Firefox 23 mixed content blocking and Galaxy

The Galaxy genomics workbench has problems with mixed content blocking in Firefox 23 when it’s running under https, which it should be based on sending logins and passwords. When you click on any of the public data sources (e.g. UCSC Tables) under Get Data, Firefox blocks it.  The solution is to turn off mixed content blocking, as described here.

Unfortunately, this is a global configuration rather than per domain.



Almost perfect day of college football yesterday

Mitigating factors:

  • it’s early, and wins were against weaker opponents.
  • couldn’t watch the Badgers, didn’t ppv for the Ags
  • Cardinal and Aggies wins still leave concerns about future success.

For the Ags, the future is next Saturday, when Alabama comes to town with vengeance on their minds for last year’s upset at their place.  TAMU was already replacing several stalwarts from last year’s defense: NFL pick DaMontre Moore, and less well-known players like Spencer Nealy (who dominated Bama’s All-America center last year) and Dustin Harris (who made a critical stop in the late goal line stand), Sean Porter, Jonathan Mathis, Jonathan Stewart and Steven Terrell. See Good Bull Hunting’s archives for more on these former students. This meant DC Mark Snyder’s squad would be young and thin even without injuries and early suspensions.  Several players will be back for Bama, but will not have any game time going in. Starting safety Floyd Raven came back from a suspension only to break his clavicle yesterday. The Tide are not who you would normally want to use to get the rust out of your game, but there’s no choice now.  Concern about the D has been high after giving up points, yards, and big plays to both Rice and Sam Houston State.

The high-flying offense led by Johnny Manziel also lost some key performers, but was expected to be less of a problem than the D. The O has put up lots of points in the two warmups, but  can the Ags do it to Bama again?  We shall see.  It’s going to be the most-hyped game at Kyle field in my time here.

The schadenfreude is especially strong in reading the fan reactions from Austin, after the ‘sips were trounced in Provo by a BYU team that had lost the week before to mighty Virginia.  I saw a little of that game while waiting for Stanford to come on in the late game.  It was actually kind of shocking to see how bad the Texas Defense looked in that game.

The best game of the day was probably South Carolina at Georgia. The momentum in that game seemed to go back and forth until Georgia opened a two-score 11-pt lead in the final quarter on an 85-yard pass play.  S. Carolina looked to cut it to less than a TD by driving deep into the red zone on the next possession.  But they were thwarted on a goal line stand with 8:28 to go where they couldn’t punch it in on 4th and goal from the 1. The Dawgs then took over and ran out the rest of the clock.

Weird, given Marissa Mayer’s rep from Google

I first heard of Marissa Mayer from a podcast of this talk from the Stanford Entrepreneurial Thought Leaders series.  As I recall, one of the intereresting things was the way Google tested UI options and gathered data about what did or did not work for users. Given that, I am kind of surprised how hideous the Yahoo Sports Blog pages have become.

John Gruber links to criticism of the new logo; this goes way beyond logo fonts.

Fix for Macports 2.2.0 upgrade problems (if /opt/local is a symlink)

I was having trouble updating MacPorts on one of our OSX servers.

Error: org.macports.extract for port gnupg returned: command execution failed
Please see the log file for port gnupg for details:
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:

It turns out that version 2.2.0 doesn’t like symlinks to /opt/local that didn’t bother earlier versions.  See here.  The solution was to edit /opt/local/etc/macports/macports.conf in order to provide the full path everywhere.


A biocurator ranking for Journals

There has been a lot of focus on impact factors for journals, and there are some interesting issues with how publishers can try to game the system.  I wonder, however, if it would be useful to publish some alternative rankings of journals based on other criteria.

Specifically, I’d love to see a ranking of journals based on the usability of their papers for biocuration. Do they have strong editorial practices to get authors to include

  • Accessions to data deposition
  • Metadata for topic classification
  • Use of nonstandard nomenclature

Of course, this is a rating I would only take credit for if I never wanted to publish in journals that might come out low in the rankings.  In my fantasy world, a virtuous cycle would cause the journals with biocurator-friendly practices to rise in impact factor.

Microfiber stylii

Most of the time, I use my finger on my iPad, just as Steve Jobs intended. But there are times when a stylus is nice:

  • Taking handwritten notes
  • Actual drawing

For a while, I’ve had a Wacom Bamboo stylus, which is one of the better ones that have soft rubber tips.  But recently I got a Boxwave Evertouch, which is one of many relatively recent offerings using microfiber tips instead of rubber. This makes the stylus slide much more smoothly than even the Wacom, and so far I like it.  It also helps that the Boxwave is much cheaper.



Can we make Science more family-friendly?

A couple of weeks ago, Jon Eisen tweeted a link to an article in the Atlantic: For Female Scientists, There’s No Good Time to Have Children

Over the past decade these issues have come to the attention of universities in the United States and abroad. Many sensible policies have been introduced in an attempt to make academia more family friendly. Two of the most common are tenure-clock stoppage and parental leave. Although these interventions are important, they are not enough on their own. They raise numerous complications, but in the interest of brevity I’ll name only two. First, these policies need to be entitlements, rather than special accommodations that have to be requested and approved. Second, they need to be available to and used by men and women alike.

I was talking to some of my colleagues with young children at a conference last week, which reminded me of the linked piece. Tenure clock extensions and parental leave are good things. However, there is a limit to how much this kind of institutional support can do if taking time off affects the productivity needed to get and keep funding.  That means that stronger parental leave benefits are may not be used by either men or women even if they are available.

There are things that could be done by both employers and the broader community to be more supportive of parent/scientists. Unfortunately, some of these things, like making day care more available and accommodating can run into regulatory hurdles. For example, when I was an organizer of the Phage Meetings I had a lot of discussions about how to make day care more available for conference participants.  On the one hand, the local day care center could not take additional children without violating local rules on the ratio of caregivers to children.  On the other hand, liability issues meant the meeting could not recommend potential external day care providers.  I was under the impression we could not even help organize parents to share childcare with each other.

For some participants the partial solution for meetings was to hire their own extra child care, either on site, or to look after kids left at home with the other spouse.  I know of a couple of universities that offer benefits to support extra child care so parents can attend conferences… but don’t tell parents about them.



So it’s a Ponzi scheme?

The Detroit Free Press defends their home town against mischaracterizations in the national press with the first installment of The Truth About Detroit

What was said: “Government employees and their overbearing unions have been on a decades-long crusade to defraud the taxpayer and unjustly enrich themselves. When everyday Americans are struggling to find job security and save for retirement with defined contribution plans, selfish and greedy public-sector unionists have unparalleled job security and retire with golden parachutes (that) would make any middle American look like a pauper in comparison.”

Reality: The average annual pension for retired Detroit police officers and firefighters is about $34,000, roughly half that of such pensions in Los Angeles and Chicago, 25% less than in Kansas City, Mo., and 36% below benefits for those in Dallas. Retirees from Detroit’s general city pension fund receive, on average, less than $20,000 a year.

“Even by Michigan standards, these are not fat pensions,” said Leon LaBrecque, , managing partner with the financial advisory firm LJPR in Troy. “I see a lot of these people, and their pay is lower and their multipliers are lower than retirees in Grand Rapids or Lansing or Warren or the (Michigan) State Police.”

One factor that has made Detroit’s pension underfunding worse: There are only 3,200 active workers paying into a system that pays benefits to 9,300 retirees. In Chicago, 12,026 actives pay into a fund that supports 9,035 retirees.

This isn’t a problem for defined contribution plans. At Forbes, Jeffrey Dorfman writes about this.