Archive for the ‘Things that annoy me’ Category

Action items in response to hateful shit

5 Apr 2016

UW-Madison faculty got an email update from Vice Provost and Chief Diversity Officer Patrick Sims regarding the things we can do in response to the hate and bias incidents on campus.

Here are the things he had mentioned yesterday at the Faculty Senate meeting:

  • Address hate/bias incidents in your curriculum to ameliorate unacceptable occurrences in our campus community.
  • Look at “bullying” language as a way to address possible hate/bias incidents in the classroom.
  • Commit to engaging in ongoing cultural competency training. Learning Communities for Institutional Change & Excellence (LCICE) as an infrastructure already provides these services campus-wide.
  • Commit to experiencing the leadership institute and become a facilitator, carving out 10-15% of your time towards these efforts.
  • Support the request for additional staff.
  • Visit the Campus Climate website

An attached letter from the Hate & Bias incident team added:

  • Your school/college/department can host a bystander intervention workshop on hate and bias. This workshop will provide tools for UW-Madison community members on when and how to intervene. If you would like to host a workshop, please contact Joshua Moon Johnson.
  • Many incidents go unreported for a variety of reasons. We encourage students and campus community members to report incidents of hate and bias to ensure that campus can best support the victim and work to prevent future incidents. We encourage you to post the link to report on your school/college/department websites.
  • Oftentimes students do not report incidents because they are unaware of the reporting process. To increase awareness of the reporting process, we encourage you to share brochures and posters with information on how and why it is important to report. These will be distributed across campus in the next few weeks.
  • Students who are victims of hate and bias incidents may need immediate support. Please be sure to refer/provide students with appropriate resources such as mental health/counseling services through University Health Services (UHS). The Multicultural Student Center also has drop-in hours with UHS counselors as well as support and discussions groups for students of color.
  • Many students who are victims of hate and bias incidents identify with an underrepresented racial group, gender identity or sexual orientation, or religious group. We encourage you to specifically reach out to marginalized student groups to raise awareness of the bystander intervention workshop and reporting process.

I got a reasonably positive response to my email to my faculty colleagues suggesting that we all commit to cultural competency training. But the training from the LCICE mentioned above looks to be semester-long, Tuesdays 4:30-7:30pm. I think I’ll have a difficult time convincing my colleagues of that. We need something in between nothing and 45 hours.

Hateful shit at UW-Madison

4 Apr 2016

I’m a privileged white male university professor. As privileged as they come, really. My father was a professor of chemistry; my mother also has an advanced degree in chemistry. The jobs I’ve held have been more about personal fulfillment than money: dancer, dance teacher, secretary for intellectual property lawyers, research and teaching assistant, professor. People assume I know what I’m talking about, even if I’m in shorts and a t-shirt.

All that’s just to say that, when it comes to the ongoing hateful acts that have been happening at the University of Wisconsin-Madison, I’m really the last one that you should be listening to. You should instead listen to UW students, such as the United Council of UW Students, who have submitted a list of 5 reasonable demands, or Vice Provost and Chief Diversity Officer Patrick Sims, who made an important 8-min video in response to a recent hateful incident that you should now go away and watch (really, stop reading what I have to say and spend 8 minutes watching that video), or Chris Walker, Asst Prof in the dance department, who spoke movingly today at the UW-Madison Faculty Senate meeting about the shit that faculty and students of color have to put up with on campus.

Lot’s of crap has been happening in Wisconsin lately. My focus has been on what Scott Walker and company have been doing to the state and to the University of Wisconsin, most recently by making huge cuts to state support to the UW System and by weakening tenure and shared governance.

That’s all been an embarrassment, and depressing, but in comparison to the hateful racist shit that’s been happening on campus, and Vice Provost Sims reported that there have been >30 reported hate or bias incidents on campus this year, tenure and funding just don’t seem that important.

Chris Walker’s speech at the Faculty Senate today really hammered this home. As a black man on campus, he’s experienced a lot of shit: worse shit then we’re seeing in the papers. And if we don’t fix this, our students can’t be successful. We must fix this.

What can a biostatistics professor do? I’m open to suggestions.

But for now, I’ll follow Patrick Sims’s suggestion and start with one of the United Council of UW Students’ demands:

We demand that the University of Wisconsin System creates and enforces comprehensive racial awareness and inclusion curriculum and trainings throughout all 26 UW Institution departments, mandatory for all students, faculty, staff, campus & system administration, and regents. This curriculum and training must be vetted, maintained, and overseen by a board comprised of students, staff, and faculty of color.

I’ve written an email to the faculty in my department, asking that we, as a department, volunteer to participate in such racial awareness training:

email_to_dept

Correction: There’s an error in my email; Chris Walker is Associate Professor, and has been for a couple of years.

Update: Chris Walker’s speech at the 4 Apr 2016 Faculty Senate meeting was recorded! Must listen.

God-awful conference websites

5 Aug 2015

What do I want in a conference website? Not this.

  • I want to be able to browse sessions to find the ones I’m interested in. That means being able to see the session title and time as well as the speakers and talk titles. A super-long web page is perfectly fine.
  • If you can’t show me everything at once, at least let me click-to-expand: for the talk titles, and then for the abstracts. Otherwise I have to keep clicking and going back.
  • I want to be able to search for people. And if I’m searching for Hao Wu, I don’t want to look at all of the Wus. Or all of the Haos. I just want the Hao Wus. If I can’t search on "Hao Wu", at least let me search on "Wu, Hao".
  • If my search returns nothing and I go back, bring me back to the same search form. Don’t make me have to click “Search for people” again.
  • I’d like to be able to form a schedule of the sessions to attend. (JSM2015 does that okay, but it’s not what I’d call “secure” and you have to find the damned things, first.) Really, I want to pick particular talks: this one in that session and that one in the other. But yeah, that seems a bit much to ask.

The JSM 2015 site is so terrible for browsing, I was happy to get the pdf of the program. (Good luck finding it on the website on your own; ASA tweeted the link to me, due to my bitching and moaning.) You can browse the pdf. That’s the way I ended up finding the sessions I wanted to attend. It also had an ad for the JSM 2015 mobile app. Did you know there was one? Good luck finding a link to that on their website, either.

The pdf is useable, but much like the website, it fails to make use of the medium. I want:

  • Bookmarks. I want to jump to where Monday’s sessions start without have to flip through the whole thing.
  • Hyperlinks. If you don’t include the abstracts, with links from the talk titles to the abstracts, at least include links to the web page that has the abstract so I don’t have to search on the web.
  • More hyperlinks. The pdf has an index, with people and page numbers. Why not link those page numbers to the corresponding page?

I helped organize a small meeting in 2013. The program on the web and the corresponding pdf illustrate much of what I want. (No scheduling feature, but that meeting had no simultaneous sessions.) I included gratuitous network graphs of the authors and abstracts. It’s 2015. No conference site is truly complete without interactive network graphs.

Update

As Thomas Lumley commented below, if you search on “Wu” you get all of the “Wu”s but also there’s one “Wulfhorst”. And if you search on “Hao” you get only people whose last name is “Hao”.

He further pointed out that if you search for the affiliation “Auckland” the results don’t include “University of Auckland” but only “Auckland University of Technology”. And actually, if you search for “University of Auckland” you get nothing. You need to search for “The University of Auckland”.

If I could do it over again, I’d self-publish

12 Aug 2014

In 2009, Śaunak Sen and I wrote a book about QTL mapping and the R/qtl software. We started working on it in the fall of 2006, and it was a heck of a lot of work.

We’d talked to several publishers, and ended up publishing with Springer. John Kimmel was the editor we worked with; I like John, and I felt that Springer (or John) did a good job of keeping prices reasonable. We were able to publish in full color with a list price of $99, so that on Amazon it was about $65. (In April, 2013, there was a brief period where it was just $42 at Amazon!)

Springer did arrange several rounds of reviews; they typically pay reviewers $100 or a few books. But the copy editing was terrible (at the very least, you want a copy editor to read the book, and it was pretty clear that our copy editor hadn’t), and the actual type-setting and construction of the index was left to us, the authors.

It feels nice to have written a proper book, but I don’t think it makes that big of a difference, for me or for readers.

And John Kimmel has since left Springer to go to Chapman & Hall/CRC, and Springer has raised the price of our book to $169, so it’s now selling for $130 at Amazon. I think that’s obnoxious. It’s not like they’ve gone back and printed extra copies, so it’s hard to see how their costs could have gone up. But in the publishing agreement we signed, we gave Springer full rights to set the price of the book.

(Update: it’s now listed at $199, though it’s still about $130 at Amazon.)

I have a hard time recommending the book at that price; I’m tempted to help people find pirated PDFs online. (And seriously, if you can’t find a pirated copy, you should work on your internet skills.)

I corresponded with an editor at Springer, on why our book has become so expensive and whether there’s anything we can do about it. They responded

  • If we do a new edition, it could be listed as $129.
  • If the book is adopted by university classes, “the pricing grid it is based on would have lower prices.”
  • Our book is available electronically, for purchase by chapter as well.

Purchase by chapter? Yeah, for $30 per chapter!

Springer has published books and allowed the authors to post a PDF, but only for really big sellers, and ours is definitely not in that category.

I’m both disgusted and embarrassed by this situation. If I could do it all over again, I’d self-publish: post everything on the web, and arrange some way for folks to have it printed cheaply.

I still don’t like it

9 Feb 2014

I got a book in the mail this week, a book I hadn’t ordered and would never have ordered. The publisher sent me a complimentary copy, as I’d reviewed the book proposal last year. (It’s the one where the author refused to allow me to have an electronic copy.)

Actually, I soundly trashed the proposal in my review. In the nicest possible way, of course. For example, I said:

And then there are things that are just plain wrong. For example, “We then express our confidence in the H0 with a p-value, which might crudely be considered the probability that the H0 is true.” That is not a crude interpretation of the p-value; that is just wrong.

It seems like if a reviewer says, “This particular book should not be adopted,” the publisher can interpret that to also mean, “and whatever you do, don’t send me a copy.”

Fixing a font problem for XeLaTeX

11 Oct 2013

If the topic sounds boring, well, it is really boring. I write it down here in case it’s useful to someone.

I was working on a talk about git & GitHub, and chose a different font (Helvetica Neue, sort of the default Apple font). I think the default font for LaTeX/Beamer is a bit too tall and thin for slides. Here’s the default:

Slide with default font

And here’s what I wanted:

Slide with Helvetica Neue

But it didn’t work on unix

It worked fine with XeLaTeX on my Mac, but it wasn’t working in Unix, and I’d like the source to be portable to others.

XeLaTex was giving two errors:

Invalid fontname `Helvetica Neue', contains ' '
Font \zf@basefont="Helvetica Neue" at 10.0pt not loadable: Metric (TFM) file
or installed font not found.

It obviously wasn’t finding the font.

I futzed about for an hour, trying to figure out where fonts are located on my Mac, and where fonts are located on Unix, and doing various web searches. But no luck.

How I solved the problem

Finally, I read this post on fonts in xelatex, and following that set of ideas, I figured out what to do.

  • Switch to the TeX Gyre Heros font. It looks just like Helvetica to me.
  • Download qhv2.004otf.zip.
  • On unix, unzip the file (which contains eight .otf files) into ~/.fonts
  • On Mac, unzip the file, double-click the .otf files and select “Install font.” This uses the Font Book application.
  • In the .tex file, use \setsansfont{TeX Gyre Heros}

Not thoroughly tested, but it works on two systems.

Complaints about the NIH grant review process

2 Oct 2013

Earlier this week, I met with a collaborator to discuss what to do with our NIH grant proposal, whose “A1” was “unscored” (ie, the revised version, and you don’t get a third try, received a “preliminary score” in the lower half and so was not discussed by the review panel and couldn’t be funded).

NIH proposals are typically reviewed by three people and given preliminary scores on five aspects (significance, approach, investigators, environment, innovation) and overall, and the top proposals based on those scores are discussed and scored by the larger panel.

One of the reviewers gave our proposal an 8 for “approach” (on a scale of 1-9, with 1 being good and 9 being terrible) with the following review comments:

4. Approach:
Strengths

  • Well described details for mining of [data] and genotyping of [subjects].

Weaknesses

  • There is no power analysis for Aim 2. Without knowing which and how many [phenotypes] will be evaluated it is not possible to estimate the statistical power.

Valid comments, but is that really all the reviewer had to say? What about Aims 1 and 3, or the other aspects of Aim 2? That is totally fucking inadequate.

Looking at this review again, I was reminded of how much I despise many aspects of the NIH review process. So it’s led me, finally, to write down some of the things that annoy me.
(more…)

$18 for a two page PDF? I still don’t get it.

2 May 2013

Yesterday, I saw this tweet by @Ananyo

Time that biologists stopped telling the public oversimplistic fairy tales on Darwinian evolution, says P Ball ($) nature.com/nature/journal…

So I clicked the link to the Nature paper and realized, “Oh, yeah. I’ve got to enter through the UW library website.”

But then I thought, “Wait…$18 for a two-page Nature comment? WTF?”

So I tweeted:

DNA: Celebrate the unknowns, like this Nature comment, which costs $18. nature.com/nature/journal…

And thinking about it some more, I got more annoyed, and tweeted:

Why do publishers charge such high per-article fees? At $18/artcl, you’d have to be desperate or stupid to pay; at $1-2, prob’ly lots would.

And then I thought, I’ll ask Nature directly:

@NatureMagazine Why is the per-article charge so high? It seems like you’d make more profit at $2/article.

And they responded:

@kwbroman For a while now, individual papers can be rented through @readcube for $3-5. A full tablet subscription to Nature costs $35.

But that didn’t quite answer my question. So I asked:

.@NatureMagazine So is the $18 charge for a 2 pg PDF just to discourage piracy?

I thought a lot about whether to put “piracy” in quotes or not, or whether to write “copyright infringement” instead.

But anyway, they responded:

@kwbroman just as with any product, the more you buy, the more you save. Media/publishing subscriptions have worked this way for decades.

That again didn’t quite answer my question.

It’s a scam

I still don’t understand the $18 business. It’s not “The more you buy, the more you save.” It’s, “Buy the whole season for $35, or buy 5 min from Episode 1 for $18.”

I understand that the cover price of Wired is $5 per issue, while I could get a year’s subscription for $15-20. But that’s not the same as $18 for one article vs $200 per year.

The $18 for a two-page PDF is like 900 numbers and paycheck advances. These are scams taking advantage of desperate or stupid people.

If they don’t want to sell the PDFs for individual articles for a reasonable price, they should just not sell them at all.

Methods before results

29 Apr 2013

It’s great that, in a step towards improved reproducibility, the Nature journals are removing page limits on Methods sections:

To allow authors to describe their experimental designs and methods in enough detail for others to interpret and replicate them, the participating journals are removing length restrictions on Methods sections.

But couldn’t they include the Methods section in the pdf for the article? For example, consider this article in Nature Genetics; the Methods section is only available in the html version of the paper. The PDF says:

Methods and any associated references are available in the online version of the paper.

Methods are important.

  • They shouldn’t be separated from the main text.
  • They shouldn’t be placed after the results (as so many journals, including PLoS, do).
  • They shouldn’t be in a smaller font than the main text (as PNAS does).
  • They certainly shouldn’t be endnotes (as Science used to do).

Supplements annoy me too

I love supplemental material: authors can give the full details, and they can provide as many supplemental figures and tables as they want.

But supplements can be a real pain.

  • I don’t want to have to click on 10 different links. Put it all in one document.
  • I don’t want to have to open Word. Put text and figures in a PDF.
  • I don’t want to have to open Excel. Put data in a plain text file, preferably as part of a git repository with related code.

At least supplements are now included at the journal sites!

This paper in Bioinformatics refers to a separate site for supplemental information:

Expression data and supplementary information are available at
http://www.rii.com/publications/2003/HE_SDS.htm.

But rii.com doesn’t exist anymore. I was able to find the supplement using the Wayback Machine, but

  • The link in the paper was wrong: It should be .html not .htm
  • The final version on Wayback has a corrupted PDF, though one can go back to previous versions that are okay.

I like Genetics and G3

Genetics and G3 put the Methods where they belong (before the results), and when you download the PDF for an article in Genetics, it includes the supplement. For a G3 article, the supplement isn’t included in the article PDF, but at least you can the whole supplement as a single PDF.

For example, consider my recent Genetics articles:

If you click on “Full Text (PDF),” you get the article plus the 3 supplemental figures and 23 supplemental tables in the former case, and article plus the 17 supplemental figures and 2 supplemental tables in the latter case.

Use meaningful URLs

10 Apr 2013

QR codes are stupid. See the well-known flowchart.

And I don’t like Drupal. Sites that use it give things URLs like http://www.genetics.wisc.edu/node/577 for their seminar list.

And can we get rid of the www?

“What’s your web site?”

“double-u double-u double-u …”

“Zzz…”

URLs should be meaningful and short. I like deep hierarchies of folders, but it makes for long URLs.

URL-shorteners help, but you don’t really want to read out (or type) one of those short URLs. And they tell you nothing about where they’re going.

What you want is something like bcaffo.com or stodden.net. Or rqtl.org.

But…I guess you could just say “I’ll send you an email.”

And customize <title>

And while I have your attention, note that the title of your web page shows up on Google (and at the top of the browser).

It’s nice to see others make use of my html code, but you shouldn’t leave my name in the title of your publication page.

Put the important words first (not like the title for my “official page”), and perhaps nothing else. For example, the title shouldn’t include “Drupal”.

Update: Read this: “URLs are for People, not Computers

I could have just given the URL:
http://www.not-implemented.com/urls-are-for-people-not-computers