The Generic Model Organism Database project: open-source software for genome-scale biological data.
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Joined November 2012
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Frontend Developer position
Required to apply @ usajobs.gov/job/771349000
-Responsible for designing, developing, testing, & debugging responsive web applications
-Using #javascript , HTML, CSS, GitHub, Jekyll & Liquid
#JobOpening #Hybrid #FrontEndDeveloper
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Did you know that you could get variant analysis, methylation and phasing in a single data analysis workflow? #EPI2ME human variation workflow, best practice @nanopore data analysis, with great reports and integrated genome browser. #nanoporeconf
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I created a Colab tutorial that checks if a gene/transcript ID has an associated crystal structure, checks if related proteins with associated crystal structures are available, and then compares those to a de novo structure prediction:
colab.research.google.com/gi…
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The application even includes jbrowse2 for no fuss viewing of read alignments straight. Analysis a manual review in a single application.
jbrowse.org/jb2/
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During the #Soybean Breeders Workshop the SoyBase team asked the workshop attendees to vote for their favorite SoyBase.org tool. The word cloud was created from the community's votes.
#soybeans #plantbreeding #research #GenomeBrowser #BLAST
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Also available in #bioconda :-)
Thanks @usejbrowse team!
JBrowse v2.2.0 released, featuring alignments track performance improvements, totally revamped documentation on our website, and lazy loading of assemblies allowing improved scalability for loading many genomes in a single config! See release notes: jbrowse.org/jb2/blog/2022/11…
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JBrowse v2.2.0 released, featuring alignments track performance improvements, totally revamped documentation on our website, and lazy loading of assemblies allowing improved scalability for loading many genomes in a single config! See release notes: jbrowse.org/jb2/blog/2022/11…
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Reminder - there are just 2 weeks remaining in @Hacktoberfest! Everyone, of all skill levels, is welcome to join. Visit hacktoberfest.com/ to see current project needs and to register! @TripalProject @usejbrowse @galaxyproject @biocurator @drupal_org #genomics #Fairdata
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Interested in Pangenome data visualisation? 👇
Congratulations Dr Durant😉
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Helena Rasche and Saskia Hiltemann talking about all the new additions to the Galaxy Training Network. Now with data science tutorials! @galaxyproject #egd2022
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Very excited to attend the European #usegalaxy Days ( #EGD2022 ), and present (by @jason_j_gill) our use of Galaxy and Apollo for undergraduate genomics education! @galaxyproject
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The Main Lab (@MainDorrie ) at @HorticultureWsu has recently relased version 1.4.0 of the Tripal MegaSearch module! It provides flexiblle querying and download of data in a @TripalProject
and @gmodproject Chado website.
Learn more here:
gitlab.com/mainlabwsu/tripal…
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For fellow biologists working on non-model organisms: @lh3lh3's new tools miniprot is like minimap for proteins. You can easily map prots from one sp to another's genome. It also outputs GFF. This will be very nice for annotating new genomes!
github.com/lh3/miniprot
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JBrowse v2.1.3 released with improvements for drawing dotplots and synteny, searching gene names, and a button to open ".jbrowse" files on desktop! jbrowse.org/jb2/blog/2022/09…
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CarrotOmics now published! doi.org/10.1093/database/baa…
This site uses Tripal to provide genomic and other resrouces for carrot breeders and researchers
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Tripal v3.8 is now released! This release consists mostly of minor bug fixes and compatibility improvements. Tripal sites can upgrade using standard Drupal upgrade steps.
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The preprint for the main @usejbrowse 2 paper is officially on bioRxiv 🧬 🎉 🥳
Really proud to have been a part of this team.
This platform offers many new opportunities, especially for exploring structural variation with long reads, and relationships between genomes.
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New release of JBrowse 2.1.0 features multi-bigwig tracks, undo/redo, and warnings if synteny datasets render out of bounds! jbrowse.org/jb2/blog/2022/07…
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We are delighted to have our HumanMine article doi.org/10.1093/database/baa… published in the Database journal 🎉. Check it out to learn how to do powerful data exploration over biological data to gain new insights!
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#JobAlert: An exciting opportunity for a #SoftwareDeveloper to join @emblebi @usejbrowse teams and work on the brand new shiny Apollo project. #Bioinformatics #SoftwareEngineering #SoftwareEngineer
Opening for a software engineer to work the #usejbrowse team and #emblebi on the new Apollo: Typescript + React + JBrowse2! Please forward to any UK-based software engineers you think might be interested:
cwjobs.co.uk/job/software-en…