Skip to content

Commit

Permalink
Fix post sidebar titles [#1005]
Browse files Browse the repository at this point in the history
Generally speaking, these sidebar titles were written to maintain the
current sidebar titles (which were formally based on file names) as
much like the existing ones as possible, while also correcting spacing
and other issues (i.e., `SARS CoV 2` is now properly `SARS-CoV-2`; `H
5 N 1` is now `H5N!`, etc.)
  • Loading branch information
genehack committed Sep 4, 2024
1 parent 1b0dcbb commit d9dbb3d
Show file tree
Hide file tree
Showing 11 changed files with 11 additions and 1 deletion.
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "James Hadfield"
date: "2018-05-14"
title: "New nextstrain.org website"
sidebarTitle: "New Nextstrain Website"
---

The data visualisation aspect of nextstrain.org has been under a lot of development over the last year, with new features and new datasets, but we've fallen behind with documentation and explanations of everything that's going on.
Expand Down
2 changes: 1 addition & 1 deletion static-site/content/blog/2019-10-21-auspice-v2.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
author: "James Hadfield"
date: "2019-10-21"
title: "Auspice v2 released"
anchorText: "Auspice v2"
sidebarTitle: "Auspice v2"
---

## What's New
Expand Down
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
---
title: Using Nextstrain narratives to explain WNV spread and evolution
sidebarTitle: Using Narratives To Explain West Nile Virus Spread
date: "2019-10-31"
author: James Hadfield
---
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "Emma B Hodcroft, James Hadfield, Richard A Neher, Trevor Bedford"
date: "2020-06-02"
title: "Year-letter Genetic Clade Naming for SARS-CoV-2 on Nextstrain.org"
sidebarTitle: "SARS-CoV-2 Clade Naming"
---

Nextstrain provides clade or lineage information for a number of pathogens it already tracks, including influenza and enterovirus D68. Nextstrain also introduced informal clade designations for SARS-CoV-2 on 4 March 2020, largely to aid internal discussions and to create URL links allowing ‘automatic zoom’ to an area of the tree that was of interest. These clades names were ad-hoc letter-number combinations (e.g. A2a) and were never intended to be a permanent naming system (and never visible by default). Nevertheless, these clades have been used by some to discuss different aspects of the phylogeny on Nextstrain, underscoring the need for a more long-term, formal proposal to designate SARS-CoV-2 clades.
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "Trevor Bedford, Emma B Hodcroft, Richard A Neher"
date: "2021-01-06"
title: "Updated Nextstrain SARS-CoV-2 clade naming strategy"
sidebarTitle: "Updated SARS-CoV-2 Clade Naming"
---

The emerging 501Y.V1 and 501Y.V2 variants have pushed the Nextstrain team to revise our strategy for Nextstrain clade labels. Here, we propose a backwards-compatible update to make clades more adaptable to the continuing pandemic situation, and more useful to people working on the pandemic today.
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "Trevor Bedford, James Hadfield, Emma Hodcroft, John Huddleston, Richard Neher, Thomas Sibley"
date: "2021-07-08"
title: "Extension of SARS-CoV-2 data processing to incorporate Open Data through GenBank"
sidebarTitle: "Ncov Open Announcement"
---

Progress towards large-scale real-time genomic surveillance of SARS-CoV-2 has been remarkable with over 2 million viral genomes shared to [GISAID](https://www.gisaid.org/) from all over the world since Jan 2020. This has allowed detailed tracking of the [emergence and spread of variants of concern](https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/) and is an essential pandemic response activity. In an unprecedented collective effort, these data were shared by hundreds of laboratories from all over the world, often within days or weeks of sample collection, and curated by GISAID. Such early sharing of unpublished data requires certain guarantees that submitters get credit for their contributions and a chance to publish on their data. Sequences submitted to the GISAID EpiCoV database are shared under [Terms of Use](https://www.gisaid.org/registration/terms-of-use/) that restrict resharing of sequence data or metadata.
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "Cornelius Roemer, Emma B Hodcroft, Richard A Neher, Trevor Bedford"
date: "2022-04-29"
title: "SARS-CoV-2 clade naming strategy for 2022"
sidebarTitle: "SARS-CoV-2 clade naming 2022"
---

The rapid dominance and increased diversity of the Omicron variant and its constituent sub-lineages has triggered another update of the Nextstrain clade naming guidelines and labels. Once again, we propose a backwards-compatible update, this time to allow more flexible and faster designation of clades as new variants appear and spread.
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "Nextstrain team"
date: "2024-03-27"
title: "Nextstrain Annual Update March 2024"
sidebarTitle: "Annual Update March 2024"
---

_The nextstrain.org blog has not seen a lot of use lately. Here we're piloting an effort to post annual updates._
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "Kim Andrews, Jover Lee, James Hadfield, Jennifer Chang, Trevor Bedford"
date: "2024-06-12"
title: "New Resources for Measles Virus"
sidebarTitle: "New Resources for Measles"
---

We now provide regularly updated phylogenetic monitoring of measles virus at [nextstrain.org/measles](https://nextstrain.org/measles). This site displays phylogenies generated using genomic data from NCBI GenBank, and is updated daily when new sequences are uploaded to NCBI. You can choose to display one of two different phylogenies based on the following data types:
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "Trevor Bedford, Jover Lee, James Hadfield, John Huddleston, Louise Moncla"
date: "2024-06-18"
title: "Phylogenetic analysis of H5N1 cattle outbreak and curated genomic data"
sidebarTitle: "H5N1 Cattle Outbreak Analysis and Resources"
---

# Phylogenetic analysis
Expand Down
1 change: 1 addition & 0 deletions static-site/content/blog/2024-09-03-augur-v25-features.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
author: "The Nextstrain team"
date: "2024-09-03"
title: "Notable changes in Augur v25"
sidebarTitle: "Augur v25 features"
---

The Nextstrain team has released several new versions of Augur – our
Expand Down

0 comments on commit d9dbb3d

Please sign in to comment.