BISON - Revision history

Floratos at 05:13, 9 July 2013

2013-07-09T05:13:46Z

Floratos at 04:53, 9 July 2013

2013-07-09T04:53:58Z

Sean at 16:03, 15 February 2007

2007-02-15T16:03:14Z

Sean: /* Concept Definition */

2007-02-14T05:07:56Z

‎ Concept Definition

Sean: /* Architecture */

2007-02-14T05:07:32Z

‎ Architecture

Sean at 18:33, 13 February 2007

2007-02-13T18:33:57Z

Sean at 18:31, 13 February 2007

2007-02-13T18:31:14Z

Sean at 18:10, 13 February 2007

2007-02-13T18:10:59Z

Sean at 22:19, 7 February 2007

2007-02-07T22:19:24Z

Sean at 22:05, 7 February 2007

2007-02-07T22:05:34Z

New page

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

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 The foundation for component interoperability in geWorkbench is 'BISON'' ('''B'''iomedical '''I'''nformatics '''S'''tructured '''ON'''tology), an application-wide data-model for the representation of bioinformatics objects, including both primary data and analysis results. geWorkbench components communicate by exchanging BISON objects, via an underlying event-driven framework.
-BISON borrows concepts from a number of popular domain models, such as [http://www.mged.org/Workgroups/MAGE/mage-om.html MAGE-OM], [http://biojava.org/ BioJava], and [http://www.biopax.org/ BioPax]. Its design strives to achieve the right balance between concrete needs and model expressiveness, to avoid creating a model too complicated to be of practically utility.
+BISON borrows concepts from a number of well established domain models, such as [http://www.mged.org/Workgroups/MAGE/mage-om.html MAGE-OM], [http://biojava.org/ BioJava], and [http://www.biopax.org/ BioPax]. Its design strives to achieve the right balance between concrete needs and model expressiveness, to avoid creating a model too complicated to be of practically utility.
 For additional information on BISON, please see the following resources:
 * [{{SERVER}}/workbench/api/index.html BISON Javadocs documentation].

← Older revision		Revision as of 04:53, 9 July 2013
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−	~~This page provides~~ a ~~quick introduction~~ to BISON ~~concepts definitions~~, ~~architecture structure and other ontology~~ resources.	+	The foundation for component interoperability in geWorkbench is 'BISON'' ('''B'''iomedical '''I'''nformatics '''S'''tructured '''ON'''tology), an application-wide data-model for the representation of bioinformatics objects, including both primary data and analysis results. geWorkbench components communicate by exchanging BISON objects, via an underlying event-driven framework.
		+
		+	BISON borrows concepts from a number of popular domain models, such as [http://www.mged.org/Workgroups/MAGE/mage-om.html MAGE-OM], [http://biojava.org/ BioJava], and [http://www.biopax.org/ BioPax]. Its design strives to achieve the right balance between concrete needs and model expressiveness, to avoid creating a model too complicated to be of practically utility.
		+
		+	For additional information on BISON, please see the following resources:
		+	* [{{SERVER}}/workbench/api/index.html BISON Javadocs documentation].

← Older revision		Revision as of 16:03, 15 February 2007
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−	This page provides a quick introduction to BISON concepts definitions, architecture structure and other ontology resources.	+	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~~.

@@ Line 8: / Line 8: @@
 ===[[BISON - Concept Definition | Concept Definition]]===
 All concepts created in BISON are defined here.
 ===[[BISON - Architecture | Architecture]]===

@@ Line 8: / Line 8: @@
 ===[[BISON - Concept Definition | Concept Definition]]===
 All concepts created in BISON are defined here.
 ===[[BISON - Architecture | Architecture]]===

@@ Line 1: / Line 1: @@
-__NOEDITSECTION__
+This page provides a quick introduction to BISON concepts definitions, architecture structure and other ontology resources.
@@ Line 12: / Line 7: @@
 ===[[BISON - Concept Definition | Concept Definition]]===
-All concepts created in BISON are defined.
+All concepts created in BISON are defined here.
 ===[[BISON - Architecture | Architecture]]===
-The architecture that shows the relationship of all concepts.
+The architecture demonstrates the relationships between concepts.
-===[[BISON - Links to MAGNET components | Links to MAGNET components]]===
+===[[BISON - Links to MAGNET Components | Links to MAGNET Components]]===
-This indicates the linkage between MAGNET components and BISON concepts.
+This indicates the linkages between MAGNET components and BISON concepts.
-===[[BISON - Other Ontology | Other Ontology]]===
+===[[BISON - Other Ontologies | Other Ontologies]]===
 This part stores the information of other ontologies.

@@ Line 1: / Line 1: @@
 __NOEDITSECTION__
-{{TutorialsTopNav}}
+{{BISONTopNav}}
-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.
+The BISON shown on this page provide a quick introduction to BISON concepts definitions, architecture structure and other ontology resources.
-===[[Tutorial - Getting_Started | Getting Started]]===
+===[[BISON - Getting_Started | Getting Started]]===
-Obtaining and installing geWorkbench.  Requirements.
+What is BISON and what make it different from other ontologies?
-===[[Tutorial - Basics | Basics]]===
+===[[BISON - Concept Definition | Concept Definition]]===
-A brief introduction to the use of geWorkbench.
+All concepts created in BISON are defined.
-===[[Tutorial - Projects and Data Files | Projects and Data Files]]===
+===[[BISON - Architecture | Architecture]]===
-Creating projects, loading microarray data files, merging into one dataset, and saving.
+The architecture that shows the relationship of all concepts.
-===[[Tutorial - Project Details | Project Details]]===
+===[[BISON - Links to MAGNET components | Links to MAGNET components]]===
-Creating projects, loading microarray data files, merging into one dataset, and saving.
+This indicates the linkage between MAGNET components and BISON concepts.
-===[[Tutorial - Data Subsets | Data Subsets]]===
+===[[BISON - Other Ontology | Other Ontology]]===
-Subsets of both markers and arrays can be defined for targeted analysis.
+This part stores the information of other ontologies.

← Older revision	Revision as of 18:10, 13 February 2007
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	+	__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.

← Older revision		Revision as of 22:19, 7 February 2007
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−	~~[[Image:(2008-02-07)comlex object.JPG ]]~~	+