#wormbase — Public Fediverse posts

I've published a new ACGT genomics blog post! This is a very rare event for me these days (having been out of the field for over a decade now).

A chance conversation this week led me to write almost 2,000 words last night about how — over two decades ago — I had to design a new form of gene identifier for the WormBase database (now part of @AllianceGenome) that would have to stand the test of time.

Here is a very deep dive into the decisions behind coming up with a bioinformatics gene identifier.

https://www.acgt.me/blog/2026/4/30/whats-in-a-gene-name

#genomics #bioinformatics #WormBase

A similar program has been successfully running in the #worm community and a lot of our program structure/surveys and ideas were adapted from those. We are very grateful to the worm program chairs and #WormBase members for supporting us in our endeavors.

Keep an eye out for emails from the GSA next week for more details. Meanwhile urging everyone in the #genetics #community to kindly please share this with trainees/faculty who will benefit from the program.

I got up pretty early to watch the WormBase workshop at #worm23 (the international c. elegans meeting) but they aren't streaming any of the workshops 😢
I can at least post a link to a video of my section of the workshop, an intro to #jbrowse2 at #WormBase: https://youtu.be/8IBOotP48Dw

I got up pretty early to watch the WormBase workshop at #worm23 (the international c. elegans meeting) but they aren't streaming any of the workshops 😢
I can at least post a link to a video of my section of the workshop, an intro to #jbrowse2 at #WormBase: https://youtu.be/8IBOotP48Dw

I got up pretty early to watch the WormBase workshop at #worm23 (the international c. elegans meeting) but they aren't streaming any of the workshops 😢
I can at least post a link to a video of my section of the workshop, an intro to #jbrowse2 at #WormBase: https://youtu.be/8IBOotP48Dw

I got up pretty early to watch the WormBase workshop at #worm23 (the international c. elegans meeting) but they aren't streaming any of the workshops 😢
I can at least post a link to a video of my section of the workshop, an intro to #jbrowse2 at #WormBase: https://youtu.be/8IBOotP48Dw

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

#biocuration2023 parallel session "AI and Text Mining" starting with Kimberly Van Auken: community curation and artificial intelligence are solutions to scale #biocuration. ACKnowledge (Author Curation to Knowledgebase) combines them at #WormBase https://afp.textpressolab.com/about

I know it. Change isn't easy. I literally just went through it last month with #WormBase, where I shut of a service that has been running for 20 years (and found out that there was one bit of functionality not replicated elsewhere--oops).

BUT. I'm not thrilled with #Gitter's migration to #matixDotOrg. Their migration documentation really is lacking WRT desktop clients (maybe they aren't ready yet? Good time to pull the trigger then, yah?). Anyway, I'm sure it will get better.

I’ve been in #DigitalCommunication / #ScienceCommunication full-time for about six years now.

Prior to that I was a #genomics researcher and I spent about 20 years working on various research and infrastructure projects (big love for #WormBase) as well as teaching bio students to #code.

My science background remains useful in making sense of all of the comms data that I have now.

@jogoodma Yeah, #WormBase 's GBrowse is going away at the end of January as well. It's been a heck of a workhorse and can go out to pasture now. Time to move on to #JBrowse2 https://jbrowse.org/ !

#Introduction (part 1)

Hi! I’m a former #genomics researcher. My PhD (that I started in 1996) was spent looking at the very first sequenced eukaryotic genomes (yeast and worm).

I spent about 20 years of working on various research and infrastructure projects (big love for #WormBase) as well as teaching bio students to #code.