From dcb0ee44b70b9d7c535cf33f74c9f70eb5e63552 Mon Sep 17 00:00:00 2001 From: John SJ Anderson Date: Fri, 23 Aug 2024 15:06:42 -0700 Subject: [PATCH 1/2] Update blog layout/style to place author list under title [#997] * Leaves date position unchanged * Removes superfluous wrapper component * Adjust styling --- static-site/src/templates/displayMarkdown.jsx | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/static-site/src/templates/displayMarkdown.jsx b/static-site/src/templates/displayMarkdown.jsx index 2f4edc79f..d75437a27 100644 --- a/static-site/src/templates/displayMarkdown.jsx +++ b/static-site/src/templates/displayMarkdown.jsx @@ -81,11 +81,9 @@ export default class GenericTemplate extends React.Component { - - {author} - {date} - + {date} {title} + {author} @@ -132,16 +130,16 @@ const PostTitle = styled.h1` font-weight: 500 !important; font-size: 38px !important; `; -const PostAuthorSurrounds = styled.div` - min-height: 2rem; +const PostAuthor = styled.div` font-size: ${(props) => props.theme.niceFontSize}; - color: ${(props) => props.theme.medGrey}; -`; -const PostAuthor = styled.span` - float: left; + font-weight: bold; + margin: 2rem 0; `; const PostDate = styled.span` + color: ${(props) => props.theme.medGrey}; float: right; + font-size: ${(props) => props.theme.niceFontSize}; + min-height: 2rem; `; const GreyOverlay = styled.div` position: absolute; From 0457cb51744ebbc19d1e3d0a9b40cd3c33007ed7 Mon Sep 17 00:00:00 2001 From: John SJ Anderson Date: Fri, 23 Aug 2024 15:10:13 -0700 Subject: [PATCH 2/2] Remove duplicated, hard-coded author lists [#997] --- static-site/content/blog/2020-06-02-SARSCoV2-clade-naming.md | 2 -- .../content/blog/2021-01-06-updated-SARS-CoV-2-clade-naming.md | 2 -- static-site/content/blog/2021-07-08-ncov-open-announcement.md | 2 -- .../content/blog/2022-04-29-SARS-CoV-2-clade-naming-2022.md | 2 -- .../content/blog/2024-06-12-new-resources-for-measles.md | 1 - .../2024-06-18-h5n1-cattle-outbreak-analysis-and-resources.md | 1 - 6 files changed, 10 deletions(-) diff --git a/static-site/content/blog/2020-06-02-SARSCoV2-clade-naming.md b/static-site/content/blog/2020-06-02-SARSCoV2-clade-naming.md index 049c253d1..81af4aff2 100644 --- a/static-site/content/blog/2020-06-02-SARSCoV2-clade-naming.md +++ b/static-site/content/blog/2020-06-02-SARSCoV2-clade-naming.md @@ -4,8 +4,6 @@ date: "2020-06-02" title: "Year-letter Genetic Clade Naming for SARS-CoV-2 on Nextstrain.org" --- -**Emma B Hodcroft, James Hadfield, Richard A Neher, Trevor Bedford** - 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. Our objective here is to introduce a naming system that facilitates discussion of large scale diversity patterns of SARS-CoV-2 and label clades that persist for at least several months and have significant geographic spread. This objective is distinct from and complementary to Rambaut et al. 2020 (1), who proposed a dynamic system for labeling transient lineages that have local epidemiological significance. Their proposal results in a large number of short lived labels that maintain some information on the hierarchical structure and facilitate discussion of local short term dynamics, but are not intended to provide large scale structure. diff --git a/static-site/content/blog/2021-01-06-updated-SARS-CoV-2-clade-naming.md b/static-site/content/blog/2021-01-06-updated-SARS-CoV-2-clade-naming.md index 86c997203..f358fb58c 100644 --- a/static-site/content/blog/2021-01-06-updated-SARS-CoV-2-clade-naming.md +++ b/static-site/content/blog/2021-01-06-updated-SARS-CoV-2-clade-naming.md @@ -4,8 +4,6 @@ date: "2021-01-06" title: "Updated Nextstrain SARS-CoV-2 clade naming strategy" --- -**Trevor Bedford**, **Emma B Hodcroft**, **Richard A Neher** - 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. In June we put forth an [initial Nextstrain clade naming strategy](/blog/2020-06-02-SARSCoV2-clade-naming/). This basic strategy of flat "year-letter" names was borne out of work with seasonal influenza, where the nested names of 3c2.A1b (etc...) can become unwieldy. In the “year-letter” scheme, years are there to make it easy to know what's being discussed in ~5 years when, for example, clade `20A` is referenced. Our June strategy called for naming of a clade when it reached >20% global frequency for more than 2 months. diff --git a/static-site/content/blog/2021-07-08-ncov-open-announcement.md b/static-site/content/blog/2021-07-08-ncov-open-announcement.md index 7c51a54aa..6bfe3a016 100644 --- a/static-site/content/blog/2021-07-08-ncov-open-announcement.md +++ b/static-site/content/blog/2021-07-08-ncov-open-announcement.md @@ -4,8 +4,6 @@ date: "2021-07-08" title: "Extension of SARS-CoV-2 data processing to incorporate Open Data through GenBank" --- -**Trevor Bedford**, **James Hadfield**, **Emma Hodcroft**, **John Huddleston**, **Richard Neher**, **Thomas Sibley** - 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. With Nextstrain, we’ve done our best to respect these Terms of Use and we encourage data generators to share data to GISAID, which allows for comprehensive analyses. With [Augur](https://github.com/nextstrain/augur), [Auspice](https://github.com/nextstrain/auspice) and our [ncov workflow](https://github.com/nextstrain/ncov), we have provided academic and public health bioinformaticians around the world with open-source tools to analyze these GISAID data. But while guarantees such as those provided by GISAID’s Terms of Use are important, these restrictions also constrict and constrain data reuse, thereby adding friction to genomic analyses conducted by researchers and public health agencies. diff --git a/static-site/content/blog/2022-04-29-SARS-CoV-2-clade-naming-2022.md b/static-site/content/blog/2022-04-29-SARS-CoV-2-clade-naming-2022.md index 77870e1ad..4f1ddf880 100644 --- a/static-site/content/blog/2022-04-29-SARS-CoV-2-clade-naming-2022.md +++ b/static-site/content/blog/2022-04-29-SARS-CoV-2-clade-naming-2022.md @@ -4,8 +4,6 @@ date: "2022-04-29" title: "SARS-CoV-2 clade naming strategy for 2022" --- -**Cornelius Roemer**, **Emma B Hodcroft**, **Richard A Neher**, **Trevor Bedford** - 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. Our initial strategy of the 'year-letter' naming has been successful in keeping Nextstrain clade names short, clear, and easy to pronounce, and over two years into the pandemic, is accomplishing our original goal of remaining a long-term solution for distinct clade naming where the aim is to have a level of granularity that matches significant differences in biological impact or circulation patterns among viruses Nextstrain clades are coarser than the fine grained [Pango lineages](https://cov-lineages.org/). diff --git a/static-site/content/blog/2024-06-12-new-resources-for-measles.md b/static-site/content/blog/2024-06-12-new-resources-for-measles.md index d28115d5e..2f449f571 100644 --- a/static-site/content/blog/2024-06-12-new-resources-for-measles.md +++ b/static-site/content/blog/2024-06-12-new-resources-for-measles.md @@ -3,7 +3,6 @@ author: "Kim Andrews, Jover Lee, James Hadfield, Jennifer Chang, Trevor Bedford" date: "2024-06-12" title: "New Resources for Measles Virus" --- -**Kim Andrews**, **Jover Lee**, **James Hadfield**, **Jennifer Chang**, **Trevor Bedford** 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: diff --git a/static-site/content/blog/2024-06-18-h5n1-cattle-outbreak-analysis-and-resources.md b/static-site/content/blog/2024-06-18-h5n1-cattle-outbreak-analysis-and-resources.md index 083e9388d..ce23c3413 100644 --- a/static-site/content/blog/2024-06-18-h5n1-cattle-outbreak-analysis-and-resources.md +++ b/static-site/content/blog/2024-06-18-h5n1-cattle-outbreak-analysis-and-resources.md @@ -3,7 +3,6 @@ author: "Trevor Bedford, Jover Lee, James Hadfield, John Huddleston, Louise Monc date: "2024-06-18" title: "Phylogenetic analysis of H5N1 cattle outbreak and curated genomic data" --- -**Trevor Bedford**, **Jover Lee**, **James Hadfield**, **John Huddleston**, **Louise Moncla** # Phylogenetic analysis