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v1.5.1 Release

· 3 min read

This is the release of v1.5.1 with a bunch of small improvements and bugfixes, including...

Cytoband overview​

We can now display the cytoband data for your genome assembly in the linear genome view overview, and this will now be available for hg19 and hg38 assembly configs on JBrowse Desktop

This can also appear in SVG exports

Plugins can integrate with "Add track" workflow better​

Plugins that register new adapter types can integrate with the "Add track" workflow by registering themselves for a particular file type or file extension with the Core-guessAdapterForLocation

Open plaintext FASTA file on JBrowse desktop​

Users can now open a plain FASTA instead of an indexed FASTA on JBrowse desktop, and it will create a .fai index on the fly

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.5.1 (2021-11-04)​

🚀 Enhancement​

  • core
    • #2488 Improve usability of the search result autocomplete when typing in via keyboard (@cmdcolin)
    • #2267 Add cytoband to overview scale bar in LGV (@cmdcolin)
    • #2447 Drawer widget tooltips and use position: fixed on fab (@cmdcolin)
    • #2299 Add new pluggable element type and properties to adapter type for registering adapter association with 'add track' workflow (@carolinebridge-oicr)
  • Other

🐛 Bug Fix​

  • Other
    • #2494 Add polyfill for text-index compatibility with node 10 (@cmdcolin)
    • #2492 Fix ability to open breakpoint split view from a BEDPE row in SV inspector (@cmdcolin)
    • #2480 Fix refName renaming on VcfAdapter for files that don't have ##contig lines (@cmdcolin)
    • #2469 Fix embedded crash when opening dialogs (@garrettjstevens)
    • #2451 Fix issue with intermittent text-index failures and improve speed (@cmdcolin)
    • #2439 Fix adding plugins on desktop (@cmdcolin)
    • #2426 Fix CLI create/upgrade failing to find the latest release (@cmdcolin)
  • core
    • #2457 Fix linear synteny view import form failure (@cmdcolin)
    • #2444 Fix crash when chromSizesLocation not specified when loading TwoBitAdapter in GUI (@cmdcolin)

📝 Documentation​

🏠 Internal​

Committers: 4​

v1.5.0 Release w/ JBrowse Desktop

· 4 min read

We are pleased to present the release of v1.5.0! We have some major new features to announce with this version!

JBrowse Desktop​

JBrowse Desktop is our fully featured desktop application available for Mac, Windows, and Linux.

Everything you can do with JBrowse Web, you can do with JBrowse Desktop! In fact, because it runs as a desktop app, JBrowse Desktop can do things that the web can't like saving sessions to a file on your computer to revisit later.

JBrowse Desktop session

JBrowse Desktop features a new landing page designed to help you manage your work. Here's a few things you can do with it:

  • re-visit saved sessions using the recent session panel
  • launch new sessions easily from the quick start panel (e.g. hg19 and hg38 are built-in)
  • create a new entries in the quick start panel (e.g. quick launch your favorite organism)
  • quickly rename or delete sessions from the landing page

JBrowse Desktop landing page

With JBrowse Desktop, your genome browser and your web browser can finally live in harmony on your taskbar! ❤️

Access authenticated resources​

This release also contains the ability to access authenticated resources. For JBrowse Desktop, the ability to open files from Google Drive and Dropbox share links is built in. For JBrowse Web, administrators can add some extra configuration to set these up.

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.5.0 (2021-10-18)​

🚀 Enhancement​

  • core
    • #2413 Bundle size savings (@cmdcolin)
    • #2390 Support plain text (non-tabix'ed) GFF files with new Gff3Adapter (@teresam856)
    • #2384 Allow docking the drawer on the left side of the screen (@cmdcolin)
    • #2387 Add bulk delete of sessions on jbrowse-desktop (@cmdcolin)
    • #2279 Add ability to access authenticated resources using pluggable internet accounts framework (@peterkxie)
  • Other
    • #2388 Create "quickstart list" on jbrowse-desktop which users can add to (@cmdcolin)
    • #2385 Ensure all dependencies are properly specified in package.json files using eslint-plugin-import (@cmdcolin)
    • #2373 Add auto update functionality for jbrowse-desktop (@cmdcolin)
    • #2369 Add tooltip with track description to track selector (@garrettjstevens)
    • #2258 Update admin-server to accept value from ?config= so that multiple configs could be edited (@cmdcolin)
    • #2321 Add show descriptions toggle box to most feature tracks (@cmdcolin)

🐛 Bug Fix​

  • Other
    • #2355 Allow prefix and exact matches jb1 text search (@cmdcolin)
    • #2348 Fix ability to use JB1 backcompat text search adapter (@teresam856)
    • #2322 Fix install plugin workflow and error handling on desktop, update to electron 15 (@cmdcolin)
    • #2329 Fix bugs preventing embedded circular genome view from rendering in some circumstances (@garrettjstevens)
  • core
    • #2352 Better keyboard navigations on text search autocomplete component (@cmdcolin)
    • #2332 Fix ability to use LocalFile on nodejs-based apps e.g. @jbrowse/img (@cmdcolin)

📝 Documentation​

🏠 Internal​

  • Other
  • core
    • #2379 Bump typescript to 4.4.3 (@cmdcolin)
    • #2363 Add some typescripting of some MST models and components (@cmdcolin)
    • #2351 Use main "module" field instead of "browser" from dependency package json files electron builds (@cmdcolin)
    • #2323 Remove session related menu items from jbrowse-desktop (@cmdcolin)

Committers: 6​

v1.4.4 Release

· 3 min read

We're excited to announce the v1.4.4 release! Some highlights of this release include:

Text searching​

Finally, we have added the ability to search by gene name!

Users will now be able to create their own text indexes with the jbrowse text-index command, which creates an index for searching by gene names, identifiers and descriptions.

searching in lgv

GIF showing the process of searching via the location search box of the Linear Genome View. Try it out yourself here, type your favorite gene name e.g. HER2, PTEN, or others in the search box https://jbrowse.org/code/jb2/v1.4.4/?config=test_data%2Fconfig_demo.json&session=share-H3vwqh1BKa&password=xYz9Z

For a quick introduction and a tutorial on how to add this feature to your JBrowse instance, check out this quick start

Like most parts of JBrowse, the text searching system is pluggable. Plugin developers can add new text index adapters to connect JBrowse to other types of text search services, indexes, or databases.

Users of the @jbrowse/react-linear-genome-view can also enable text searching functionality, see https://jbrowse.org/storybook/lgv/v1.4.0/?path=/story/text-searching--page

Note that 1.4.0-1.4.3 had issues during publish, so we moved all release notes for them to here. Thanks to @bbimber for letting us know about these issues.

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.4.4 (2021-09-14)​

🚀 Enhancement​

  • Other
    • #2287 Use react-popper to reduce tooltip lag on pages with many elements (@cmdcolin)
    • #2294 Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views (@cmdcolin)
    • #2272 Auto adjust box RefNameAutocomplete width based on refName length (@cmdcolin)
    • #2243 Import bookmarks functionality for grid bookmark widget (@cmdcolin)
  • core
    • #2247 New jbrowse-desktop start screen design (@cmdcolin)
    • #2254 Better error reporting from web worker and chrom sizes adapter errors (@cmdcolin)
    • #1881 Add new text searching functionality to core, with jbrowse text-index CLI command to generate trix index (@teresam856)

🐛 Bug Fix​

  • core
    • #2320 Fix issue where add track widget doesn't infer adapters on second usage (@cmdcolin)
    • #2250 Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available (@cmdcolin)
  • Other
    • #2309 Fix mouseover selection appearing across unrelated blocks (@cmdcolin)
    • #2283 Fix ability for the variant detail panel to create breakpoint split view for <TRA> elements (@cmdcolin)
    • #2268 Fix autocomplete height on small displays (@cmdcolin)

📝 Documentation​

  • #2300 Release announcement draft v1.4.0 (@teresam856)
  • #2310 Add cancer demos to the demos page on website (@cmdcolin)
  • #2253 Add note about legacy-peer-deps to embedded component readme (@cmdcolin)
  • #2262 Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks (@cmdcolin)

🏠 Internal​

Committers: 3​

v1.3.5 Release

· 3 min read

We're excited to announce the v1.3.5 release of JBrowse! Some highlights of this release include:

New embedding build of @jbrowse/react-linear-genome-view​

This release adds a new UMD build of our @jbrowse/react-linear-genome-view React component. This build will allow users to use our React Linear Genome View in a website that doesn't otherwise use React. See a tutorial for how to get started using this build:

A preliminary beta version of this build was used in a tutorial at BOSC2020, and that tutorial was also on our website. If you've used that version, the interface has changed somewhat, so come check out the new tutorial for the official released version!

Bookmark widget​

A new widget has been added that is accessible from the Linear Genome View view menu or when you click and drag over a region in the header (a.k.a rubber band selection). This view keeps a list of bookmarked regions, which you can add custom labels to, and also which you can use to navigate back to that region. The bookmarks can also be exported.

Bookmark widget in use

Note to plugin developers​

If your plugin adds menu items or context menu items to a track, or customizes renderProps, there may be some changes that affect how those menu items work, particularly in #2226 and #2229. Also see an updated example of context menu items here.

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.3.5 (2021-08-23)​

🚀 Enhancement​

  • Other
    • #2163 Add new embeddable React Circular Genome View (@garrettjstevens)
    • #2229 Use extendPluggableElement for context menu items (@garrettjstevens)
    • #2233 Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs (@cmdcolin)
    • #2199 Make the BED parser not interpret general tab delimited data as BED12 (@cmdcolin)
    • #2241 Restore previous window location when re-opening on desktop (@garrettjstevens)
    • #2203 Add a helpful message if there is a 404 on config.json error (@cmdcolin)
    • #2204 Hide reads with unmapped flag by default in alignments tracks (@cmdcolin)
    • #2198 Add better inversion visualization to read vs reference visualizations (@cmdcolin)
    • #2154 Add UMD build of react-linear-genome-view for plain-js use (@garrettjstevens)
  • core

🐛 Bug Fix​

📝 Documentation​

🏠 Internal​

  • core
    • #2057 Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance (@cmdcolin)
    • #2231 Export offscreenCanvasUtils (@cmdcolin)
    • #2226 Use superRenderProps and superTrackMenuItems for better simulated inheritance model (@cmdcolin)
    • #1874 Add aborting to CoreGetFeatures rpcManager call (@cmdcolin)
  • Other

Committers: 4​

v1.3.3 Release

· 2 min read

This is a small bugfix release that includes notable fixes for the methylation/modifications drawing (the negative strand reads displayed the data incorrectly) and the reference name selector

Please check the release notes for more details!

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.3.3 (2021-08-02)​

🚀 Enhancement​

🐛 Bug Fix​

  • Other
    • #2159 Stop local storage quota-exceeded errors preventing the app from starting (@cmdcolin)
    • #2161 Remove outline from clicking on SVG chord tracks (@cmdcolin)
    • #2157 Fix rendering of negative strand alignment modifications/methylation (@cmdcolin)
    • #2131 Fix mouseovers/click handlers after "force load" button pressed (@cmdcolin)
    • #2128 Fix using the "Color by modifications" setting on files that need ref renaming (@cmdcolin)
    • #2115 Fix bug where sometimes plugin could not be removed from UI (@garrettjstevens)
    • #2119 Fix loading indicator on the reference sequence selector getting stuck (@cmdcolin)
  • core
    • #2101 Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item (@teresam856)

🏠 Internal​

Committers: 3​

v1.3.2 Release

· One min read

This is a hotfix release that fixes a bug that prevented the @jbrowse/react-linear-genome-view component from being used in v1.3.1

It also contains a couple other small improvements

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.3.2 (2021-07-07)​

🚀 Enhancement​

🐛 Bug Fix​

  • #2109 Make sure to wait for assembly to load before downloading canonical refnames in SV inspector (@cmdcolin)
  • #2111 Fix "Can't resolve '@jbrowse/plugin-legacy-jbrowse'" in @jbrowse/react-linear-genome-view (@garrettjstevens)

Committers: 2​

v1.3.1 Release

· 3 min read

Hello everyone! This release offers a couple important bug fixes.

For users of @jbrowse/react-linear-genome-view, we have fixes that improve speed, CSS style consistency, and theming. We also have another speed improvement for users with many scaffolds or contigs. Please see the release notes below for more details!

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.3.1 (2021-07-06)​

🚀 Enhancement​

🐛 Bug Fix​

  • Other
    • #2097 Improve speed for laying out features for embedded/mainthreadrpc scenarios (@cmdcolin)
    • #2096 Fix issue with page reload after editing session title (@cmdcolin)
    • #2074 Fix support for opening local files in spreadsheet/SV inspector (@cmdcolin)
    • #2061 Fix issue with using --force error when no track was previously loaded (@cmdcolin)
    • #2024 Flip drawing of negative strand PAF features in linear synteny and dotplot views (@cmdcolin)
    • #2023 Fix infinite loop in adding some plugins on desktop (@cmdcolin)
    • #2019 Fix session import to use blob map for opening local files (@cmdcolin)
  • core
    • #2071 Add indicator to the end of ref name dropdown to suggest user to type the searchbox for more (@teresam856)
    • #2056 Fix infinite recursion in FromConfigAdaptor by avoiding mutating the passed in data when using SimpleFeature (@cmdcolin)
    • #2018 Fix 3'UTR in sequence detail panels when no UTRs are in gff (@cmdcolin)

🏠 Internal​

Committers: 5​

v1.3.0 Release

· 4 min read

We're excited to announce the v1.3.0 release of JBrowse Web! Some highlights of this release include:

In-app plugin store​

Building on the plugin store on our website in the last release, we're now excited to announce that plugins can be installed from within JBrowse Web! Plugins from our plugin store can now be installed with the click of a button.

Screenshot of plugin store with MsaView plugin installed and open

Open local files​

JBrowse Web now has the ability for tracks to use files on your local hard drive. This is a great option if you want to visualize files you have locally without uploading them to a server. These files will need to be re-opened each time the app is opened or refreshed, but more robust handling of local files will be available when we release JBrowse Desktop.

Screenshot of selector in URL and File states

Color by MM and MP/ML tags in BAM/CRAM​

The MM and MP/ML tags can be used to color alignments tracks by either base modifications or by methylation. The modifications mode is exciting because it can show arbitrary DNA/RNA modifications, and the methylation mode uses specific CpG context to show both modified and unmodified CpGs.

Screenshot of alignments tracks colored by methylation and base modification

In this screenshot, the top alignments track is colored by methylation and the bottom alignments track is colored by base modification.

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.3.0 (2021-05-24)​

🚀 Enhancement​

  • Other
    • #2001 Make tracks added using the add track widget a session track if not in adminMode (@cmdcolin)
    • #1980 Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist (@cmdcolin)
    • #1977 Upgrade @material-ui/data-grid (@cmdcolin)
  • core
    • #1982 Allow manually specifying adapter type if filename does not match expected pattern (@cmdcolin)
    • #1975 Allow local files on the users computer to be opened as tracks in jbrowse-web (@cmdcolin)
    • #1865 Show modified bases using MM and MP/ML tags in BAM/CRAM (@cmdcolin)
    • #1984 Better feature details when there are short arrays of json supplied as feature data (@cmdcolin)
    • #1931 Create in app graphical plugin store (@elliothershberg)

🐛 Bug Fix​

  • core
    • #1985 Avoid error calculating UTR on features that have no exon subfeatures (@cmdcolin)
    • #1954 Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering (@cmdcolin)
    • #1963 Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components (@cmdcolin)
    • #1945 Fix hic not being able to render due to incorrect lazy loading (@cmdcolin)
  • Other

📝 Documentation​

  • #2002 Add @jbrowse/img to homepage (@cmdcolin)
  • #2007 Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details (@cmdcolin)
  • #1976 reorganize the demo page to emphasize the cancer sv demo more (@rbuels)
  • #1952 Add demo for 1000 genomes extended trio dataset to website (@cmdcolin)
  • #1862 Add example for using a build-time included plugin to storybook (@cmdcolin)

🏠 Internal​

  • Other
    • #2003 Make SNPCoverage independently generate the modifications tag-color mapping (@cmdcolin)
  • core, development-tools

Committers: 4​

v1.2.0 Release

· 4 min read

We're excited to announce the v1.2.0 release of JBrowse Web!

New plugin store added to website​

One of the core aspects of JBrowse 2 is that it is an extensible platform for biological visualization that can be extended with plugins. We are excited to introduce the first version of our plugin store, where we list the current external plugins that are available. Check it out here. In the coming weeks, we will also be bringing this plugin store directly into the application, allowing plugin installation with the click of a button. Stay tuned!

SVG export​

We're excited to introduce a new feature to JBrowse Web: built-in SVG export of track visualizations! This feature currently supports the linear genome view, and will be extended to more views in future releases.

With the addition of this feature, it is now even easier to create publication-ready screenshots of JBrowse views.

Virtualized track lists​

An important consideration for genomics software is scaling to very large datasets. We have implemented a virtualization of our hierarchical track selector, enabling it to support arbitrarily large track lists.

Lazy loading​

We have expanded our use of lazy loading, which optimizes app performance and improves load times.

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.2.0 (2021-05-03)​

🚀 Enhancement​

  • core
    • #1125 Export SVG (@cmdcolin)
    • #1867 Virtualized tree for tracklist to support having thousands of tracks (@cmdcolin)
    • #1660 Allow connections to have multiple assemblies (@garrettjstevens)
    • #1864 Add Material UI's DataGrid to re-exports (@garrettjstevens)
    • #1875 Make drawer widget titles stay visible when scrolling inside the widget (@cmdcolin)
    • #1877 Add ability to copy the text produced by the feature details sequence panel to MS Word/Google Docs and preserve styling (@cmdcolin)
    • #1854 Make "About track" dialog available from tracklist and for non-LGV tracks (@cmdcolin)
    • #1853 Add mouseovers in feature details that show field descriptions for VCF fields (@cmdcolin)
  • Other
    • #1892 Create new JB2 plugin store (@elliothershberg)
    • #1901 Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink (@cmdcolin)
    • #1850 Add true breakend ALT strings to the feature details panel (@cmdcolin)
    • #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
    • #1861 Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict (@cmdcolin)

🐛 Bug Fix​

  • core
    • #1924 Fix import of BED and navToLocString from spreadsheet views (@cmdcolin)
    • #1918 Fix issue with some falsy values being hidden in feature details (@cmdcolin)
    • #1911 Fix breakpoint split view visualizations for files that need ref renaming (e.g. chr1 vs 1) (@cmdcolin)
    • #1904 Fix issue with synteny polygons displaying slightly offset (@cmdcolin)
    • #1884 Fix rIC ponyfill for use on Safari (@cmdcolin)
  • Other
    • #1912 Fix reloading of local sessions when using React.StrictMode (@cmdcolin)
    • #1900 Make clicking away from autocomplete popup on track container work (@cmdcolin)
    • #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
    • #1871 Fix crash on dotplot/linear synteny import form and when closing linear synteny track (@cmdcolin)
    • #1860 Fix alignments read filter jexl syntax (@cmdcolin)

📝 Documentation​

  • #1914 Use MDX to add proper image captions in web and pdf documentation (@cmdcolin)
  • #1855 Add download page in website header and new super-quick-start guide (@cmdcolin)

🏠 Internal​

Committers: 4​

v1.1.0 Release

· 3 min read

We're pleased to announce a new release of JBrowse Web!

Changed callbacks language from JavaScript to Jexl​

To allow users to safely and seamlessly share advanced configurations in sessions, we now use Jexl to express configuration callbacks. Note that this is a breaking change, function()-style callbacks will no longer work.

For details, see the callbacks section of our configuration guide.

Fetch intron and upstream/downstream sequences​

We also have several other improvements including the ability to get intron and upstream/downstream sequence in the feature details

Interactive documentation using Storybook​

Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View. The docs contain live examples of how the LGV component can be used, along with source-code examples. The site can be found here.

Enhanced navigation to drawer widget stack​

We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web.

See below for demos of the new navigation UI.

Minimize button demo

Demo of using the minimize button in the drawer

Downloads​

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.1.0 (2021-03-29)​

🚀 Enhancement​

  • core
    • #1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
    • #1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
    • #1816 Remove some animation effects (@cmdcolin)
    • #1778 Adds dropdown to show drawer widget stack (@teresam856)
    • #1685 Change callbacks language from JavaScript to Jexl (@peterkxie)
  • Other
    • #1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
    • #1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
    • #1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
    • #1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)

🐛 Bug Fix​

📝 Documentation​

🏠 Internal​

Committers: 6​