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James Hawley

I'm a PhD candidate in Medical Biophysics at the University of Toronto studying epigenetics and cancer. Math and physics background taking a step into bioinformatics and evolution

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James Hawley

If you ever want a crash course in bad web design, try submitting a journal article or asking for access to data from an institution. Few things bug me more than trying to fill out these absolutely horrendous online web forms.

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James Hawley boosted
Craig Maloney ☕

Are there any good books on how to do beautiful layout in LaTeX? I have most of the Addison Wesley / Pearson / InformIT books but wondered if there was some brave soul out there that has something more like a tutorial of not only "put these commands here to make this work" but also goes into the "why" of the design they chose.

(Note: this is a specific question for a specific item. Alternatives are not requested. Spitballing web searches are not helpful. I want an artifact, not Stack Overflow).

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James Hawley

They don't throw a ton of data at you because they don't even need a lot of experiments.
It's just a careful, mathematically-based, and biologically-inspired analysis with clearly stated conclusions.

More of this, please.

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James Hawley

Instead of relying on a trendy idea in the field, they slow down, develop toy models of gene regulation based on existing literature, explore how these models might function, then make the models more complex as needed.

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James Hawley

It's so refreshing to see a paper like this one by Xiao, Hafner, and Boettiger treat the conflicting observations about TAD perturbations and enhancer-promoter contacts seriously.

elifesciences.org/articles/643

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c o r c r a

ordered "Regression and Other Stories", can't wait to finally learn statistics

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James Hawley

Ouch, I definitely tempted the Monkey's Paw on this one.

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James Hawley

My manuscript has been through a true quarantine, can it get released now?

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James Hawley boosted
c o r c r a

dreaming of an open-source EHR

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James Hawley boosted
the bioinformatics chat

For the 60th episode of the #bioinformatics chat, we're excited to bring you a conversation with Mike Love about his classic package DESeq2
bioinformatics.chat/deseq2

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James Hawley boosted
M. Grégoire

Snarking at techbros 

@bgcarlisle
I wasn't aware that Linux kernel developers were doing unethical research on scholar.social , or defending those who did so. Maybe the victims of unethical research should sympathise with each other and work together against the problem?

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James Hawley

I submitted my journal article earlier this week and I got approval from my committee to write my thesis and plan my oral examination! The end is in sight!

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James Hawley boosted
c o r c r a

hello everyone, I'm stephanie (she/her)!

I'm a researcher at a big tech company, based in the UK. I did my phd in computational biology+medicine. I focus very much on ML for health, specifically critical care, physiological time series, "how to do ML well in health", etc.

Non-research activities include rollerskating/derby, gaming (computer/table-top/board), sewing, looking at birds.

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James Hawley

I gave a talk yesterday as part of the Fragile Nucleosome Seminar Series. The talk was recorded and put online, so if anyone wants to learn about prostate cancer, the 3D genome, and structural variants, take a look!

youtube.com/watch?v=YsFFN2AY62

Like all my scientific work, feedback and questions are always appreciated

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James Hawley boosted
the bioinformatics chat

Today on the #bioinformatics chat, Lindsay Pino discusses the difficulties of comparing proteomic (mass spec) measurements across different samples, potentially acquired in different labs, as well as a method she has developed recently for calibrating these measurements without the need for expensive reagents

bioinformatics.chat/proteomics

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James Hawley

This was a really neat discussion of various computer processes and how they can get slowed down or take up lots of space.

gregoryszorc.com/blog/2021/04/

The most interesting one, for me, was about the slowness of zlib. In bioinformatics, I use gzipped files all the time, and I've always wondered about the silly FASTQ format (zipped or unzipped). I wonder how much faster and more compressed things would be if we used zstandard instead

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James Hawley boosted
Yo Yehudi

All too often I hear "how can we justify funds to maintain research software?"

But really, we should be asking "How can we justify _not_ funding it?"

My colleagues and I wrote a thing: nature.com/articles/s43588-021

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James Hawley boosted
James Hawley

Wow, I just had my first interaction with GitHub's dependabot.

It was able to
1. detect the requirements.txt file with Python packages
2. recognize the vulnerable version
3. test for compatibility with the other package requirements
4. open a new branch and PR that addresses the security issue
5. display all the relevant information in an easy to read format

That's amazing, to be honest. Just wow

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James Hawley boosted
~ashwinvis

Vim scripting for Python dev 

#IMadeThis @vim command to auto-generate #ctags from a directory and #Python virtual environment or conda environment.

source.coderefinery.org/ashwin

#Vim

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James Hawley

I got my hands on an old Illumina NextSeq flow cell and got to tear it apart.

jrhawley.ca/2021/03/13/flow-ce

There's a lot of cool design choices and stuff in here! As a computational biologist, I don't see this kind of stuff that often, but it was fun to see this side of sequencing machines.

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