Help Change Log

Change Log

v1.5.2 (2020-09-07)

A divergent region summary track has been added to the primer indel tool.
Sweep haplotypes have been added to the latest release.

v1.5.1 (2020-08-30)

The primer indel tool has been released.

v1.5 (2020-08-15)

The primary data model has moved from isotypes to strains.
The backend of the site has been substantially restructured to improve maintainability.
A table of strains with issues has been added to the data releases page.
The variant data table has been removed from isotype pages.
New strain collection images have been added.
The API has been removed. It did not see a lot of usage and become cumbersome to maintain.
A new collaborators page has been added.
Software and Methods have been moved to be per-release, as the pipeline is ever-evolving.
Data links have been removed from isotype pages; They are still available on the release pages.
Reports for Alignment, Concordance, And Variant calling are now produced for all releases.
Publications have been updated.
The public mappings page was removed as our mapping infrastructure is changing.
A new tool for calculating heritability has been released.
A tool for generating primers for genotyping indels will be released soon.

Genome Browser

IGVjs has been upgraded and has a number of new tools.
A track for repeat_masker, and Dust data has been added.
A track for transposons from Laricchia et al. 2017 been added.
Tracks for divergent regions from Lee et al. 2020 have been added.

v1.3.4 (2020-02-23)

Logins now redirect to the previous page.
Fixed Github authentication issues. A public email is no longer required.

v1.3.3 (2020-02-04)

Fixed Google authentication issues.

v1.3.2 (2019-10-20)

Update Strain map background to ESRI worldmap tileset.
Add a publications page listing publications that have cited CeNDR.
Fixed a bug that broke the statistics page.
Updated internal software to improve security.

v1.3.1 (2019-02-17)

Use a natural sort for strain names on global strain map.
Update software versions.
Improvements to ordering form.
Add code of conduct.
Add issue tracker link.

v1.3.0 (2018-10-03)

Add interval data to reports

v1.2.9 (2018-04-15)

New dataset release: 20180527
Added collection photos.
Added variant counts.
Fixed issue with early reports missing.
Added variant correlation plot.

v1.2.8 (2018-03-18)

Fix link on data page
Fix error with ordering

v1.2.7 (2018-03-01)

Fix site error when strain URL not found.
Fix warning banner for users attempting to access their profile that are not logged in.
Update sqlite schema.

v1.2.6 (2018-02-23)

Fix error with v1 reports that are not significant.

v1.2.5 (2018-02-23)

Prevent queries on browser from exceeding 100kb and crashing the site.
Fix v1 report links
Fix LD plots on v1 reports
Fix homepage link
Fix errant API calls on gene pages
Fix broken link on outreach page.

v1.2.4 (2018-02-21)

Fix issue with the way private reports are organized.

v1.2.3 (2018-02-21)

Fix genome browser URLs.

v1.2.2 (2018-02-21)

Removed extraneous information from v2 report.

v1.2.1 (2018-02-21)

Quick fix for certain v2 reports that would not load properly

v1.2.0 (2018-02-21)

New Pages

A statistics page has been added that details strains/isotypes collected over time, visitors over time, and

Site Infrastructure

Added login system
Moved codebase to Python 3.
Improved robustness of forms using python module WTForms.
Switched database to a single SQLite flatfile + Google Datastore
Moved BAMs to AWS.

Mapping Pipeline

Moved mapping infrastructure to AWS Fargate
Added new description field
The embargo option has been dropped for publishing reports
Added tooltips to report allele distribution maps.
Mapping reports have been removed from gene pages. The new database infrastructure makes it difficult to incorporate these.

Browser

Add allele frequency (AF) as column on variant output.
Added BAMs for strains
Reorganized variant data table output. Variants that affect multiple transcripts are now grouped together.

Public Mappings

The waffle chart has been removed.

Data

CRAMS files and downloads have been removed.

v1.1.2 (2017-12-05)

Fixed a bug preventing the download button from working properly.

v1.1.1 (2017-10-18)

Fixed Drawing of the Tajimas D plot on report pages.
Added ability to view all genotypes on the variant viewer

v1.1.0 (2017-06-16)

A revamped genome browser, which offers the ability to download data in a tab-delimited format (TSV).
The release of a larger set of strains (our 2017-05-31 set). The site now has 249 isotypes available, and a fourth set of strains.
The Data page has been renamed as the 'releases' page to reflect the fact that our set of genomic data continues to evolve.
Many other bug-fixes and minor enhancements.

v1.0.9 (2017-01-24)

Released transposon data.

v1.0.8 (2016-12-20)

Fixed issue with ordering page

v1.0.7 (2016-12-19)

Fixed issue with css on strain pages.

v1.0.6 (2016-12-03)

Added additional error checking to mapping submission page.
Changed submissions to run 'on demand.'

v1.0.5 (2016-12-01)

Fixed an issue with GWA submission.

v1.0.4 (2016-11-28)

Fixed an issue regarding encoding of strain meta info.

v1.0.3 (2016-11-18)

Fixed searching on public mappings.
Fixed the calendar heatmap on public mappings.
Fixed caching on reports.
Updated phenotype histogram to use plotly-js.
Genotypes are now shown beneath variants on the browser page. We are working on methods for exporting data.

v1.0.2 (2016-11-02)

Fixed an issue that prevented variant correlation tables from being output.

v1.0.1 (2016-10-18)

A change log has been added. You are looking at it.
A link to the change log was added to the homepage.
A link to the CeNDR paper and Nucleic Acids Research was added to the homepage.
Fixed an issue that prevented the phastCons track from showing on the browser.
Fixed sorting of news items.