Recent changes to Home

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Thu, 20 Mar 2014 21:45:09 -0000

--- v13
+++ v14
@@ -1,37 +1 @@
-# Virtual Fly Brain web application
-
-[Virtual Fly Brain](http://www.virtualflybrain.org) (VFB) is a data integration hub for Drosophila neurobiology.  It allows users to search, browse and query information about Drosophila neuroanatomy.  
-
-Auto-complete driven searches across an extensive dictionary of structure names and synonyms allow users to find anatomical structures and cell types using almost any term they find in the Drosophila neurobiology literature.  Each term found includes a textual description with references, a list of synonyms, images (if available) and a set of relationships to other terms via which users can browse to find details of related anatomical structures.  A range of queries are available from each term including anatomical queries, queries for images, queries for expression of genes or transgenes and queries for phenotypes.  
-
-Users can also browse a painted 3D stack of a Drosophila brain using a system which allows viewing of virtual sections through the stack in any arbitrary plane. Structures can be identified via tool-tips, prompted by floating the cursor over a region and selected. by clicking on the stack or on a part-tree of painted structures.  We have a large library of annotated 3D images that are registered to the standard brain used in our stack browser.  This includes > 16000 single neuron images from [FlyCircuit](http://www.flycircuit.tw), several thousand GAL4 line images from the [Rubin lab](http://www.janelia.org/lab/rubin-lab) and > 200 images of lineage clones from the labs of [Tzumin Lee](http://www.janelia.org/lab/lee-tzumin-lab) and [Kei Ito](http://www.k.u-tokyo.ac.jp/pros-e/person/kei_ito/kei_ito.htm) (to be released in July 2013).  Users can add 3D images to the stack and view serial sections of them.  A system allowing multiple overlaid to be displayed is under development and will be release shortly.
-
-The central component that binds VFB into a queryable whole is an [ontology of Drosophila anatomy](https://sourceforge.net/p/fbbtdv/) in [OWL2](http://www.w3.org/TR/owl2-primer/). The logical component of this ontology includes axioms about the properties of neurons including synaptic partners and the locations of synaptic terminals \[1\]. All VFB queries use OWL reasoning software to query the ontology, returning inferences about neuroanatomy. For anatomy queries, these are used directly to generate query results pages. For queries of expression and phenotype the resulting lists of anatomy terms are used to query across 10s of thousands of annotations in a local instance of the [FlyBase CHADO database](http://gmod.org/wiki/Public_Chado_Databases).  Queries of images use OWL queries over the ontology combined with a formal representation of what the images depict as OWL individuals.
-
-[[members limit=20]]
-
-### Publications
-
- 1. _Osumi-Sutherland D., Reeve S., Mungall C., Ruttenberg A. Neuhaus F, Jefferis G.S.X.E, Armstrong J.D._ (2012) A strategy for building neuro-anatomy ontologies. [Bioinformatics __28__(9): 1262-1269.](http://bioinformatics.oxfordjournals.org/content/28/9/1262.full)
- 1. _Milyaev N., Osumi-Sutherland D., Reeve S., Burton N., Baldock R.A., Armstrong J.D._ (2012) The Virtual Fly Brain Browser and Query Interface. [Bioinformatics __28__(3): 411-415](http://bioinformatics.oxfordjournals.org/content/28/3/411.full)
-
-### Annotating your own data using our system
-
-We maintain a page on [the Drosophila anatomy ontology wiki](https://sourceforge.net/p/fbbtdv/wiki/Annotate_your_data/) outlining the advantages of annotating your own data using our system and providing links to resources for doing so.
-
-#### Documentation
-Please note.  This is a work in progress. Most documentation currently lives in a google doc. We are in the process of transferring it to this wiki.
-
- * __Functional Description__
-     * [User scenarios](user_scenarios)
-     * [Description and functions of pages](page_descriptions)
- * __Technical Description__
-     * [Static content](static_content)
-     * [Dynamic content](dynamic_content)
-     * [Java](java)
- * __Data structures__
-     * [FlyBase CHADO](FBChado)
-     * [VFB link path DB](VFB_DB)
-     * [Ontologies](ont)
-     * [OWL individuals](owl_ind)
- * [__Stack Browser__](stack_browser)
+We've moved to GitHub: https://github.com/VirtualFlyBrain/VFB

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Fri, 07 Jun 2013 14:01:49 -0000

--- v12
+++ v13
@@ -28,6 +28,7 @@
  * __Technical Description__
      * [Static content](static_content)
      * [Dynamic content](dynamic_content)
+     * [Java](java)
  * __Data structures__
      * [FlyBase CHADO](FBChado)
      * [VFB link path DB](VFB_DB)

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Thu, 06 Jun 2013 11:40:28 -0000

--- v11
+++ v12
@@ -10,16 +10,16 @@

 [[members limit=20]]

-# Publications
+### Publications

  1. _Osumi-Sutherland D., Reeve S., Mungall C., Ruttenberg A. Neuhaus F, Jefferis G.S.X.E, Armstrong J.D._ (2012) A strategy for building neuro-anatomy ontologies. [Bioinformatics __28__(9): 1262-1269.](http://bioinformatics.oxfordjournals.org/content/28/9/1262.full)
  1. _Milyaev N., Osumi-Sutherland D., Reeve S., Burton N., Baldock R.A., Armstrong J.D._ (2012) The Virtual Fly Brain Browser and Query Interface. [Bioinformatics __28__(3): 411-415](http://bioinformatics.oxfordjournals.org/content/28/3/411.full)

-# Annotating your own data using our system
+### Annotating your own data using our system

 We maintain a page on [the Drosophila anatomy ontology wiki](https://sourceforge.net/p/fbbtdv/wiki/Annotate_your_data/) outlining the advantages of annotating your own data using our system and providing links to resources for doing so.

-# Documentation
+#### Documentation
 Please note.  This is a work in progress. Most documentation currently lives in a google doc. We are in the process of transferring it to this wiki.

  * __Functional Description__

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Thu, 06 Jun 2013 11:39:58 -0000

--- v10
+++ v11
@@ -15,6 +15,10 @@
  1. _Osumi-Sutherland D., Reeve S., Mungall C., Ruttenberg A. Neuhaus F, Jefferis G.S.X.E, Armstrong J.D._ (2012) A strategy for building neuro-anatomy ontologies. [Bioinformatics __28__(9): 1262-1269.](http://bioinformatics.oxfordjournals.org/content/28/9/1262.full)
  1. _Milyaev N., Osumi-Sutherland D., Reeve S., Burton N., Baldock R.A., Armstrong J.D._ (2012) The Virtual Fly Brain Browser and Query Interface. [Bioinformatics __28__(3): 411-415](http://bioinformatics.oxfordjournals.org/content/28/3/411.full)

+# Annotating your own data using our system
+
+We maintain a page on [the Drosophila anatomy ontology wiki](https://sourceforge.net/p/fbbtdv/wiki/Annotate_your_data/) outlining the advantages of annotating your own data using our system and providing links to resources for doing so.
+
 # Documentation
 Please note.  This is a work in progress. Most documentation currently lives in a google doc. We are in the process of transferring it to this wiki.

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 16:52:08 -0000

--- v9
+++ v10
@@ -29,4 +29,4 @@
      * [VFB link path DB](VFB_DB)
      * [Ontologies](ont)
      * [OWL individuals](owl_ind)
- * [Stack Browser](stack_browser)
+ * [__Stack Browser__](stack_browser)

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 16:51:27 -0000

--- v8
+++ v9
@@ -18,13 +18,13 @@
 # Documentation
 Please note.  This is a work in progress. Most documentation currently lives in a google doc. We are in the process of transferring it to this wiki.

- * [Functional Description](func_desc)
+ * __Functional Description__
      * [User scenarios](user_scenarios)
      * [Description and functions of pages](page_descriptions)
- * [Technical Description](tech_desc)
+ * __Technical Description__
      * [Static content](static_content)
      * [Dynamic content](dynamic_content)
- * [Data structures](data_strucs)
+ * __Data structures__
      * [FlyBase CHADO](FBChado)
      * [VFB link path DB](VFB_DB)
      * [Ontologies](ont)

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 11:15:40 -0000

--- v7
+++ v8
@@ -4,7 +4,7 @@

 Auto-complete driven searches across an extensive dictionary of structure names and synonyms allow users to find anatomical structures and cell types using almost any term they find in the Drosophila neurobiology literature.  Each term found includes a textual description with references, a list of synonyms, images (if available) and a set of relationships to other terms via which users can browse to find details of related anatomical structures.  A range of queries are available from each term including anatomical queries, queries for images, queries for expression of genes or transgenes and queries for phenotypes.  

-Users can also browse a painted 3D stack of a Drosophila brain using a system which allows viewing of virtual sections through the stack in any arbitrary plane. Structures can be identified via tool-tips, prompted by floating the cursor over a region and selected. by clicking on the stack or on a part-tree of painted structures.  We have a large library of annotated 3D images that are registered to the standard brain used in our stack browser.  This includes > 16000 single neuron images from [FlyCircuit](http://www.flycircuit.tw), several thousand GAL4 line images from the [Rubin lab](http://www.janelia.org/lab/rubin-lab) and > 200 images of lineage clones from the labs of [Tzumin Lee](http://www.janelia.org/lab/lee-tzumin-lab) and [Kei Ito](http://www.k.u-tokyo.ac.jp/pros-e/person/kei_ito/kei_ito.htm) (to be released in July).  Users can add 3D images to the stack and view serial sections of them.  A system allowing multiple overlaid to be displayed is under development and will be release shortly.
+Users can also browse a painted 3D stack of a Drosophila brain using a system which allows viewing of virtual sections through the stack in any arbitrary plane. Structures can be identified via tool-tips, prompted by floating the cursor over a region and selected. by clicking on the stack or on a part-tree of painted structures.  We have a large library of annotated 3D images that are registered to the standard brain used in our stack browser.  This includes > 16000 single neuron images from [FlyCircuit](http://www.flycircuit.tw), several thousand GAL4 line images from the [Rubin lab](http://www.janelia.org/lab/rubin-lab) and > 200 images of lineage clones from the labs of [Tzumin Lee](http://www.janelia.org/lab/lee-tzumin-lab) and [Kei Ito](http://www.k.u-tokyo.ac.jp/pros-e/person/kei_ito/kei_ito.htm) (to be released in July 2013).  Users can add 3D images to the stack and view serial sections of them.  A system allowing multiple overlaid to be displayed is under development and will be release shortly.

 The central component that binds VFB into a queryable whole is an [ontology of Drosophila anatomy](https://sourceforge.net/p/fbbtdv/) in [OWL2](http://www.w3.org/TR/owl2-primer/). The logical component of this ontology includes axioms about the properties of neurons including synaptic partners and the locations of synaptic terminals \[1\]. All VFB queries use OWL reasoning software to query the ontology, returning inferences about neuroanatomy. For anatomy queries, these are used directly to generate query results pages. For queries of expression and phenotype the resulting lists of anatomy terms are used to query across 10s of thousands of annotations in a local instance of the [FlyBase CHADO database](http://gmod.org/wiki/Public_Chado_Databases).  Queries of images use OWL queries over the ontology combined with a formal representation of what the images depict as OWL individuals.

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 11:15:06 -0000

--- v6
+++ v7
@@ -6,7 +6,7 @@

 Users can also browse a painted 3D stack of a Drosophila brain using a system which allows viewing of virtual sections through the stack in any arbitrary plane. Structures can be identified via tool-tips, prompted by floating the cursor over a region and selected. by clicking on the stack or on a part-tree of painted structures.  We have a large library of annotated 3D images that are registered to the standard brain used in our stack browser.  This includes > 16000 single neuron images from [FlyCircuit](http://www.flycircuit.tw), several thousand GAL4 line images from the [Rubin lab](http://www.janelia.org/lab/rubin-lab) and > 200 images of lineage clones from the labs of [Tzumin Lee](http://www.janelia.org/lab/lee-tzumin-lab) and [Kei Ito](http://www.k.u-tokyo.ac.jp/pros-e/person/kei_ito/kei_ito.htm) (to be released in July).  Users can add 3D images to the stack and view serial sections of them.  A system allowing multiple overlaid to be displayed is under development and will be release shortly.

-The central component that binds VFB into a queryable whole is an ontology of neuroanatomy in [OWL2](http://www.w3.org/TR/owl2-primer/). The logical component of this ontology encodes information about the properties of neurons including synaptic partners and the locations of synaptic terminals \[1\]. All VFB queries use OWL reasoning software to query the ontology, returning inferences about neuroanatomy. For anatomy queries, these are used directly to generate query results pages. For queries of expression and phenotype the resulting lists of anatomy terms are used to query across 10s of thousands of annotations in a local instance of the [FlyBase CHADO database](http://gmod.org/wiki/Public_Chado_Databases).  Queries of images use OWL queries over the ontology combined with a formal representation of what the images depict as OWL individuals.
+The central component that binds VFB into a queryable whole is an [ontology of Drosophila anatomy](https://sourceforge.net/p/fbbtdv/) in [OWL2](http://www.w3.org/TR/owl2-primer/). The logical component of this ontology includes axioms about the properties of neurons including synaptic partners and the locations of synaptic terminals \[1\]. All VFB queries use OWL reasoning software to query the ontology, returning inferences about neuroanatomy. For anatomy queries, these are used directly to generate query results pages. For queries of expression and phenotype the resulting lists of anatomy terms are used to query across 10s of thousands of annotations in a local instance of the [FlyBase CHADO database](http://gmod.org/wiki/Public_Chado_Databases).  Queries of images use OWL queries over the ontology combined with a formal representation of what the images depict as OWL individuals.

 [[members limit=20]]

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 10:49:47 -0000

--- v5
+++ v6
@@ -6,7 +6,7 @@

 Users can also browse a painted 3D stack of a Drosophila brain using a system which allows viewing of virtual sections through the stack in any arbitrary plane. Structures can be identified via tool-tips, prompted by floating the cursor over a region and selected. by clicking on the stack or on a part-tree of painted structures.  We have a large library of annotated 3D images that are registered to the standard brain used in our stack browser.  This includes > 16000 single neuron images from [FlyCircuit](http://www.flycircuit.tw), several thousand GAL4 line images from the [Rubin lab](http://www.janelia.org/lab/rubin-lab) and > 200 images of lineage clones from the labs of [Tzumin Lee](http://www.janelia.org/lab/lee-tzumin-lab) and [Kei Ito](http://www.k.u-tokyo.ac.jp/pros-e/person/kei_ito/kei_ito.htm) (to be released in July).  Users can add 3D images to the stack and view serial sections of them.  A system allowing multiple overlaid to be displayed is under development and will be release shortly.

-The central component that binds VFB into a queryable whole is an ontology of neuroanatomy in [OWL2](http://www.w3.org/TR/owl2-primer/). The logical component of this ontology encodes information about the properties of neurons including synaptic partners and the locations of synaptic terminals \[1\]. All VFB queries use OWL reasoning software to query the ontology, returning inferences about neuroanatomy. For anatomy queries, these are used directly to generate query results pages. For queries of expression and phenotype the resulting lists of anatomy terms are used to query across 10s of thousands of annotations in FlyBase CHADO.  Queries of images use OWL queries over the ontology combined with a formal representation of what the images depict as OWL individuals.
+The central component that binds VFB into a queryable whole is an ontology of neuroanatomy in [OWL2](http://www.w3.org/TR/owl2-primer/). The logical component of this ontology encodes information about the properties of neurons including synaptic partners and the locations of synaptic terminals \[1\]. All VFB queries use OWL reasoning software to query the ontology, returning inferences about neuroanatomy. For anatomy queries, these are used directly to generate query results pages. For queries of expression and phenotype the resulting lists of anatomy terms are used to query across 10s of thousands of annotations in a local instance of the [FlyBase CHADO database](http://gmod.org/wiki/Public_Chado_Databases).  Queries of images use OWL queries over the ontology combined with a formal representation of what the images depict as OWL individuals.

 [[members limit=20]]

@@ -30,4 +30,3 @@
      * [Ontologies](ont)
      * [OWL individuals](owl_ind)
  * [Stack Browser](stack_browser)
-

Home modified by David Osumi-Sutherland

David Osumi-Sutherland — Wed, 05 Jun 2013 10:47:09 -0000

--- v4
+++ v5
@@ -20,7 +20,7 @@

  * [Functional Description](func_desc)
      * [User scenarios](user_scenarios)
-     * Description and functions of pages (page_descriptions)
+     * [Description and functions of pages](page_descriptions)
  * [Technical Description](tech_desc)
      * [Static content](static_content)
      * [Dynamic content](dynamic_content)