Monthly Archives: August 2013

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.