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Michael Hoffman @michaelhoffman.bsky.social
@michaelhoffman
Chair, Comp Bio & Medicine Program, Princess Margaret Cancer Centre, @UHN. Assoc Prof, Medical Biophysics, University of Toronto. COI github.com/michaelmhoffma…
Toronto
Joined May 2008
Posts
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    I don't log in here much anymore. Try Bluesky. Also, when I do log in I don't check notifications since they've just been polluted with non-notification stuff I don't want like Elon's latest missive.
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    This is amazing. "Do boring speakers really talk for longer?" Nature (2018) 561:464. nature.com/articles/d4158…
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    Proud to announce my latest collaboration with @slanketgoals, now available in @biorxivpreprint. Meet Naomi Estelle Olson-Hoffman, a high-impact baby!
    Naomi Estelle Olson-Hoffman in bioRxiv onesie
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    1/Folks with mainly biology training sometimes ask me for resources that can help them learn bioinformatics. This short thread has my recommendations at various levels.
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    I've tried this "artificial intelligence" plant identification app multiple times on the same tree and get a different answer each time. They must be using random forest
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    The @uoftmedicine Dean's Office said I have been approved for promotion to Associate Professor, effective July 1. Thanks to the Hoffman Lab for your scientific work and to all my colleagues for your support. Getting to keep working with such awesome people is a privilege. 🎉🎉🎉
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    Canada finally substantially above the U.S. in COVID hospitalizations per capita for the first time in the pandemic. Well done to the provincial premiers who have made this happen. Also, for restricting testing to make it harder to know how we're doing. ourworldindata.org/grapher/curren…
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    BV: It's hard to cure humans, but we can cure mice. My lab has cured so many mice. If you are a mouse I advise you to come to my lab. I can give you hope, especially if I've injected you with a tumor a couple of weeks before. #ASHG19
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    eLife buys big into a "publish, then review" model of publishing: "From July 2021 eLife will only review manuscripts already published as preprints, and will focus its editorial process on producing public reviews to be posted alongside the preprints." elifesciences.org/articles/64910
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    Hey, people writing scientific documents! Here's one easy technique that increases readability dramatically: Shorten your sentences.
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    I have a data joke, which is available on reasonable request.
    I have a bioinformatics joke, but I need to reformat and clean it up.
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    pdfcomments: turns comments placed directly on a PDF into a text file with a list of comments for pasting into a journal reviewer comments form or emailing to a student after a PhD examination. Hope making it available will help others! github.com/hoffmangroup/p…
    # pdfcomments: extract comments from PDF

pdfcomments extracts comments from a PDF and puts them in a text file.
It is most useful for turning text comments and sticky notes into a list of comments with page numbers.

By default all comments are minor.
You can specify a major comment by adding an asterisk at its beginning.

## Example output

Say you have `test.pdf` and you add the following comments with Acrobat Reader, PDFExpert, or your annotation tool of choice:
- page 1: a text comment, `Text is unclear.`
- page 2: a sticky note, `Sticky note.`
- page 2: a text comment, `* Important comment.`

Run `pdfcomments test.pdf` and it will produce the following output file:

```text
Major comments:

p2: Important comment.

Minor comments:

p1: Text is unclear.
p2: Sticky note.
```
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    To my colleagues, who are highly accomplished geniuses in a variety of fields: now is not the time to start an independent public health or infectious disease modeling practice if you have no expertise in these areas. Please get an expert to check your work. Don't just post.