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Posts by J.J. Emerson 艾偉傑 🖥️🧬

Of course not.

I'll just link to a recent response and some IHE discussion on the issue in the context of standardized testing.

bsky.app/profile/jjem...

www.insidehighered.com/admissions/a...

4 months ago 0 0 1 0

I am anti-punitive and I don't like forcing students to seek accommodations in the first place. But I'm not DS. I never once suggested students be punished, tested, ferreted out, etc.

4 months ago 0 0 0 0

DS is creating inequity, especially among populations with less access to healthcare and proper diagnosis to obtain this rationed accommodation. This is before we even consider the minority of students who seek advantage by circumventing DS accommodation conditions.

4 months ago 0 0 1 0

I've explained myself several times. But I'll clarify once more. I do not seek to ration accommodations. I did not set up these circumstances. DS does by rationing accommodations. I would prefer that everyone be given ample time in a quiet testing center without rationing.

4 months ago 0 0 1 1

To put it simply: I would love to give everyone more than enough time to complete the assessments. However, DS rations how much time students get to complete assessments. I wouldn't. The rationing and how it is apportioned is the problem to begin with. That is all.

4 months ago 0 0 0 0

Yup. Already addressed this sentiment upthread. For me, YES! And if that ends the conversation for you, so be it. For the institution, what you said. This is somebody's job, even if it isn't mine or yours.

4 months ago 0 0 1 0

Cheaters circumvent that.

4 months ago 0 0 1 0

I don't think it's cheating. But if I scheduled my exams so that everyone had extra time, DS would view that as the baseline and extend the time even more for a subset of students. So, clearly, part of what they are trying to accomplish is giving those without accommodations LESS time.

4 months ago 0 0 1 0

Sure, that's a get out of jail free card for faculty, but not the universities. That shifts the question to disability services. By allowing cheaters, DS undermines accommodations. Otherwise, why not give the entire class the same accommodation? Like Jason, I don't care and just do what DS tells me.

4 months ago 0 0 2 0
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I literally wrote a Shiny App that automates tasks for the track leader that theoretically can be done in Slate, but I can't actually figure out how to do. I'm told Slate is super awesome actually, but I have neither the access permissions nor the training to get much out of it. And the interface...

4 months ago 1 0 0 0

I'm supervising two admissions tracks this year, and I couldn't agree more if I tried. My most successful reviewer recruiting tool is promising "You won't have to interact with Slate to complete your reviews!"

4 months ago 3 0 1 0

Certifications should be outside of the university and should be universal. That would eliminate grade inflation and preference for "easy" professors that simply assign less or less challenging work. Students would prefer professors whose pupils perform well on certifications.

4 months ago 1 0 0 0

As per usual, I think the whole discussion is a bit of a red herring. The real problem is using university assessments as certifications. Personally speaking, I think universities should be thought of places of learning rather than of certification. The consumer of grades should be the student.

4 months ago 1 0 1 0

I also think that accommodation expectations undermine instructor autonomy. I literally can't design an assessment that factors in common time accommodations. It is assumed that I didn't do that and accommodations are stretched from that baseline. So, I'm herded into designed for the modal student.

4 months ago 0 0 1 0

As a kid, I always got chiltepin and chili pequin confused. Only learned the difference as an adult. We put chiltepins into an empty Tabasco Sauce bottle with vinegar to make pickled peppers. After a while, it was an awesome little sauce to put on greens and the like. Or on my tongue when I cursed.

4 months ago 1 0 1 0

Time to just use all of UTF-8.

5 months ago 4 0 0 0

That's so egregious!

5 months ago 1 0 0 0

The fact that you don't know the original fastp is exacerbated by the collision. You are totally not to blame!

5 months ago 1 0 0 0

This isn't only about whether researchers know the history. It's also about due diligence during development and peer review. The original literally shows up in the search results, or at least it would have before SEO got swamped with the new software. And that's the point about avoiding collisions.

5 months ago 2 0 1 0
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At 5,000 citations and the OG of the naming convention for the most widespread bioinformatics file format, it's probably not too much to ask that bioinformaticians know their own field well enough to avoid a collision. Heck, just google it!

5 months ago 1 0 1 0

If these pieces of software were applied to different domains, that's probably fine. However, the reason the text 'fast' is applied to nt sequences is because of the fastp and fasta software by Lipman and Pearson. For context, the fasta format is derived from the fasta software. fastp preceded both.

5 months ago 1 0 1 0
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Rapid and Sensitive Protein Similarity Searches An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases. Because of the algorithm's efficien...

Did nobody at Bioinformatics suggest maybe, just maybe, it's bad practice to simply reuse the name of a piece of foundational software, like the original fastp package from Lipman and Pearson from 1985? Are we TRYING to make using bioinformatics tools hard???

www.science.org/doi/10.1126/...

5 months ago 5 0 2 0
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fastp: an ultra-fast all-in-one FASTQ preprocessor AbstractMotivation. Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a differ

Wow, I never really noticed this 'fastp' software. I'm apparently the only one though.

They simply re-used an existing name already employed by popular and historically significant software. How is this kind of thing possible?

academic.oup.com/bioinformati...

5 months ago 6 1 1 1
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a man with a mustache is wearing a hat and pointing his finger . ALT: a man with a mustache is wearing a hat and pointing his finger .

<looks at watch: 10 minutes remaining>
<looks at slides: 30 remaining>

I'm going to switch gears here.

5 months ago 2 0 0 0
The Specificity of the Hidden Defect in the Human Bio Element – EVROPSKÝ POLITICKÝ A PRÁVNÍ DISKURZ

Here's a fun paper! The bibliography is fire. I wonder what they have to say about evolutionary genomics?

eppd13.cz?page_id=2587

5 months ago 0 0 0 0

I totally agree with this approach. There's no real benefit to collecting replies from randos. I'm not Ash Ketchum and replies aren't Pokemón. I do not need to catch 'em all.

5 months ago 4 1 0 0

Relatedly, I think it's presumptuous to assume whether Puerto Rico would join or how their representatives would vote if they did. Nothing good ever comes from assuming a whole region's population is a monolith.

5 months ago 1 0 1 0
Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

12/12 This work provides a new map of variation for these "recalcitrant" regions, opening the door to studying how their variation affects essential biological functions. Check out the full paper here: genome.cshlp.org/content/35/9...

5 months ago 0 0 0 0
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11/12 The histone cluster was just one part. We also characterized the complex Stellate loci, which influence male fertility. Our new assembly also significantly improves the reference for the proximal side of the X chromosome, a notoriously difficult region.

5 months ago 0 0 1 0

10/12 These anchors were critical. They gave us a window to map the complex structural changes (like duplications and deletions) happening in this locus. Without them, we couldn't have confidently made our observations about the scale of rearrangement in the cluster.

5 months ago 0 0 1 0