Web app for visualizing pathogen evolution

version 1.21.2 - 2018/06/07

version 1.21.1 - 2018/06/04

version 1.21.0 - 2018/06/01

  • Untangling via a simple algorithm upon 2nd tree load
  • Segment names displayed above trees (if 2 trees)
  • Fix hover-info-box date bug -- issue 572

version 1.20.3 - 2018/05/30

  • Narratives now accessed via /narratives/... URLs
  • App now works without needing a manifest file (but the datasets dropdown needs it)
  • Initial load simplified
  • Sidebar doesn't appear until the data is ready to be displayed

version 1.20.2 - 2018/05/21

  • Changes to the frequencies threshold

version 1.20.1 - 2018/05/21

  • Changes to the frequencies threshold
  • Narratives restored

version 1.20.0 - 2018/05/15

Auspice is now served via the nextstrain.org server together with the static (gatsbyjs) site * Changes to the server code organisation * Static content removed * New splash page listing the (should only be accessed from local instances or 404s, live site splash is via the static site) * Improved page navigation API * Travis CI 🎉 * Auspice version is displayed in the footer * Release script modified (Travis CI listens to release and pushes a successful build to S3 which is fetched by the live server)

version 1.19.1 - 2018/05/09

  • Fixed a bug where proteins starting with a number (e.g. 2K) were assumed to be nucleotide genotypes.

version 1.19.0 - 2018/05/09

  • Improved sidebar styling on both mobile & desktop
  • Reset layout button doesn't re-instantiate the PhyloTree object, rather it resets the branch thicknesses & sets the whole tree to be in view
  • Padding improvements - tip labels are now visible, and small clades render better.
  • Tip names now shown for up to 100 taxa
  • Branch thickness restored -- issue 544
  • Tree panning has been removed (we no longer use react-svg-pan-zoom)

version 1.18.10 - 2018/05/07

  • Separate Nucleotide mutations from gaps / Ns in info-box - thanks @emmahodcroft PR 552
  • Frequencies y-axis is no longer rounded to the nearest 0.05

version 1.18.9 - 2018/05/03

  • update flu footer
  • start using travis CI

version 1.18.8 - 2018/05/02

  • temporary fix for map transmissionIndices errors (bug still exists, issue 547)

version 1.18.7 - 2018/05/02

  • Fix frequencies panel x-axis bug
  • Linting
  • Minor style changes

version 1.18.6 - 2018/04/30

  • update WNV footer

version 1.18.5 - 2018/04/27

  • update WNV footer

version 1.18.4 - 2018/04/26

  • Use exponential notation for the clock rate

version 1.18.3 - 2018/04/23

  • Updated the footer for LASV & WNV

version 1.18.2 - 2018/04/16

  • LBI color scale domain is [0, 0.7] Issue 541
  • Fix bug with antigenic advance & frequencies Issue 540
  • Hovering over a tree legend value of zero now correctly highlights matching tips
  • Undefined color traits are now grey on a discrete scale
  • Removed all references to node.attr.strain (tree JSON) and seq_author_map (meta JSON)

version 1.18.1 - 2018/04/15

  • Make date slider spacing consistent between animation and drag

version 1.18.0 - 2018/04/14

  • Tanglegrams enabled! (bugfixes & reinstate controls dropdown)
  • Status pages: nextstrain.org/status & nextstrain.org/status/staging
  • Narrative files are sourced from nextstrain.org repository

version 1.17.4 - 2018/04/10

  • Updated LASV footer

version 1.17.3 - 2018/04/04

  • Allowed arbitrary user manifests to be served
  • Changed how the tanglegram updates, so that it is now triggered straight after the trees update.
  • Updated the files downloaded from get_data.sh
  • Add lassa (LASV) footer acknowledgments.

version 1.17.2 - 2018/04/02

  • Job ad on splash page.

version 1.17.1 - 2018/03/28

version 1.17.0 - 2018/03/26

Narrative

  • Now exposed via a "hidden" URL query. E.g. flu/h3n2/3y?n=1
  • Frequencies added to narrative
  • block in focus is part of the URL query, and can be reloaded via the URL

Second Tree / Tanglegram

  • Second tree can be loaded via a URL (e.g. ?tt=na). Sidebar dropdown currently disabled.
  • In this mode, trees are forced to be rectangular, and the map & frequencies are not displayed.
  • Tanglegram exists, but no untangling (yet)
  • Bugs still exist (which is why the sidebar has been disabled)

Internals

  • All JSONs (incl. frequencies, narrative) are loaded within a single Promise & dispatch
  • phylotree.change() only ever called once, and always in componentDidUpdate (fixes bugs where it fired in both CWRP and CDU)
  • old & deprecated code removed

version 1.16.5 - 2018/03/26

  • Authors filter is now an explicit setting in the JSONs PR 532

version 1.16.4 - 2018/03/22

  • Flu footer updated
  • Fix bug in genotype colouring PR 531
  • Adjust vaccine cross styling & remove dashed line PR 529

version 1.16.3 - 2018/03/21

  • Flu footer updated

version 1.16.2 - 2018/03/21

version 1.16.1 - 2018/03/16

  • Fix bug in the color scales where clades were coloured white after switching trees.

version 1.16.0 - 2018/03/16

Browser support

  • Now works on Internet Explorer 11 (tested on windows 7)
  • Grid layout issue fixed for Firefox on linux/windows
  • Embedding Nextstrain in an iFrame works - see /scripts/gisaid_iframe.html

version 1.15.1 - 2018/03/14

version 1.15.0 - 2018/03/12

  • Multiple genotypes (for the same amino acid) by typing in multiple comma separated AA/nuc positions. PR 523.

version 1.14.4 - 2018/03/05

version 1.14.3 - 2018/03/01

  • Bug fix where tip colours reverted to their initial colours after a layout change. issue 519

version 1.14.2 - 2018/02/28

  • PR 518
    • Frequency y-axis is now dynamic
    • Frequency text box is more readable
    • Frequency normalisation has been removed

version 1.14.1 - 2018/02/27

  • Style tip stroke separately from branch stroke (node.stroke replaced with node.branchStroke & node.tipStroke)

version 1.14.0 - 2018/02/27

Features

  • Strain search (using awesomplete). This highlights the path to a single tip and increases the tip radius. Strain is stored in the URL query (s=...) and can be restored via URL. Selected strain also appears in the info panel (top of screen).
  • Amino acid branch labels (for every tree) as well as clade labels if specified by the clade_annotation attribute. AA labels are shown where the descendent visible tips account for more than 5% of the total visible tips (same as nextflu). Clade labels are always displayed.
  • Default geneotype gene is now HA1 if available (previously nucleotide).
  • ColorBy ordering (sidebar dropdown) is now ordered (via an array in globals.js)

Internals

  • The JSON processing on initial load has been shifted from the reducers to a single action - fewer dispatches, fewer potential bugs, faster code.
  • Frequencies are initialised in a single action (previously 2).
  • tip-frequencies are now downloaded via get_data.sh
  • Frequency actions are not dispatched unless the frequency panel is loaded.

version 1.13.2 - 2018/02/26

  • Improve consistency of panel controls
  • Show unassigned in tree legend (if applicable)

version 1.13.1 - 2018/02/26

  • Tree button "reset layout" now at top right

version 1.13.0 - 2018/02/26

Features

  • Frequencies are now displayed via a stream graph panel - see PR 497. These require the fetching of a separate tip-frequencies JSON, and must be specified in the panels array of the meta.JSON.
  • "Panels To Display" toggles in the sidebar allow customisation of the display, and this is reflected in the URL.
  • The + - buttons in the tree have been replaced by a "reset tree" button. This resets the bounds to the entire tree & completely re-renders the tree (filters are maintained). Pan behaviour is unchanged.

Internals

  • React-PhyloTree interface is completely rewritten to use phylotree.change() - see PR 501 for the API. The new interface is both easier to understand and quicker.
  • changePageQuery (used for changing narrative blocks) is now a single action
  • Ongoing narrative work (still disabled).
  • React sidebar has been removed (no UI changes).

version 1.12.0 - 2018/02/14

Features

  • Vaccine strains are shown at their use date (in temporal trees), with dotted lines connecting them to their tips (representing collection date) (PR 498)

Internals

  • updateGeometryFade uses counters to know when transitions are finished rather than setTimeout

version 1.11.0 - 2018/02/05

Features

  • Vaccine strains are now displayed if they are specified in metaJSON.vaccine_choices (PR 490)

Internals

  • Tree components and PhyloTree have been reorganized (in src/components/tree) and the syntax improved (PR 493)
  • Upgraded to React 16, as well as upgrading redux & react-svg-pan-zoom (PR 494)

version 1.10.0 - 2018/02/05

Features

  • Local Branching Index (LBI) coloring can be calculated in auspice (code identical to nextflu) if specified in color_options (meta JSON) (PR 491)

Internals

  • get_data.sh script updated to no longer download sequences & entropy JSONs
  • action logging middleware available for debugging / development

version 1.9.0 - 2018/01/30

Animation

  • Animations can now loop! This is selected via a toggle in the sidebar.
  • While animating, the URL displays information which defines the animation (bounds, looping, cumulative, speed). This allows the animation to start automatically by linking to this URL.
  • The code for the animation (i.e. the setInterval code) has been moved out of Map and into a separate AnimationController component.
  • Animation is stopped & started by examining redux state, rather than with imperative controls.

misc

  • The narrative machinery has been moved forward, but this functionality is still disabled and not present in production code.
  • The (rather expensive) calendarToNumeric calculations have become part of state.controls so that components no longer have to calculate them from the string form.

version 1.8.0 - 2018/01/18

entropy calculated via tree

  • The entropy panel data is now computed within auspice by examining mutations throughout the tree, and is throttled to improve speed under load.
  • Both entropy and number of mutations are available via a toggle similar to AA/NT
  • This results in entropy.JSON no longer being fetched.
  • The entropy data is stored in redux state rather than the react component
  • The D3 code has been reorganised
  • Note that the entropy values are slightly different to those exported by augur in some situations - see https://github.com/nextstrain/auspice/pull/478#issuecomment-358496901

genotype calculated via tree

  • This results in sequences.JSON no longer being fetched.
  • Augur was updated to export annotations which are needed for entropy gene display.

middleware / react router

  • All changes to the URL are now performed via middleware rather than side-effects within the action definition.
  • React router has been removed
  • Browser back/forward is detected via window.addEventListener('popstate', this.onURLChanged) which also fires on initial page load.
  • Pages are selected via the <PageSelect> component.

other

  • The number of proteins displayed while hovering over a branch has been limited to 7 (issue #484)
  • The presence of author data is checked before display (issue #488)
  • This changelog has been created and a step in the releaseNewVersion script added to prepend the version number upon release.

version 1.7.2 - 2018/1/4

Narrative / situational report

  • Functionality has been added, but is currently disabled via a flag in globals.js.
  • This is currently rendered in a right-hand sidebar. This feature is not yet complete.

URL queries

  • The following state has been added to the URL query:
    • filters, e.g. f_authors=Tong_et_al,Capobianchi_et_al&f_division=kerouane
    • genotype URLs (these were previously set as the URL but not parsed)
    • panel layout (grid/full)
  • A number of bugs regarding URL query state parsing (esp with genotype colorBys) have been fixed.

version 1.7.1 - 2017/10/31

  • Added mumps acknowledgment

version 1.7.0 - 2017/10/17

version - 2018/01/18