From c345785e9e461dade8859be8d0918f6627165c1d Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Fri, 19 Jan 2024 10:32:45 -0700 Subject: [PATCH] [update docs] 2023 year in review blog post (#4166) --- website/blog/2023-12-26-yearinreview.md | 122 ++++++++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 website/blog/2023-12-26-yearinreview.md diff --git a/website/blog/2023-12-26-yearinreview.md b/website/blog/2023-12-26-yearinreview.md new file mode 100644 index 0000000000..affd412728 --- /dev/null +++ b/website/blog/2023-12-26-yearinreview.md @@ -0,0 +1,122 @@ +--- +title: 2023 year in review +date: 2023-12-26 +--- + +Hello all, as we wrap up the year, we can see that 2023 was a big year for +JBrowse 2! + +## New "Faceted track selector" feature + +We added a new "Faceted track selector" feature to JBrowse 2, similar to the +JBrowse 1 version! This provides a data grid view of your tracks, with multiple +levels of filtering capability + +![](https://user-images.githubusercontent.com/6511937/216159433-e2ef2994-dd85-4283-a942-23cecbb75356.png) + +## New theming features with dark mode support + +We added the ability to choose between custom themes, which was specifically +beneficial for delivering better dark mode support + +![](https://user-images.githubusercontent.com/6511937/221064203-d19352fe-915a-41bc-9ec3-dc22ae94c40f.png) + +## SVG export of all view types + +SVG export is a highly requested feature, as it enables publication quality +exports of the JBrowse 2 visualizations. + +This made it so synteny views, dotplot views, breakpoint split view, and +circular view were all supported by the SVG export functionality! + +![](https://user-images.githubusercontent.com/6511937/221062560-346cc4e7-1053-496f-80a8-bded420041a7.png) + +## Publication of the JBrowse 2 paper + +We finally published our JBrowse 2 paper! This followed our biorxiv pre-print +almost a year earlier +https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02914-z + +## Mac M1/M2 builds for JBrowse Desktop + +This let's JBrowse Desktop take advantage of speed improvements in Mac M1/M2. + +Note: we only realized we weren't publishing the right builds after a user told +us that JBrowse Desktop required virtualization! + +Moral of the story, feel free to let us know if you run into any problems :) + +## New @jbrowse/react-app NPM package + +The `@jbrowse/react-app` package enables the NPM installation of the +`jbrowse-web` (which is otherwise deployed as a folder of pre-built +js/css/html). + +We still envision `jbrowse-web` to be the typical way that most users deploy the +app, but we think the availability of the NPM package is important for certain +use cases. + +## Office hours and community meeting outreach effort + +In Fall 2023, we created a new effort to do office hours where users can +schedule 1-on-1 meetings with the dev team. + +We have already conducted + +- 6 1-on-1 office hours meetings +- 3 community meetings + +We met a diverse group of users via these sessions who we had not talked to +through other channels like GitHub issues/discussions. We look forward to +continuing these meetings through the new year! + +## New structural variant visualization features + +We have long had the 'circos' view of structural variants, but in 2023 we added +'arc style' rendering of SVs in the normal linear genome view from either +"breakend style" VCF, "symbolic style" VCF (`, , , `), or +BEDPE + +![](https://user-images.githubusercontent.com/6511937/281789167-aef6ccd2-c7e4-444e-b213-f3876fedabf9.png) + +## Improved synteny scalability + +In v2.10.0, we created a new way to load 'indexed PAF files' that we call PIF +files. + +This greatly improves the speed and scalability of loading synteny data, since +it allows you to load just the alignment data in a region of interest instead of +the whole file! + +![](https://user-images.githubusercontent.com/6511937/290839304-dc5a6abe-9258-4b94-8a2e-7a369ec7d249.png) + +## Track selector improvements + +We created a new feature for keeping track of your "Recently used tracks" and +"Favorite tracks", which we think will be helpful especially for instances with +large track lists! + +![](https://user-images.githubusercontent.com/6511937/287035460-c5705fc9-d90c-4fe1-ad23-e05389047c53.png) + +## New JBrowseR and jbrowse-jupyter releases + +We have renewed our efforts and released new versions of JBrowseR and +jbrowse-jupyter. + +Notebook style usages of JBrowse 2 with R and Python are very compelling for +certain use cases, and we look forward to seeing more usages of this in the new +year! + +## New plugins + +This year we introduced a new JBrowse 2 MAFViewer plugin +(https://github.com/cmdcolin/jbrowse-plugin-mafviewer), for viewing multiple +alignment format files. We have already seen integrations where a Cactus +pangenome can be exported into MAF and loaded into the MAFViewer track using +workflows from +https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#maf + +## Looking forward! + +We look forward to the new year, and thank everyone for their support, bug +reports, and participation