Documentation refactoring

.gitignore

@@ -2,6 +2,9 @@ public/*
 .DS_Store
 /.venv
 transcript.en.vtt
+.idea/*
+.hugo_build.lock
+resources/*
 __pycache__
 __pycache__/
 __pycache__/*.pyc

Dockerfile

@@ -1,3 +1,4 @@
 FROM klakegg/hugo:ext-alpine
 
-RUN apk add git
+RUN apk add git && \
+  git config --global --add safe.directory /src

content/en/about/citeus.md

@@ -24,8 +24,8 @@ Court, Robert, et al. "Virtual Fly Brain—An Interactive Atlas of the Drosophil
 Court, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, McLachlan, Alex, Larkin, Aoife et al. "Virtual Fly Brain—An interactive atlas of the Drosophila nervous system." *Frontiers in Physiology* 14, (2023). https://doi.org/10.3389/fphys.2023.1076533.
 
 ### BibTeX
-```bibtex
-@article{10.3389/fphys.2023.1076533,
+```BibTeX
+@article{Court_2023,
   author = {Robert Court and Marta Costa and Clare Pilgrim and Gillian Millburn and Alex Holmes and Alex McLachlan and Aoife Larkin and Nicolas Matentzoglu and Huseyin Kir and Helen Parkinson and Nicolas H. Brown and Cahir J. O'Kane and J. Douglas Armstrong and Gregory S. X. E. Jefferis and David Osumi-Sutherland},
   title = "{Virtual Fly Brain—An interactive atlas of the Drosophila nervous system}",
   journal = {Frontiers in Physiology},
@@ -35,7 +35,7 @@ Court, Robert, Costa, Marta, Pilgrim, Clare, Millburn, Gillian, Holmes, Alex, Mc
   month = {jan},
   abstract = "{As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of available data, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.}",
   issn = {1664-042X},
-  doi = {https://doi.org/10.3389/fphys.2023.1076533},
+  doi = {10.3389/fphys.2023.1076533},
   url = {https://doi.org/10.3389/fphys.2023.1076533},
 }
 ```

content/en/about/collaborators.md

@@ -16,5 +16,6 @@ weight: 500
 
   [![flybase.gif](https://v2.virtualflybrain.org/images/vfb/project/logos/flybase.gif)](http://www.flybase.org/)
 
-  **Expression data** is collaboratively curated by VFB and [FlyBase](http://www.flybase.org/). 
-  <i>Phenotype data</i> is curated by FlyBase. Expression and phenotype data displayed on VFB is stored and maintained by FlyBase.
+  **Expression data** is collaboratively curated by VFB and [FlyBase](http://www.flybase.org/) and stored and maintained at FlyBase. 
+
+  **Phenotype data** is curated, stored, and maintained by FlyBase.

content/en/about/funding.md

@@ -4,13 +4,13 @@ date: 2025-06-11
 weight: 500
 tags: [VFB,funding]
 categories: [funding,acknowledgements,who we are]
-description: "VirtualFlyBrain has been supported by grants from multiple UK research councils and charitable foundations since 2009."
+description: "Virtual Fly Brain has been supported by grants from multiple UK research councils and charitable foundations since 2009."
 ---
 ## Current Funding (2022-2027)
 
 **Wellcome Trust Grant 223741/Z/21/Z**
 - Duration: April 1, 2022 to March 31, 2026 (extended to March 31, 2027)
-- Supporting ongoing VirtualFlyBrain development and maintenance
+- Supporting ongoing Virtual Fly Brain development and maintenance
 
 ## Historical Funding
 
@@ -50,17 +50,16 @@ description: "VirtualFlyBrain has been supported by grants from multiple UK rese
 
 ## Institutional Partners
 
-VirtualFlyBrain is a collaborative project between:
+Virtual Fly Brain is a collaborative project between:
 
 - **University of Edinburgh** - School of Informatics
-- **University of Cambridge** - Multiple departments including Genetics, Physiology Development & Neuroscience, and Zoology
-- **EMBL's European Bioinformatics Institute (EMBL-EBI)** - Hinxton, UK
+- **University of Cambridge** - Departments of Physiology Development & Neuroscience, and Zoology
 - **Wellcome Sanger Institute** - Hinxton, UK
 - **MRC Laboratory for Molecular Biology** - Cambridge
 
 ## Data Partnerships
 
-VirtualFlyBrain integrates data from multiple sources through collaborative partnerships rather than direct funding arrangements:
+Virtual Fly Brain integrates data from multiple sources through collaborative partnerships rather than direct funding arrangements:
 
 - FlyBase Consortium
 - FlyCircuit Project (National Tsing Hua University, Taiwan)
@@ -69,7 +68,7 @@ VirtualFlyBrain integrates data from multiple sources through collaborative part
 
 ## Site Visualization Tools
 
-VirtualFlyBrain utilizes multiple visualization technologies:
+Virtual Fly Brain utilizes multiple visualization technologies:
 
 **Geppetto Framework**
 - Open source 3D visualization platform co-developed with MetaCell Corporation

content/en/blog/releases/geppetto/_index.md → content/en/about/geppetto.md

@@ -1,7 +1,7 @@
 ---
 title: "Geppetto"
 linkTitle: "Geppetto"
-weight: 21
+weight: 800
 tags: [Geppetto,MetaCell]
 description: >
     The ultimate neuroscience platform.

content/en/about/members.md

@@ -1,93 +1,77 @@
 ---
-title: Virtual Fly Brain Members and Their Contributions
-description: "Meet the interdisciplinary team behind Virtual Fly Brain, including developers, curators, ontology experts, and researchers from leading UK institutions who collaborate to maintain and enhance this comprehensive Drosophila neuroscience resource."
+title: The Virtual Fly Brain Team
+description: "Meet the interdisciplinary team behind Virtual Fly Brain based in leading UK institutions. Our collaborative approach brings together expertise in informatics, neuroscience, ontology development, and data curation to maintain and enhance this comprehensive Drosophila neuroscience resource."
 tags: [VFB,staff]
 categories: [acknowledgements,who we are]
 weight: 400
 ---
 
-# Virtual Fly Brain Team
+## Current Team Members
 
-Virtual Fly Brain is developed and maintained by an interdisciplinary team of researchers, developers, and curators across multiple UK institutions. Our collaborative approach brings together expertise in informatics, neuroscience, ontology development, and data curation.
+- [Robert Court](https://www.inf.ed.ac.uk/people/staff/Robert_Court.html) (Lead DevOps) [1]
+- [Clare Pilgrim](https://orcid.org/0000-0002-1373-1705) (Ontology Editor/Curator) [2]
+- [Alex McLachlan](https://orcid.org/0000-0002-5214-8125) (Curator/UX Tester) [2]
+- [Gillian Millburn](https://orcid.org/0000-0002-1139-1145) (Senior Curator) [2]
 
-## 3D Viewer, Online Tools, Server, and Website
+- [Douglas Armstrong](https://www.inf.ed.ac.uk/people/staff/James_Armstrong.html) (Current Project PI) [1]
+- [Nick Brown](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Current Project PI) [2]
+- [Greg Jefferis](http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/gregory-jefferis/) (Current Project PI) [4,5]
+- [David Osumi-Sutherland](https://orcid.org/0000-0002-7073-9172) (Current Project Co-I) [3]
+- [Marta Costa](http://www.neuroscience.cam.ac.uk/directory/profile.php?mcosta) (Current Project Co-I) [4]
 
-<a href='http://www.anc.ed.ac.uk/index.php?option=com_content&task=view&id=12&Itemid=68' target='_blank'>
-  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/InformaticsLogo.gif' style="max-width: 50%"/>
-</a>
-
-### Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh
-
-- [Robert Court](https://www.inf.ed.ac.uk/people/staff/Robert_Court.html) (Lead DevOps)
-- [Douglas Armstrong](https://www.inf.ed.ac.uk/people/staff/James_Armstrong.html) (Current Project PI)
-- Nestor Milyaev (2009-2012)
-
-## Ontology Editing, FlyBase Support, and Data Annotation
-
-<a href='http://www.gen.cam.ac.uk/' target='_blank'>
-  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/CUnibig.png' style="max-width: 50%"/>
-</a>
-
-### Department of Genetics, University of Cambridge
 
-- [Cahir O'Kane](http://www.neuroscience.cam.ac.uk/directory/profile.php?cokane) (Current Project PI)
-- Michael Ashburner (Original PI and Grant Holder)
-- Simon Reeve (2009-2011)
-- Nicole Staudt (2015-2016)
-- Alex Holmes (2017-2019)
+## Past Team Members
+- Nestor Milyaev (2009-2012) [1]
+- Alex Holmes (2017-2019) [2]
+- [Aoife Larkin](https://orcid.org/0000-0003-4970-5901) (2017-2019) [2]
+- [Huseyin Kir](https://www.ebi.ac.uk/people/person/huseyin-kir/) (2021-2024) [6]
+- [Nico Matentzoglu](https://orcid.org/0000-0002-7356-1779) (2018-2022) [6]
+- Simon Reeve (2009-2011) [7]
+- Nicole Staudt (2015-2016) [7]
 
-### Department of Physiology, Development and Neuroscience
+- [Helen Parkinson](https://www.ebi.ac.uk/about/people/helen-parkinson) (Former PI) [6]
+- [Cahir O'Kane](http://www.neuroscience.cam.ac.uk/directory/profile.php?cokane) (Former PI) [7]
+- [Michael Ashburner](https://orcid.org/0000-0002-6962-2807) (Original PI and Grant Holder) [7]
 
-- [Clare Pilgrim](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Senior Ontology Editor/Curator)
-- [Alex McLachlan](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Curator/UX Tester)
-- [Aoife Larkin](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Curator)
-- [Gillian Millburn](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Senior Curator)
-- [Nick Brown](https://www.pdn.cam.ac.uk/research/groups/flybase/flybase-group-members) (Current Project PI)
+### Affiliations
+1. Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh
+2. Department of Physiology, Development and Neuroscience
+3. Wellcome Sanger Institute, Cambridge
+4. Department of Zoology, University of Cambridge
+5. MRC Laboratory of Molecular Biology, Cambridge
+6. European Bioinformatics Institute (EMBL-EBI), Cambridge
+7. Department of Genetics, University of Cambridge
 
-### Department of Zoology, University of Cambridge
+## [MetaCell](http://www.metacell.us)
 
-- [Marta Costa](http://www.neuroscience.cam.ac.uk/directory/profile.php?mcosta) (Current Project Co-I)
-
-## Image Processing, Registration, and NBLAST Neuron Search
+MetaCell collaborates with Virtual Fly Brain on the development and enhancement of the open source [Geppetto](http://www.geppetto.org) visualization platform that powers our 3D brain viewer.
 
-<a href='http://www2.mrc-lmb.cam.ac.uk/' target='_blank'>
-  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/MRC-LMB_logo.png' style="max-width: 50%"/>
+---
+<!--- width set to 55 here to prevent bunching onto same line -->
+<a href='http://www.anc.ed.ac.uk/index.php?option=com_content&task=view&id=12&Itemid=68' target='_blank'>
+  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/InformaticsLogo.gif' style="max-width: 55%"/>
 </a>
 
-### MRC Laboratory of Molecular Biology, Cambridge
-
-- [Greg Jefferis](http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/gregory-jefferis/) (Current Project PI)
-
-## Schema Development & Web Development
-
-<a href='https://www.sanger.ac.uk/' target='_blank'>
-  <img src='https://virtualflybrain.org/images/logo-sanger-blue.svg' style="max-width: 50%"/>
+<a href='http://www.gen.cam.ac.uk/' target='_blank'>
+  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/CUnibig.png' style="max-width: 55%"/>
 </a>
 
-### Wellcome Sanger Institute, Cambridge
+<a href='https://www.sanger.ac.uk/' target='_blank'>
+  <img src='https://virtualflybrain.org/images/logo-sanger-blue.svg' style="max-width: 55%"/>
+</a>  
 
-- [David Osumi-Sutherland](https://www.linkedin.com/in/osumisutherland) (Current Project Co-I)
+<a href='http://www2.mrc-lmb.cam.ac.uk/' target='_blank'>
+  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/MRC-LMB_logo.png' style="max-width: 55%"/>
+</a>  
 
 <a href='http://www.ebi.ac.uk/' target='_blank'>
-  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/EMBL_EBI_logo_180pixels_RGB.png' style="max-width: 50%"/>
-</a>
-
-### European Bioinformatics Institute (EMBL-EBI), Cambridge
-
-- [Huseyin Kir](https://www.ebi.ac.uk/people/person/huseyin-kir/) (Developer)
-- [Nico Matentzoglu](https://www.researchgate.net/profile/Nicolas_Matentzoglu2) (Developer)
-- [Helen Parkinson](https://www.ebi.ac.uk/about/people/helen-parkinson) (Current Project PI)
-
-## Software Engineering, Geppetto Customisation, Graphics Design
+  <img src='https://v2.virtualflybrain.org/images/vfb/project/logos/EMBL_EBI_logo_180pixels_RGB.png' style="max-width: 55%"/>
+</a>  
 
 <a href='http://www.metacell.us/' target='_blank'>
-  <img src='https://github.com/tarelli/bucket/raw/master/MetaCellLogoWhite300ppi.png' style="max-width: 50%"/>
+  <img src='https://github.com/tarelli/bucket/raw/master/MetaCellLogoWhite300ppi.png' style="max-width: 55%"/>
 </a>
 
-### [MetaCell](http://www.metacell.us)
-
-MetaCell collaborates with Virtual Fly Brain on the development and enhancement of the open source [Geppetto](http://www.geppetto.org) visualization platform that powers our 3D brain viewer.
-
 ---
 
 For questions about team members or collaboration opportunities, please [contact us](mailto:data@virtualflybrain.org).

content/en/about/whatisvfb.md

@@ -1,9 +1,9 @@
 ---
 title: What is Virtual Fly Brain?
 description: Virtual Fly Brain (VFB) - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of Drosophila melanogaster.
-weight: 100
+weight: 10
 ---
 
 Welcome to **Virtual Fly Brain (VFB)** - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity, and gene expression of _Drosophila melanogaster_. Our goal is to make it easier for researchers to find relevant anatomical information and reagents.
 
-We integrate the neuroanatomical and expression data from the published literature, as well as image datasets onto the same brain template, making it possible to run cross searches, find similar neurons, and compare image data on our [3D Viewer](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto).
+We integrate the neuroanatomical and expression data from the published literature, and align image datasets onto the same nervous system [templates](/docs/data/templates), making it possible to run cross searches, find similar neurons, and compare image data on our [3D Viewer](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto).

content/en/blog/news/_index.md

@@ -1,6 +1,6 @@
 
 ---
-title: "News about Virtual Fly Brain (VFB)"
+title: "Virtual Fly Brain News"
 linkTitle: "News"
 weight: 20
 cascade:

content/en/blog/news/neurofly2026.md

@@ -8,6 +8,6 @@ description: >
 
 The 21st Biennial European Drosophila Neurobiology Conference, NeuroFly 2026, will be held at the University of Cologne, Germany, from September 7th to 11th, 2026. This conference continues the tradition of bringing together researchers from around the world to discuss the latest advancements in Drosophila neurobiology, including studies on neuronal circuits, synapses, connectome, signal transmission, behavior, development, and more. The event emphasizes interdisciplinary interactions in an inclusive environment, featuring a mix of invited talks and abstracts from both junior and senior researchers.
 
-Virtual Fly Brain (VFB) is excited about the upcoming conference and is exploring opportunities to host a workshop/tutorial on connectomics and transcriptomics data we have available, similar to our previous successful sessions such as [NeuroFly 2024](neurofly2024.md) titled 'Bridging connectomics and transcriptomics' ([workshop notebook](http://tinyurl.com/workshopVFB)). This new workshop will introduce available connectomes and transcriptomics data, highlight important differences between datasets, and demonstrate how to perform your own analysis using the latest [tools](/docs/Tutorials/APIs/Connectome/tools) and [APIs](/docs/Tutorials/APIs/) for integrating Drosophila neuroscience data. Stay tuned for updates on our participation.
+Virtual Fly Brain (VFB) is excited about the upcoming conference and is exploring opportunities to host a workshop/tutorial on connectomics and transcriptomics data we have available, similar to our previous successful sessions such as the one at [NeuroFly 2024](neurofly2024.md) titled 'Bridging connectomics and transcriptomics' ([workshop notebook](http://tinyurl.com/workshopVFB)). This new workshop will introduce available connectomes and transcriptomics data, highlight important differences between datasets, and demonstrate how to perform your own analysis using the latest [tools](/docs/past-workshops/connectome/tools) and [APIs](/docs/tutorials/apis/) for integrating Drosophila neuroscience data. Stay tuned for updates on our participation.
 
 For more information about NeuroFly 2026, including registration, abstract submission, and program details, visit the official website at [https://neurofly.org/home/](https://neurofly.org/home/) or the 2026 conference page at [https://neurofly.org/y2026/](https://neurofly.org/y2026/).

content/en/blog/ontologies/_index.md

@@ -0,0 +1,20 @@
+---
+title: "Ontologies and Vocabularies Used in the Current VFB Release"
+linkTitle: "Ontologies"
+tags: [ontologies,annotation]
+date: 2021-12-24
+categories: [ontologies,annotations]
+weight: 50
+Description: >
+  The external ontologies and controlled vocabulary terms used to create VFB. 
+cascade:
+- type: "docs"
+  _target:
+    path: "/**"
+---
+
+These are mostly open source projects and contributions are welcome. VFB actively maintains FBbt, FBcv, dpo and FBdv and contributes to FlyBase and RO. 
+
+
+
+

content/en/blog/releases/_index.md

@@ -3,7 +3,7 @@ title: "Release Information"
 linkTitle: "Releases"
 weight: 20
 description: >
-    The Virtual Fly Brain (VFB) site consists of open source software projects we contribute to and actively develop as well as ontologies that we actively curate into and utilise in building the data for our servers. Here we provide details of these.
+    Virtual Fly Brain (VFB) is regularly updated with new data and software improvements. Information about the latest release can be found here.
 cascade:
 - type: "docs"
   _target: