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| --- | ||
| title: 2023 year in review | ||
| date: 2023-12-26 | ||
| --- | ||
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| Hello all, As we wrap up the year, we can see that it was a big year for JBrowse | ||
| 2! | ||
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| ## New "Faceted track selector" feature | ||
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| 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 | ||
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|  | ||
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| ## New theming features with dark mode support | ||
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| We added the ability to choose between custom themes, which was specifically | ||
| beneficial for delivering better dark mode support | ||
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|  | ||
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| ## SVG export of all view types | ||
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| SVG export is a highly requested feature, as it enables publication quality | ||
| exports of the JBrowse 2 visualizations. | ||
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| This made it so synteny views, dotplot views, breakpoint split view, and | ||
| circular view were all supported by the SVG export functionality! | ||
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|  | ||
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| ## Publication of the JBrowse 2 paper | ||
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| 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 | ||
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| ## Mac M1/M2 builds for JBrowse Desktop | ||
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| This let's JBrowse Desktop take advantage of speed improvements in Mac M1/M2. | ||
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| Note: we only realized we weren't publishing the right builds after a user told | ||
| us that JBrowse Desktop required virtualization! | ||
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| Moral of the story, feel free to let us know if you run into any problems :) | ||
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| ## New @jbrowse/react-app NPM package | ||
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| 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). | ||
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| 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. | ||
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| ## Office hours and community meeting outreach effort | ||
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| In Fall 2023, we created a new effort to do office hours where users can | ||
| schedule 1-on-1 meetings with the dev team. | ||
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| We have already conducted | ||
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| - 6 1-on-1 office hours meetings | ||
| - 3 community meetings | ||
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| 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! | ||
|
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| ## New structural variant visualization features | ||
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| 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 (`<INV>, <DEL>, <DUP>, <CNV>`), or | ||
| BEDPE | ||
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|  | ||
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| ## Improved synteny scalability | ||
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| In v2.10.0, we created a new way to load 'indexed PAF files' that we call PIF | ||
| files. | ||
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| 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! | ||
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|  | ||
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| ## Track selector improvements | ||
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| 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! | ||
|
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|  | ||
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| ## New JBrowseR and jbrowse-jupyter releases | ||
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| We have renewed our efforts and released new versions of JBrowseR and | ||
| jbrowse-jupyter. | ||
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| 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! | ||
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| ## New plugins | ||
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| 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 |
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