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2023 year in review

· 3 min read

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

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

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!

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 (<INV>, <DEL>, <DUP>, <CNV>), or BEDPE

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!

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!

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