CeNDR.News CeNDR News 2022-01-29T08:00:48.196802+00:00 CeNDR Admin erik.andersen@northwestern.edu python-feedgen http://ex.com/logo.jpg This is a cool feed! Open Beta Open Beta 2022-01-29T08:00:48.244547+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>Open Beta</h4> <p><a href="https://www.elegansvariation.org">elegans variation</a> is now in an open beta!</p> 2016-02-05T00:00:00-06:00 May 2016 CeNDR Updates May 2016 CeNDR Updates 2022-01-29T08:00:48.241483+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>May 2016 CeNDR Updates</h4> <ul> <li>A <a href="/data/browser/">variant browser</a> has been added!</li> <li>The feedback system has been changed and now utilizes a google form.</li> <li>Reports have been reworked to utilize the full width of pages.</li> <li>Caching has been enabled.</li> <li>Interactive version of the allele distribution and Tajima's D have been added.</li> <li>The ordering system has been updated. Strain sets are now treated as individual items.</li> <li>A <a href="/about/donate/">Donation</a> page has been added.</li> <li>A <a href="/about/funding/">Funding</a> page has been added.</li> <li>Strain metadata is available, click <a href="/strain/metadata.tsv">here</a> to download.</li> <li>Report text and content has been edited for clarity.</li> </ul> 2016-05-25T00:00:00-05:00 Transposon Data Transposon Data 2022-01-29T08:00:48.239608+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>January 2017 CeNDR Updates</h4> <p>We have recently performed an anaysis characterizing Transposon variation in _C. elegans_. The dataset will be further integrated with the site resources as time goes on. For now, the raw data are available below, and on the data page.</p> <p><br /> <a href="https://storage.googleapis.com/andersenlab.org/publications/2017Laricchia/tes_cender.bed" type="button" class="btn btn-default btn-block btn-success">Download Transposon Data</a></p> 2017-01-24T00:00:00-06:00 Version 1.1.0 Version 1.1.0 2022-01-29T08:00:48.237547+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>June 2017 CeNDR Updates</h4> <p>The site has undergone a large update! Our 1.1.0 release brings the following:</p> <ul> <li>A revamped genome browser, which offers the ability to download data in a tab-delimited format (TSV).</li> <li>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.</li> <li>The Data page has been renamed as the 'releases' page to reflect the fact that our set of genomic data continues to evolve.</li> <li>Many other bug-fixes and minor enhancements.</li> </ul> <p>As always, we highly value community feedback. Please let us know what issues you run in to and how we can continue to improve the site.</p> 2017-06-16T00:00:00-05:00 Version 1.2.0 Version 1.2.0 2022-01-29T08:00:48.233637+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>January 2018 CeNDR Updates</h4> <p>Version 1.2.0 brings many updates to the site.</p> <p><strong>New Pages</strong></p> <ul> <li>A statistics page has been added that details strains/isotypes collected over time, visitors over time, and </li> </ul> <p><strong>Site Infrastructure</strong></p> <ul> <li>Added login system</li> <li>Moved codebase to Python 3.</li> <li>Improved robustness of forms using python module WTForms.</li> <li>Switched database to a single SQLite flatfile + Google Datastore</li> <li>Moved BAMs to AWS.</li> </ul> <p><strong>Mapping Pipeline</strong></p> <ul> <li>Moved mapping infrastructure to AWS Fargate</li> <li>Added new description field</li> <li>The embargo option has been dropped for publishing reports</li> <li>Added tooltips to report allele distribution maps.</li> <li>Mapping reports have been removed from gene pages. The new database infrastructure makes it difficult to incorporate these.</li> </ul> <p><strong>Browser</strong></p> <ul> <li>Add allele frequency (AF) as column on variant output.</li> <li>Added BAMs for strains</li> <li>Reorganized variant data table output. Variants that affect multiple transcripts are now grouped together.</li> </ul> <p><strong>Public Mappings</strong></p> <ul> <li>The waffle chart has been removed.</li> </ul> <p><strong>Data</strong></p> <ul> <li>CRAMS files and downloads have been removed.</li> </ul> 2018-01-23T00:00:00-06:00 Version 1.2.5 Version 1.2.5 2022-01-29T08:00:48.231428+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>August 2018 CeNDR Updates Updates</h4> <ul> <li>Release 20180527 is out! This release brings the total number of isotypes to 330, with 766 total strains.</li> <li>Added haplotype plots for new releases.</li> <li>Improvements to ordering.</li> <li>Upgraded internal packages for improved stability.</li> <li>Elevation is now rounded to the nearest integer.</li> <li>Enabled searching of reference, strain, and isotype on the global map.</li> <li>Fixed language on ordering pages to reflect payment type.</li> <li>Fixed an issue with missing phenotype plots.</li> </ul> 2018-08-03T00:00:00-05:00 Version 1.3.0 Version 1.3.0 2022-01-29T08:00:48.229702+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>October 2018 CeNDR Updates</h4> <ul> <li>Variant lists from the variant summaries are now output with reports.</li> <li>Variant correlation is now performed regardless of interval size.</li> </ul> 2018-10-03T00:00:00-05:00 Version 1.3.4 Version 1.3.4 2022-01-29T08:00:48.228161+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>February 2020 CeNDR Updates</h4> <p>With version 1.3.4 we hope to have resolved login issues.</p> 2020-02-23T00:00:00-06:00 Version 1.3.5 Version 1.3.5 2022-01-29T08:00:48.226331+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>Version 1.3.5</h4> <p>With version 1.3.5 we have addressed an issue that was preventing mappings from working.</p> 2020-03-04T00:00:00-06:00 Version 1.3.6 Version 1.3.6 2022-01-29T08:00:48.224381+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>Version 1.3.6</h4> <ul> <li>A new Tools menu is available. Currently, the tools listed are placeholders. Full functionality will be added soon.</li> <li>At this time we are unable to accept new strain orders until further notice.</li> </ul> 2020-03-15T00:00:00-05:00 Version 1.5.0 Version 1.5.0 2022-01-29T08:00:48.219969+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>Version 1.5</h4> <p>CeNDR <code>1.5.0</code> has now been released. Version <code>1.5.0</code> is a substantial update.</p> <p><strong>Release Notes</strong></p> <ul> <li>The primary data model has moved from isotypes to strains.</li> <li>The backend of the site has been substantially restructured to improve maintainability.</li> <li>A table of strains with issues has been added to the data releases page.</li> <li>The variant data table has been removed from isotype pages.</li> <li>New strain collection images have been added.</li> <li>The API has been removed. It did not see a lot of usage and become cumbersome to maintain.</li> <li>A new <a href="/about/collaborators">collaborators</a> page has been added.</li> <li>Software and Methods have been moved to be per-release, as the pipeline is ever-evolving.</li> <li>Data links have been removed from isotype pages; They are still available on the release pages.</li> <li>Reports for Alignment, Concordance, And Variant calling are now produced for all releases.</li> <li>Publications have been updated.</li> <li>The public mappings page was removed as our mapping infrastructure is changing.</li> <li>A new tool for calculating <a href="/tools/heritability">heritability</a> has been released.</li> <li>A tool for generating primers for genotyping indels will be released soon.</li> </ul> <p><strong>Genome Browser</strong></p> <ul> <li>IGVjs has been upgraded and has a number of new tools.</li> <li>A track for repeat_masker, and Dust data has been added.</li> <li>A track for transposons from <a href="https://andersenlab.org/publications/2017Laricchia.pdf"><em>Laricchia et al.</em> 2017</a> been added.</li> <li>Tracks for divergent regions from <a href="https://andersenlab.org/publications/2020LeebioRxiv.pdf"><em>Lee et al.</em> 2020</a> have been added.</li> </ul> 2020-08-15T00:00:00-05:00 Version 1.5.1 Version 1.5.1 2022-01-29T08:00:48.218260+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>Version 1.5.1</h4> <p><strong>Release Notes</strong></p> <ul> <li>The <a href="/tools/pairwise_indel_finder">primer indel tool</a> has been released.</li> </ul> 2020-08-30T00:00:00-05:00 Version 1.5.2 Version 1.5.2 2022-01-29T08:00:48.216460+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>v1.5.2 (2020-09-08)</h4> <ul> <li>A divergent region summmary track has been added to the primer indel tool.</li> <li>Sweep haplotypes have been added to the latest release.</li> </ul> 2020-09-08T00:00:00-05:00 Version 1.5.3 Version 1.5.3 2022-01-29T08:00:48.214424+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>v1.5.3 (2020-09-27)</h4> <ul> <li>The Strain catalogue has been opened.</li> </ul> 2020-09-27T00:00:00-05:00 Version 1.5.7 Version 1.5.7 2022-01-29T08:00:48.202454+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>v1.5.7 (2021-04-12)</h4> <ul> <li>Fix to Mapboxes</li> <li>New dataset released</li> </ul> 2021-04-12T00:00:00-05:00 Version 1.6.0 Version 1.6.0 2022-01-29T08:00:48.200146+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>v1.6 (2021-03-29)</h4> <ul> <li>Reorganize content and update link names</li> <li>Create Cloud Configuration for dynamic creation of Dataset Releases</li> <li>Add support for SAML/Shibboleth User authentication</li> <li>Add username/password User authentication</li> <li>Migrate user auth from Session to JWT</li> <li>Add user roles</li> <li>Create Site Admin views for managing site content</li> <li>Migrates some existing content from AWS to GCP</li> </ul> 2021-04-15T00:00:00-05:00 Version 1.7.0 Version 1.7.0 2022-01-29T08:00:48.197241+00:00 CeNDR Admin erik.andersen@northwestern.edu <h4>v1.7.0a (2021-06-20)</h4> <ul> <li>Major updates to site look and feel and user experience</li> <li>Introduction of a Genetic mapping tool for analyzing a single trait of interest using the NemaScan Nextflow Pipeline and Google Lifesciences</li> <li>Introduction of Strain Annotated Variant tool for browsing relationships between strains, genetic variants, and sequence consequences</li> <li>Users can now store and view their results from the Pairwise Indel Finder, Heritability Calculator, and Genetic Mapping analysis</li> <li>Multiple bugfixes and site architecture cleanup</li> </ul> 2021-06-20T00:00:00-05:00