@gmodproject

The Generic Model Organism Database project: open-source software for genome-scale biological data.

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gmod.org
Joined November 2012
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This is Scott; my contract working on GMOD related tasks (including JBrowse, Chado, and Tribal) and other projects like wormbase.org and alliancegenome.org/ is likely to come to and end soon. If you know of anybody looking for help with things like this, (1/2)
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(2/2) Please steer them my way. My resume and publication list are on my personal website: scottca.in/
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SoyBase.org@SoyBaseDatabase
24 Jan 2024
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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#JBrowse2 workshop about to start at #pag31 in town and country D. Get some updates and a hands on tutorial for setting up your own JBrowse 2!
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Cristina Gamba@gamba_cristina
26 Sep 2023
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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Chris Wright@chrisnrg
6 Dec 2022
The application even includes jbrowse2 for no fuss viewing of read alignments straight. Analysis a manual review in a single application. jbrowse.org/jb2/

JBrowse — Next generation genome browser

JBrowse is a genome browser that runs on the web, on your desktop, or embedded in your app — with linear, circular, dotplot, and synteny views, structural variant inspection, and an extensible plugin...

jbrowse.org
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I am happy to announce that the #JBrowse2 paper has be published in Genome Bio. There is lots of cool stuff: synenty, structural variation, plugins, multi chromosome and multi genome views, a graphical configuration editor, a desktop and easy-to-embed apps genomebiology.biomedcentral.…

JBrowse 2: a modular genome browser with views of synteny and structural variation

Genome Biology - We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core...

link.springer.com
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Here's figure 1 to whet your appetite.
Seven panels: A The Linear Genome View displaying gene annotations, quant signals, and a Hi-C track. B whole genome overview showing tumor vs normal sequencing coverage in the COLO829 cell line. C The Circular View gives an overview of long-range relationships within and between chromosomes (translocations in an SKBR3 cancer genome). D The Dotplot View shows relationships between two sequences (in this case the relationship between hg19 and hg38 human genomes). E The Tabular View summarizes features in a sortable, filterable list, showing in this example the SKBR3 variant calls from Sniffles. F The Linear Synteny View shows relationships between two genomes (in this case, peach and grape). G The SV Inspector allows inspection of structural variants by combining a Tabular View and a Circular View. H The Breakpoint Split View shows events such as gene fusions and translocations by aligning two Linear Genome Views and tracing the split or paired read mappings across the two views

ALT Seven panels: A The Linear Genome View displaying gene annotations, quant signals, and a Hi-C track. B whole genome overview showing tumor vs normal sequencing coverage in the COLO829 cell line. C The Circular View gives an overview of long-range relationships within and between chromosomes (translocations in an SKBR3 cancer genome). D The Dotplot View shows relationships between two sequences (in this case the relationship between hg19 and hg38 human genomes). E The Tabular View summarizes features in a sortable, filterable list, showing in this example the SKBR3 variant calls from Sniffles. F The Linear Synteny View shows relationships between two genomes (in this case, peach and grape). G The SV Inspector allows inspection of structural variants by combining a Tabular View and a Circular View. H The Breakpoint Split View shows events such as gene fusions and translocations by aligning two Linear Genome Views and tracing the split or paired read mappings across the two views

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(Geez, squeezing the description of this figure into 1000 characters was hard!)
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SoyBase.org@SoyBaseDatabase
13 Mar 2023
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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It's that time again: I'm going to start bugging people for letters of support for the @usejbrowse project. If you have time and are a #JBrowse user, please consider writing a letter. JBrowse is a big part of many genomics projects, and we want to make sure it continues to grow.
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My friends at CIRAD Montpellier, France are looking for bioinformatics web developer familiar with #GMOD tools (@TripalProject @galaxyproject, @usejbrowse) to work on a rubber and palm tree genome project: recrutement.cirad.fr/job/emp…
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To go along with the #JBrowse2 tutorial at #PAG30, we also have three talks by JBrowse folks: @rbuels gave an intro: youtu.be/oxdhe_ZLGYs @cmdcolin gave an overview of features: youtu.be/jl0BzcBhGqk Caroline Bridge talked about the plugins: youtu.be/hJmV97odZ1w
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At #PAG30 earlier this month, we presented a hands on #JBrowse2 tutorial, where the attendees logged into a server, ran through setting up a JBrowse 2 instance and added a lot of data, including #synteny and #structuralVariation gmod.org/wiki/JBrowse2_Tutor…
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#GMOD at #PAG today: #JBrowse workshop 1:30 in T&C D (including hands on tutorial), #JBrowse from an implementer's perspective in Next Gen Annotation in Pacific E at 4:20 (blaze!)
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Join the #tripal folks for their #PAG30 session: plan.core-apps.com/pag_2023/… Topics include v4, biocuration, #jbrowse integration, intro to planosphere.stowers.org , and a retrospective by @FicklinStephen
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Darn it, I forgot to include useful things like time and location (I've gotten used to longer posts elsewhere so was worried about keeping it brief!): the session is at 4:00 in Town & Country D (the computer demo room)
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Björn Grüning@bjoerngruening
6 Nov 2022
Also available in #bioconda :-) Thanks @usejbrowse team!
JBrowse@usejbrowse
4 Nov 2022
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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