Monthly Archives: April 2014

Genomes and phenomes

Via Jonathan Eisen, NSF is using a wiki to get input on genomes and phenomes

BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO’s future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to

I agree withthat phenome is a #badomics term but not with this:

How exactly is this different from “phenotype”?

Phenotype is singular.  Phenomes, for lack of a better term, are collections of all phenotypes. Part of what makes it a #badomics term, IMO, is that the good omics terms like genome, transcriptome and proteome describe sets where completeness makes sense. Phenotypes, as observable manifestations of genotypes in environments, depend on the capabilities of the observer. New technology can create new phenotypes. While new technology can improve our ability to detect genes or transcripts or proteins, they did not come into existence by virtue of our being able to see them.

Incidentally, I’m wondering why I didn’t get the email. Perhaps it’s because I don’t currently have an NSF grant. However, I’ve reviewed for NSF a lot, I participated in the NSF-funded Phenotype Research Coordination Network workshop in Arizona earlier this year. And I work on the NIH-funded Ontology for Microbial Phenotypes. We have to get OMP into better shape and publish for our renewal application this summer, but we’ve talked about it at Biocurator meetings.

Updating to Mavericks Server

We have a mini that we got to support a program to train undergrads in bioinformatics. Over the past week or so I’ve been working on updating it to run Mavericks and Mavericks Server.  I first decided to go with OSX servers back when I had a G5 blade running Panther Server for the user-friendly GUI management system. But since then OSX server has gotten to be steadily more annoying in that:

  • The Server and Server Admin apps have never been backward compatible with earlier versions. This means I have to do remote administration of older machines – some of which cannot be updated to the latest OK – through either ssh or vnc. The former defeats the purpose of having the GUI. The latter is sluggish.
  • The amount of control the admin gets over things has been steadily declining. In the first versions of Server, there that gave you pretty fine-grained control over configuration. That’s all gone.

So, as with Lion Server, which is what I’m upgrading from, I think I’m going to end up running everything via MacPorts, and not use the Or look into converting it to a Linux Box.

Open source communities are different

Via Althouse, Farhad Manjoo argues in the NYT that Brendan Eich had to resign because:

Mozilla is not a normal company. It is an activist organization. Mozilla’s primary mission isn’t to make money but to spread open-source code across the globe in the eventual hope of promoting “the development of the Internet as a public resource.”

As such, Mozilla operates according to a different calculus from most of the rest of corporate America.

Like all software companies, Mozilla competes in two markets. First, obviously, it wants people to use its products instead of its rivals’ stuff. But its second market is arguably more challenging — the tight labor pool of engineers, designers, and other tech workers who make software.

When you consider the importance of that market, Mr. Eich’s position on gay marriage wasn’t some outré personal stance unrelated to his job; it was a potentially hazardous bit of negative branding in the labor pool, one that was making life difficult for current employees and plausibly reducing Mozilla’s draw to prospective workers.

A commenter or Manjoo’s piece adds:

I wonder why this man was given this position in the first place if his views are so counter cultural at Mozilla. Or, if the views were unknown, what does that say about management of the company?

A reply points out that Brendan Eich, as a cofounder of Mozilla, might be in a better position to be familiar with the culture of Mozilla than Eleanor from Augusta Maine. There’s a basic problem with this argument: it presumes that the labor pool is contains more talented people who object to Mr. Eich’s private political activity than talented people who now will avoid working for Mozilla due to concerns about working for a project where outside activities are a litmus test. The idea that programmers and engineers are homogeneously enlightened progressives is… let’s just say counterintuitive. Eich is himself the counterexample to political homogeneity of talent. He’s not a John Scully from Pepsi going to Apple. The man invented Javascript, which runs a large fraction of the current web.

In my view Manjoo and Mozilla’s management have it exactly backwards. Depending on a community makes it even more important to defend the right of people you disagree with on extracurricular matters to participate. Importantly to this question, as far as I can tell, there have been no reports that Eich’s political beliefs manifested as creating a hostile work environment beyond those who are sensitive to the existence of those beliefs per se. It’s not like I’m seeing reports that Eich did anything like the infamous Larry Summers talk about women in science (I find this story interesting in part because of parallel issues in academia and science).