carnegie Institution For Science
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The BioCyc Collection of PathwayGenome Databases PowerPoint PPT Presentation
The BioCyc Collection of PathwayGenome Databases - Acids. Res. 33:D334 2005 ASM News 70:25 2004 Science 293:2040 ... Nucleic Acids Research 34:D511-D516 2006. SRI International. Bioinformatics. Comparative Tools ...
Acids. Res. 33:D334 2005 ASM News 70:25 2004 Science 293:2040 ... Nucleic Acids Research 34:D511-D516 2006. SRI International. Bioinformatics. Comparative Tools ...
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Introduction to Bioinformatics - Tutorial no. 13 PowerPoint PPT Presentation
Introduction to Bioinformatics - Tutorial no. 13 - Introduction to Bioinformatics - Tutorial no. 13 Probe Design Gene Networks Probe design problem Given a genome with a set of genes. Recall that each gene is ...
Introduction to Bioinformatics - Tutorial no. 13 Probe Design Gene Networks Probe design problem Given a genome with a set of genes. Recall that each gene is ...
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Reconstructing the metabolic network of a bacterium from its genome: the construction of LacplantCyc PowerPoint PPT Presentation
Reconstructing the metabolic network of a bacterium from its genome: the construction of LacplantCyc - In silico reconstruction of the metabolic pathways of ... determine orthology (use phylogeny and gene-context to determine evolutionary relationship) ...
In silico reconstruction of the metabolic pathways of ... determine orthology (use phylogeny and gene-context to determine evolutionary relationship) ...
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PathoLogic: More about Matching Enzyme Names to Reactions PowerPoint PPT Presentation
PathoLogic: More about Matching Enzyme Names to Reactions - ... you to specify additional name-reaction mappings not present in ... The name matcher indexes names from: reaction frames (e.g., official names assigned by EC) ...
... you to specify additional name-reaction mappings not present in ... The name matcher indexes names from: reaction frames (e.g., official names assigned by EC) ...
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Biological Pathways PowerPoint PPT Presentation
Biological Pathways - Biological Pathways ... PPI databases Many databases DIP Established in 1999 in UCLA extract and integrate protein-protein info and build a user-friendly ...
Biological Pathways ... PPI databases Many databases DIP Established in 1999 in UCLA extract and integrate protein-protein info and build a user-friendly ...
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Advanced Editing of Pathway/Genome Databases PowerPoint PPT Presentation
Advanced Editing of Pathway/Genome Databases - (import-compounds '(CPD-ID) (kb-of-organism 'meta) (kb-of-organism 'ecoli)) (import-reactions '(ID-RXN) (kb-of-organism 'meta) (kb-of-organism 'ecoli) ...
(import-compounds '(CPD-ID) (kb-of-organism 'meta) (kb-of-organism 'ecoli)) (import-reactions '(ID-RXN) (kb-of-organism 'meta) (kb-of-organism 'ecoli) ...
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The Pathway/Genome Navigator PowerPoint PPT Presentation
The Pathway/Genome Navigator - The Pathway/Genome Navigator
The Pathway/Genome Navigator
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Bio-Trac 25 (Proteomics: Principles and Methods) PowerPoint PPT Presentation
Bio-Trac 25 (Proteomics: Principles and Methods) - Title: Protein Family Classification for Functional Genomics Author: wuc Last modified by: zh9 Created Date: 3/9/2001 10:06:29 PM Document presentation format
Title: Protein Family Classification for Functional Genomics Author: wuc Last modified by: zh9 Created Date: 3/9/2001 10:06:29 PM Document presentation format
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Bio-Trac 25 (Proteomics: Principles and Methods) PowerPoint PPT Presentation
Bio-Trac 25 (Proteomics: Principles and Methods) - Molecular Biology Database Collection (http://nar.oupjournals.org/cgi/content ... WIT: Functional Curation and Metabolic Models. BRENDA: Enzyme Database ...
Molecular Biology Database Collection (http://nar.oupjournals.org/cgi/content ... WIT: Functional Curation and Metabolic Models. BRENDA: Enzyme Database ...
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Overview of the Pathway Tools Software and Pathway/Genome Databases PowerPoint PPT Presentation
Overview of the Pathway Tools Software and Pathway/Genome Databases - What do you hope to get out of the tutorial? SRI International. Bioinformatics. SRI ... Mike McLeod, University of British Columbia, Rhodococcus sp. RHA1 ...
What do you hope to get out of the tutorial? SRI International. Bioinformatics. SRI ... Mike McLeod, University of British Columbia, Rhodococcus sp. RHA1 ...
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Jacques van Helden Jacques'van'Heldenulb'ac'be PowerPoint PPT Presentation
Jacques van Helden Jacques'van'Heldenulb'ac'be - With the advent of high-throughput methods, we dispose of ... ChIP (Chromatin Immunoprecipitation) on chip to detect protein-DNA binding. Mutant phenotypes. ...
With the advent of high-throughput methods, we dispose of ... ChIP (Chromatin Immunoprecipitation) on chip to detect protein-DNA binding. Mutant phenotypes. ...
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Functional annotation PowerPoint PPT Presentation
Functional annotation - Functional annotation Datasources Konstantinos Mavrommatis Head of Omics group DOE-JGI Kmavrommatis@lbl.gov
Functional annotation Datasources Konstantinos Mavrommatis Head of Omics group DOE-JGI Kmavrommatis@lbl.gov
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The Pathway/Genome Navigator PowerPoint PPT Presentation
The Pathway/Genome Navigator - By name/frame ID must be exact (though there are synonyms) ... Synonyms, classification (GO), link to browser. Unification links, gene-reaction schematic ...
By name/frame ID must be exact (though there are synonyms) ... Synonyms, classification (GO), link to browser. Unification links, gene-reaction schematic ...
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Protein Pathways and Pathway Databases PowerPoint PPT Presentation
Protein Pathways and Pathway Databases - All pathways are networks of interactions, however not all networks are ... Chemical substructure comparison. Enzymes,Transcription Factors. Genes: Blast search ...
All pathways are networks of interactions, however not all networks are ... Chemical substructure comparison. Enzymes,Transcription Factors. Genes: Blast search ...
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Editing Pathway/Genome Databases PowerPoint PPT Presentation
Editing Pathway/Genome Databases - The database is separate from the user interface. The Navigator ... Curate information about enzymes and genes, including evidence codes for all enzymes. ...
The database is separate from the user interface. The Navigator ... Curate information about enzymes and genes, including evidence codes for all enzymes. ...
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Update on The Pathway Tools Software PowerPoint PPT Presentation
Update on The Pathway Tools Software - Chemical substructure comparison. Enzymes, Transporters, ... Query compounds by name, MW, formula, substructure. Reference list displayed at bottom of page ...
Chemical substructure comparison. Enzymes, Transporters, ... Query compounds by name, MW, formula, substructure. Reference list displayed at bottom of page ...
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Pathways PowerPoint PPT Presentation
Pathways - M.A. Ott (CMBI) Pathways & Molecules Contents Enzymes and Metabolites Metabolic Pathways: Cholesterol Biosynthesis Metabolic Disorders BioMeta Database ...
M.A. Ott (CMBI) Pathways & Molecules Contents Enzymes and Metabolites Metabolic Pathways: Cholesterol Biosynthesis Metabolic Disorders BioMeta Database ...
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Global changes in Staphylococcus aureus gene expression during human prosthetic joint infection PowerPoint PPT Presentation
Global changes in Staphylococcus aureus gene expression during human prosthetic joint infection - Global changes in Staphylococcus aureusgene expression during human prosthetic joint infection. AAU. trt@teknologisk.dkwww.cmc.aau.dk. I n t r o d u c t i o n
Global changes in Staphylococcus aureusgene expression during human prosthetic joint infection. AAU. trt@teknologisk.dkwww.cmc.aau.dk. I n t r o d u c t i o n
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CalbiCyc, Metabolic Pathways at the Candida Genome Database PowerPoint PPT Presentation
CalbiCyc, Metabolic Pathways at the Candida Genome Database - Pathways are just one of the types of data we provide, and they account for a ... Found that it was easier to make progress by making a focused 'project' out of ...
Pathways are just one of the types of data we provide, and they account for a ... Found that it was easier to make progress by making a focused 'project' out of ...
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Creating the right chemistry in Pathways PowerPoint PPT Presentation
Creating the right chemistry in Pathways - Systems biology ...not in ten years. Pathways which? ... Tautomerism (variable positions of hydrogens) Other 'chemical' flexibility. Protonation state ...
Systems biology ...not in ten years. Pathways which? ... Tautomerism (variable positions of hydrogens) Other 'chemical' flexibility. Protonation state ...
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Overview of Genome Databases PowerPoint PPT Presentation
Overview of Genome Databases - Definition of Bioinformatics ... For many years, the majority of bioinformatics DBs did not employ a DBMS ... Warehouse schema defines many bioinformatics datatypes ...
Definition of Bioinformatics ... For many years, the majority of bioinformatics DBs did not employ a DBMS ... Warehouse schema defines many bioinformatics datatypes ...
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The Ocelot Frame Knowledge Representation System PowerPoint PPT Presentation
The Ocelot Frame Knowledge Representation System - ... Knowledge Representation Systems. Long history of development in the AI knowledge ... Aka DB, Knowledge Base, KB, PGDB. An Ocelot database is a ...
... Knowledge Representation Systems. Long history of development in the AI knowledge ... Aka DB, Knowledge Base, KB, PGDB. An Ocelot database is a ...
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PathoLogic Pathway Predictor PowerPoint PPT Presentation
PathoLogic Pathway Predictor - Transform existing genome to PGDB form. Infer metabolic pathways ... Coloring scheme aids in assessing pathway evidence. Phase I: Prune extra variant pathways ...
Transform existing genome to PGDB form. Infer metabolic pathways ... Coloring scheme aids in assessing pathway evidence. Phase I: Prune extra variant pathways ...
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BioTrac 25 Proteomics: Principles and Methods PowerPoint PPT Presentation
BioTrac 25 Proteomics: Principles and Methods - BioTrac 25 Proteomics: Principles and Methods
BioTrac 25 Proteomics: Principles and Methods
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Subsystem Approach to Genome Annotation PowerPoint PPT Presentation
Subsystem Approach to Genome Annotation - Subsystem Approach to Genome Annotation National Microbial Pathogen Data Resource www.nmpdr.org Claudia Reich NCSA, University of Illinois, Urbana
Subsystem Approach to Genome Annotation National Microbial Pathogen Data Resource www.nmpdr.org Claudia Reich NCSA, University of Illinois, Urbana
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Digital Cells Nano-Bio-Info Technology PowerPoint PPT Presentation
Digital Cells Nano-Bio-Info Technology - Digital Cells Nano-Bio-Info Technology Introduction to Nanotechnology Image by John Alsop Outline Concept of a gene (extended) Gene Regulatory Networks (GRN) GRN and ...
Digital Cells Nano-Bio-Info Technology Introduction to Nanotechnology Image by John Alsop Outline Concept of a gene (extended) Gene Regulatory Networks (GRN) GRN and ...
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Protein and Proteome Annotation PowerPoint PPT Presentation
Protein and Proteome Annotation - Objective - identify and describe all the physico-chemical, ... SCOP. http://scop.mrc-lmb.cam.ac.uk/scop/ Lecture 2.5. 20. Expression Databases. Swiss 2D Page ...
Objective - identify and describe all the physico-chemical, ... SCOP. http://scop.mrc-lmb.cam.ac.uk/scop/ Lecture 2.5. 20. Expression Databases. Swiss 2D Page ...
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BIO-TRAC 25 (Proteomics: Principles and Methods) PowerPoint PPT Presentation
BIO-TRAC 25 (Proteomics: Principles and Methods) - Transmembrane Helix: TMHMM, TMAP. 2D Prediction (a-helix, b-sheet, Coiled-coils): PHD, JPred ... Transmembrane Helix (http://www.cbs.dtu.dk/services/TMHMM/) 29 ...
Transmembrane Helix: TMHMM, TMAP. 2D Prediction (a-helix, b-sheet, Coiled-coils): PHD, JPred ... Transmembrane Helix (http://www.cbs.dtu.dk/services/TMHMM/) 29 ...
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Overview of Biochemical Pathways PowerPoint PPT Presentation
Overview of Biochemical Pathways - Bioinformatics, Vol. 19 Suppl. 1 2003, pages i331 i339. Yizhar Regev ... Bioinformatics, Vol. 17 no.9, 829-837. Problem 1. No graphical modelers can represent ...
Bioinformatics, Vol. 19 Suppl. 1 2003, pages i331 i339. Yizhar Regev ... Bioinformatics, Vol. 17 no.9, 829-837. Problem 1. No graphical modelers can represent ...
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Writing Programs that Analyze PathwayGenome Databases PowerPoint PPT Presentation
Writing Programs that Analyze PathwayGenome Databases - Types of Credit: Created, Reviewed, Revised. Home Pages for Authors ... used for Stoichiometry Coefficients, Compartments, Citations, etc. Principal Classes 1 ...
Types of Credit: Created, Reviewed, Revised. Home Pages for Authors ... used for Stoichiometry Coefficients, Compartments, Citations, etc. Principal Classes 1 ...
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Using CDK applications in the BioMeta database PowerPoint PPT Presentation
Using CDK applications in the BioMeta database - 'Creating the right chemistry' in Pathways. M.A. Ott. Enzymes don't ... FAD, FADH2. FMN, FMNH2. SAM, SAH. Coenzyme A. Glutamate/2-Oxoglutarate. Phosphorylation ...
'Creating the right chemistry' in Pathways. M.A. Ott. Enzymes don't ... FAD, FADH2. FMN, FMNH2. SAM, SAH. Coenzyme A. Glutamate/2-Oxoglutarate. Phosphorylation ...
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48x36 Poster Template PowerPoint PPT Presentation
48x36 Poster Template - Title: 48x36 Poster Template Subject: Free PowerPoint poster templates Author: A. Kotoulas Keywords: poster presentation, poster design, poster template
Title: 48x36 Poster Template Subject: Free PowerPoint poster templates Author: A. Kotoulas Keywords: poster presentation, poster design, poster template
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Bereich 3: V10 - Integrative Biologie PowerPoint PPT Presentation
Bereich 3: V10 - Integrative Biologie - Title: Computational Biology - Bioinformatik Author: Volkhard Helms Last modified by: Volkhard Helms Created Date: 1/8/2002 4:03:31 PM Document presentation format
Title: Computational Biology - Bioinformatik Author: Volkhard Helms Last modified by: Volkhard Helms Created Date: 1/8/2002 4:03:31 PM Document presentation format
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Drawing, clustering and visualization of biological pathways. PowerPoint PPT Presentation
Drawing, clustering and visualization of biological pathways. - Drawing, clustering and visualization of biological pathways. ... David Auber (Bordeaux Labri) Yves Chiricota (Chicoutimi UQAM) Thank you for your attention ...
Drawing, clustering and visualization of biological pathways. ... David Auber (Bordeaux Labri) Yves Chiricota (Chicoutimi UQAM) Thank you for your attention ...
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Bio-Trac 25 (Proteomics: Principles and Methods) PowerPoint PPT Presentation
Bio-Trac 25 (Proteomics: Principles and Methods) - Proteomic Resources 2D-Gel Image Databases Slide 49 PRIDE: centralized, standards compliant, public data repository for proteomics data Slide 51 ...
Proteomic Resources 2D-Gel Image Databases Slide 49 PRIDE: centralized, standards compliant, public data repository for proteomics data Slide 51 ...
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Pathway Tools: Recent Developments PowerPoint PPT Presentation
Pathway Tools: Recent Developments - RGD (Rat), Medical College of Wisconsin. WormBase (C. elegans), Caltech. Large scale users: ... Will use dictionary of biomedical terms. New sequence retrieval dialog ...
RGD (Rat), Medical College of Wisconsin. WormBase (C. elegans), Caltech. Large scale users: ... Will use dictionary of biomedical terms. New sequence retrieval dialog ...
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Community Standards and Comparative Genomics PowerPoint PPT Presentation
Community Standards and Comparative Genomics - Community Standards and Comparative Genomics
Community Standards and Comparative Genomics
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CHALLENGE PowerPoint PPT Presentation
CHALLENGE - CHALLENGE
CHALLENGE
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BioWarehouse: The BioSPICE Bioinformatics Database Warehouse PowerPoint PPT Presentation
BioWarehouse: The BioSPICE Bioinformatics Database Warehouse - Create a toolkit for integrating a set of bioinformatics databases into one ... Representational tricks to decrease schema bloat. Single space of primary keys ...
Create a toolkit for integrating a set of bioinformatics databases into one ... Representational tricks to decrease schema bloat. Single space of primary keys ...
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The aims of the Gene Ontology project are threefold: PowerPoint PPT Presentation
The aims of the Gene Ontology project are threefold: - ... gene products with GO terms (annotation) GO employs three ontologies to describe gene product attributes: ... NUTRITIONAL COMPOSITION. DIET GO. RELATED PRODUCTS ...
... gene products with GO terms (annotation) GO employs three ontologies to describe gene product attributes: ... NUTRITIONAL COMPOSITION. DIET GO. RELATED PRODUCTS ...
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Guest Lecture PowerPoint PPT Presentation
Guest Lecture - Database concepts - what is a 'good' database (DB) How is data stored and ... has open interfaces (APIs) for query requests. Bad DB: ... APIs, Mashups, SQL ...
Database concepts - what is a 'good' database (DB) How is data stored and ... has open interfaces (APIs) for query requests. Bad DB: ... APIs, Mashups, SQL ...
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Genome Annotation and Pathway Mining PowerPoint PPT Presentation
Genome Annotation and Pathway Mining - Sift results for biological relevance. Pathway mining. E.g. 'Can my organism ... Again, sift results for biological relevance. Example: GO. Find ... sift ...
Sift results for biological relevance. Pathway mining. E.g. 'Can my organism ... Again, sift results for biological relevance. Example: GO. Find ... sift ...
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