geWorkbench - User contributions [en]

BISON

2007-02-15T16:03:14Z

Sean:

This page provides a quick introduction to BISON concepts definitions, architecture structure and other ontology resources.

File:(2008-02-07)set objects.JPG

2007-02-14T05:10:06Z

Sean:

File:(2008-02-07)singleton object.JPG

2007-02-14T05:09:59Z

Sean:

File:(2008-02-07)Overall-view.JPG

2007-02-14T05:09:45Z

Sean:

BISON

2007-02-14T05:07:56Z

Sean: /* Concept Definition */

This page provides a quick introduction to BISON concepts definitions, architecture structure and other ontology resources.

===[[BISON - Getting_Started | Getting Started]]===
What is BISON and what make it different from other ontologies?

===[[BISON - Concept Definition | Concept Definition]]===
All concepts created in BISON are defined here.

===[[BISON - Architecture | Architecture]]===
The architecture demonstrates the relationships between concepts.

===[[BISON - Links to MAGNET Components | Links to MAGNET Components]]===
This indicates the linkages between MAGNET components and BISON concepts.

===[[BISON - Other Ontologies | Other Ontologies]]===
This part stores the information of other ontologies.

BISON

2007-02-14T05:07:32Z

Sean: /* Architecture */

This page provides a quick introduction to BISON concepts definitions, architecture structure and other ontology resources.

===[[BISON - Getting_Started | Getting Started]]===
What is BISON and what make it different from other ontologies?

===[[BISON - Concept Definition | Concept Definition]]===
All concepts created in BISON are defined here.

[[BISON | BISON Home]]

===[[BISON - Architecture | Architecture]]===
The architecture demonstrates the relationships between concepts.

===[[BISON - Links to MAGNET Components | Links to MAGNET Components]]===
This indicates the linkages between MAGNET components and BISON concepts.

===[[BISON - Other Ontologies | Other Ontologies]]===
This part stores the information of other ontologies.

BISON

2007-02-13T18:33:57Z

Sean:

BISON

2007-02-13T18:31:14Z

Sean:

__NOEDITSECTION__
{{BISONTopNav}}

The BISON shown on this page provide a quick introduction to BISON concepts definitions, architecture structure and other ontology resources.

===[[BISON - Getting_Started | Getting Started]]===
What is BISON and what make it different from other ontologies?

===[[BISON - Concept Definition | Concept Definition]]===
All concepts created in BISON are defined.

===[[BISON - Architecture | Architecture]]===
The architecture that shows the relationship of all concepts.

===[[BISON - Links to MAGNET components | Links to MAGNET components]]===
This indicates the linkage between MAGNET components and BISON concepts.

===[[BISON - Other Ontology | Other Ontology]]===
This part stores the information of other ontologies.

BISON

2007-02-13T18:10:59Z

Sean:

__NOEDITSECTION__
{{TutorialsTopNav}}

The tutorials shown on this page provide a quick introduction to the most important features of geWorkbench. Additional information can be found in the User Guide (in preparation) and in the Online Help section of the program.

All data sets used in the tutorials are available from the [[Download#Tutorial_data | download area]] of our site.

===[[Tutorial - Getting_Started | Getting Started]]===
Obtaining and installing geWorkbench. Requirements.

===[[Tutorial - Basics | Basics]]===
A brief introduction to the use of geWorkbench.

===[[Tutorial - Projects and Data Files | Projects and Data Files]]===
Creating projects, loading microarray data files, merging into one dataset, and saving.

===[[Tutorial - Project Details | Project Details]]===
Creating projects, loading microarray data files, merging into one dataset, and saving.

===[[Tutorial - Data Subsets | Data Subsets]]===
Subsets of both markers and arrays can be defined for targeted analysis.

===[[Tutorial - Viewing a Microarray Dataset | Viewing a Microarray Dataset]]===
Survey of geWorkbench visusaliztion tools for microarray data.

===[[Tutorial - Filtering and Normalizing | Filtering and Normalizing]]===
geWorkbench provides numerous methods for filtering and normalizing microarray data.

===[[Tutorial - EVD | Expression Value Distribution]]===
View and manipulate a histogram of the distribution of expression values for each array.

===[[Tutorial - Differential Expression | Differential Expression]]===
Several variants of the t-test are available.

===[[Tutorial - Clustering | Clustering]]===
Data can be clustered using a fast hierarchical clustering routine, as well as SOMs.

===[[Tutorial - Marker Annotations | Marker Annotations]]===
Marker annotations can be retrieved, including BioCarta pathway diagrams.

===[[Tutorial - Sequence Retrieval | Sequence Retrieval]]===
Genomic sequences for markers can be retrieved for further analysis.

===[[Tutorial - BLAST | BLAST]]===
geWorkbench can run BLAST jobs on the JCSB cluster.

===[[Tutorial - Pattern Discovery | Pattern Discovery]]===
Upstream seqeunce can be analyzed for conserved sequence patterns.

===[[Tutorial - Promoter Analysis | Promoter Analysis]]===
Search a set of sequences against a promoter database.

===[[Tutorial - Reverse Engineering | Reverse Engineering]]===
Simple network reverse engineering - microarray datasets can be analyzed for interactions between genes.

===[[Tutorial - ARACNE | ARACNE]]===
Formal method for reverse Engineering - microarray datasets can be analyzed for interactions between genes.

===[[Tutorial - Network Browser| Network Browser]]===
Provides visualization of adjacency matrix generated by ARACNE, using Cytoscape.

===[[Tutorial - GO Term Enrichment | GO Term Enrichment]]===
Determine if particluar Gene Ontology terms are overrepresented in a data subset.

===[[Tutorial - Synteny | Synteny]]===
Compare genomic sequence from two different species.

===[[Tutorial - Jmol | Jmol]]===
Jmol is a molecular structure viewer for viewing PDB format files.

Project Documentation

2007-02-07T22:23:38Z

Sean:

* '''Tutorials''': The most current source of documentation is the online help system within the application. In addition, [[Tutorials | a growing number of tutorials]] is under development. These tutorials will explain how to perform a number of common tasks using geWorkbench.

* '''User Guide''': The [[Media:GeWorkbench1.0_UserGuide.pdf |User Guide for geWorkbench v1.0]] provides detailed description for of the geWorkbench plugins.

* '''Training Slides''': A set of [[Media:GeWorkbench-HandsOnTraining_year1.zip|PowerPoint training slides]] has been created which covers the basics of using geWorkbench plus several of the more advanced modules, such as Network Reverse Engineering and annotation retrieval.

* '''[[BISON]]''': A formal Biomedical Informatics Structured Ontology for the representation of bioinformatics data-structure and data-structure transformation.

Project Documentation

2007-02-07T22:20:46Z

Sean:

* '''Tutorials''': The most current source of documentation is the online help system within the application. In addition, [[Tutorials | a growing number of tutorials]] is under development. These tutorials will explain how to perform a number of common tasks using geWorkbench.

* '''User Guide''': The [[Media:GeWorkbench1.0_UserGuide.pdf |User Guide for geWorkbench v1.0]] provides detailed description for of the geWorkbench plugins.

* '''Training Slides''': A set of [[Media:GeWorkbench-HandsOnTraining_year1.zip|PowerPoint training slides]] has been created which covers the basics of using geWorkbench plus several of the more advanced modules, such as Network Reverse Engineering and annotation retrieval.

* [[BISON]]: A formal Biomedical Informatics Structured Ontology for the representation of bioinformatics data-structure and data-structure transformation.

Design Documentation

2007-02-07T22:20:01Z

Sean:

{{DevelopersTopNav}}

* [[Framework | Component architecture framework]]: a high level description of how component instantiation and communication are handled within geWorkbench.
* [[Properties | Configuration properties]]: A description of how to set and get configuration properties for your component.

Coming soon:
* Use cases.
* Design docs for various plugin components.

BISON

2007-02-07T22:19:24Z

Sean:

Project Documentation

2007-02-07T22:18:48Z

Sean:

* '''Tutorials''': The most current source of documentation is the online help system within the application. In addition, [[Tutorials | a growing number of tutorials]] is under development. These tutorials will explain how to perform a number of common tasks using geWorkbench.

* '''User Guide''': The [[Media:GeWorkbench1.0_UserGuide.pdf |User Guide for geWorkbench v1.0]] provides detailed description for of the geWorkbench plugins.

* '''Training Slides''': A set of [[Media:GeWorkbench-HandsOnTraining_year1.zip|PowerPoint training slides]] has been created which covers the basics of using geWorkbench plus several of the more advanced modules, such as Network Reverse Engineering and annotation retrieval.

* '''BISON''': The [[Media:GeWorkbench1.0_UserGuide.pdf |User Guide for geWorkbench v1.0]] provides detailed description for of the geWorkbench plugins.

BISON

2007-02-07T22:05:34Z

Sean:

[[Image:(2008-02-07)comlex object.JPG ]]

File:(2008-02-07)comlex object.JPG

2007-02-07T22:03:11Z

Sean:

Design Documentation

2007-02-07T20:48:12Z

Sean:

{{DevelopersTopNav}}

* [[Framework | Component architecture framework]]: a high level description of how component instantiation and communication are handled within geWorkbench.
* [[Properties | Configuration properties]]: A description of how to set and get configuration properties for your component.
* [[BISON]]: A formal Biomedical Informatics Structured Ontology for the representation of bioinformatics data-structure and data-structure transformation.

Coming soon:
* Use cases.
* Design docs for various plugin components.