New Alliance release available
Check out the new Alliance release 7.0.0. To learn more about this release please see the release notes.
If you don’t already know about the Alliance of Genome Resources (Alliance), it is a consortium of 7 model organism databases (MODs) and the Gene Ontology (GO) Consortium whose goal is to provide an integrated view of their data to all biologists, clinicians and other interested parties. You can look at harmonized C. elegans data such as disease model annotations in the context of other species. You can find ortholog data easily right on a gene page. Note that we are in the process of transitioning data types f...
Source: WormBase - February 29, 2024 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news release notes Alliance of Genome Resources new release Source Type: news
Attend the microPublication Workshop at TAGC 2024!
Heading to The Allied Genetics Conference in Washington? Make sure to attend the microPublication Workshop! Get insights into the project, engage with editors and researchers who have authored or peer-reviewed articles, and assess if your results are suitable for microPublication. micropublication.org emphasizes speed, brevity, scientific rigor, and proper credit for your work—offering fast, concise, and easily draftable publications that undergo peer review and are citable.
When: Thursday, March 7th, 7:00 am-8:00 am
Where: Baltimore Room 1-2
Schedule
7:00am – 7:10am Introduction/Overview – ...
Source: WormBase - February 28, 2024 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news micropublication TAGC24 Source Type: news
Curate your paper for ACKnowledge at the GSA Allied Genetics Conference!
Attention Worm researchers! Are you planning to attend The Allied Genetics Conference (TAGC) in Washington in March? If so, come to the WormBase booth to learn more about the ACKnowledge project and community curation. You will have the chance to win a gift card by completing the ACKnowledge community curation form and filling out a brief survey. To participate in the challenge sign up here. We look forward to seeing you next March! (Source: WormBase)
Source: WormBase - November 30, 2023 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community meetings news ACKnowledge TAGC24 Source Type: news
New chapter about lineage specification in WormBook, GENETICS
Check out the new chapter, “Mechanisms of lineage specification in Caenorhabditis elegans” by Jun Liu and John Murray in WormBook, GENETICS. (Source: WormBase)
Source: WormBase - October 30, 2023 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community external website news wormbook WormBook GENETICS Source Type: news
C. elegans community at the GSA Allied Genetics Conference
We are excited to work with the Genetics Society of America to bring the worm community into the Allied Genetics Meeting and would like to announce that abstract submission is open. This will be a great opportunity for us to come together in C. elegans sessions to hear the latest on cell biology, small RNAs, aging, neurobiology, and all of our other favorite topics. We have some great keynote speakers, worm games, and lots of talks from the abstracts, and the best poster prize winners will get registration/domestic travel to the C. elegans appropriate topic meeting. Also, check out this link for info on undergraduate tr...
Source: WormBase - October 9, 2023 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: community external website news meetings TAGC TAGC24 Source Type: news
New JBrowse 2 release
We decided to release an updated JBrowse 2 after feedback from users at the International Worm Meeting. There are several new items in this release:
There is now a Help menu item specifically for WormBase users.The CRISPR related tracks have been ported over from JBrowse 1.The CeNDR track has been returned to functioning.The details panel for genes now has a link to that gene at the Alliance of Genome Resources
Of course, if you experience any issues with JBrowse 2 or any other part of WormBase, please let us know. (Source: WormBase)
Source: WormBase - July 14, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: news jbrowse2 Source Type: news
JBrowse 2: Sharing views
Sharing views in JBrowse 2 is not as easy as it is in JBrowse 1, but there is also more power in the ability to share views and data. In JBrowse 1, the entire state of the “core” view is always encoded in the URL: if you copy the URL from the browser’s location bar and send it to someone, they will get the same view as the original user. This has several limits though: if the user has loaded local data, no information about it would get into the URL. The same is true if the user has created a sequence search track: that information is not encoded in the URL.
JBrowse 2, on the other hand, does not encod...
Source: WormBase - July 14, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: news tutorials jbrowse2 Source Type: news
JBrowse 2: Adding your own data
JBrowse 2 provides considerable support for adding your own data. The first point about adding your own data is this: it doesn’t get uploaded to anywhere. The data you add always stays where it starts, there is no “uploading” of the data. This is an important point if you are worried about the privacy of your data.
JBrowse supports several common formats for genomics data, including GFF, VCF, BED, BigWig, BigBed, and BAM/CRAM. For a complete list of supported formats, see the JBrowse 2 documentation. For supported formats, the only caveat is that the reference sequence names should be names that the WormBase JBrow...
Source: WormBase - June 23, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: tutorials jbrowse2 Source Type: news
JBrowse 2: Comparative data
JBrowse 2 has the ability to display pairwise comparative data. At WormBase, we have comparative data between these species/assemblies:
C. elegans N2C. elegans Hawaiian strainC. elegans VC2010C. brenneriC. briggsaeC. inopinataC. japonicaC. remanei
These comparisons are made with minimap2 with the option to generate CIGAR strings. The CIGAR strings allow JBrowse to show the inserts and deletions between the compared genomes. These pre-computed comparisons can be found in a few ways from WormBase’s JBrowse.
The most straightforward way to find them is to turn on the synteny tracks when browsing the linear ...
Source: WormBase - June 22, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: tutorials jbrowse2 Source Type: news
JBrowse 2: Working with lists, bookmarks and sessions
Spreadsheet view
JBrowse 2 has a “spreadsheet view” that looks much like you might expect: a simple spreadsheet. The primary way a WormBase user might interact with the spreadsheet view is if you have a file that has a list of genomic locations that are of interest and you’d like to step through. For example, consider this list of locations that have comments separated by a tab (so that this is a tsv file–JBrowse supports tsv, csv, VCF, BED and BEDPE files in the spreadsheet view:
I:16,632..17,470 site 1
I:314,852..315,768 site 2
I:382,162..383,013 site 3--this is ...
Source: WormBase - June 21, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: tutorials jbrowse2 Source Type: news
JBrowse 2: Working lists, bookmarks and sessions
Spreadsheet view
JBrowse 2 has a “spreadsheet view” that looks much like you might expect: a simple spreadsheet. The primary way a WormBase user might interact with the spreadsheet view is if you have a file that has a list of genomic locations that are of interest and you’d like to step through. For example, consider this list of locations that have comments separated by a tab (so that this is a tsv file–JBrowse supports tsv, csv, VCF, BED and BEDPE files in the spreadsheet view:
I:16,632..17,470 site 1
I:314,852..315,768 site 2
I:382,162..383,013 site 3--this is the good one
I:397,470..3...
Source: WormBase - June 21, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: tutorials jbrowse2 Source Type: news
JBrowse 2: Searching for features and sequences
Searching in JBrowse 2 is quite similar to searching in JBrowse 1. The most common way you would look for a feature would be to type the name of a feature in the location field (that is, the field that has the current location in it, like this:
Anything that you could search for in JBrowse 1 you can search for in JBrowse 2, and there is a good reason for that: they are using exactly the same data and search indexes. So, you can look for gene and transcript names, identifiers like WBGene00006749, and allele names like pkP649. Of course, you can also enter a location like II:100000..200000. The only difference i...
Source: WormBase - June 21, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: tutorials jbrowse2 Source Type: news
JBrowse 2: Getting Sequence
In JBrowse 2 there are multiple ways to obtain sequence information. One is via a context menu when region is selected by clicking and dragging on the “number line” part of the linear genome view:
Selecting “Get sequence” from the context menu will open a dialog where you will have a few options for how to get your sequence:
To get the sequence, you have the option to either save it as a file in your browser’s default download folder or you can copy the sequence to your clipboard. Additionally, you can both complement and reverse the sequence before saving the sequence. Finally, note that the ...
Source: WormBase - June 21, 2023 Category: Genetics & Stem Cells Authors: Scott Cain Tags: tutorials jbrowse2 Source Type: news
Bring your questions, comments and suggestions to WormBase staff at IWM 2023!
WormBase is excited and looking forward to being in Glasgow for IWM 2023! We have many activities scheduled including a plenary talk in the evening on June 24th, the WormBase workshop in the afternoon of June 25th which will present and discuss data and tools in WormBase and the Alliance of Genome Resources, and the WormBase and ACKnowledge booths that will be open from June 25th to June 27th. Come visit us with your questions, comments and suggestions at any of these occassions, we’d be happy to talk to you! (Source: WormBase)
Source: WormBase - June 14, 2023 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community meetings news Source Type: news
Three more days to contribute to WB community curation to WIN PRIZES at the IWM in Glasgow!
You have 3 more days to make it to the top 10! Submit your data now, the deadline for submission is June 10th, 2023. The top submitter (Paul Sternberg, excluded!) will win a voucher for a microPublication ($250 value!). Additional prizes will be awarded at the WormBase booth. Access the submission forms here. (Source: WormBase)
Source: WormBase - June 7, 2023 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: community news community curation IWM 2023 Source Type: news
