Current projects

For anyone who’s interested, here are the projects I’ve got going right now. Many of them could use some help, so take a look and let me know if you’re interested in any. Roughly in my order of interest:

  • Add the Sugar desktop environment for OLPC — it’s in my overlay, but it segfaults on startup of sugar-emulator somewhere in sugar-shell code. Try it out and see whether you can come up with a fix.
  • Port LTSP to Gentoo — pioto, straaken and perhaps another person or two are working with me on this. This involves changes to the client-building plugins, init scripts, and adding some ebuilds. Also, probably creating Seeds for the client and server.
  • Get the rest of the system-config-* GUI tools from Red Hat working — some remain masked. Would appreciate testing and fixing on any that remain masked.
  • Add virt-manager into the main tree from my overlay — haven’t got a Xen instance to test it with yet. If anyone would like to test this and let me know, that’d be great.
  • Fix our X init scripts to be more like upstream intended, then fixing upstream to be current. havner is taking the lead on this, and I look forward to seeing his work.
  • Add some new science packages, including KiNG and friends from the Richardson lab, CCP4MG, CCTBX and more.
  • The infamous bug #44132 — make multiple MPI implementations simultaneously installable.
  • Resume my occasional series of blog posts on Gentoo in the enterprise, embedded, cluster etc environments. One post I want to make is how to use the Gentoo installer’s CLI frontend to make large, automated installations easy.

And of course these are beyond the usual ongoing maintenance of X, science packages and cluster packages.

Web 2.0 blog software

I brought this up in #redmonk, and sog suggested I stick it here and ask the LazyWeb for ideas. So here it is, with added capitalization and punctuation (no extra charge!).

There needs to be Web 2.0 blog software. The default blog page would show either just topics or perhaps topics and the first paragraph. Click, and you get a simple expansion or compression on the same page, instead of redirecting to a new one. This turns a blog’s homepage into effectively a featureful blog reader, especially when coupled with possibility of people logging in so you can track what they’ve read. Every time I see one of those annoying 1-paragraph things that trails off and I have to click to read the full post, I think about it.

Academic papers in Linux

We’re beginning to put an academic paper together, and of course I’d like to do this using open-source software if I can. My PI (principal investigator, the head of the lab) uses Word — so whatever ends up getting used, it needs some capability to at least export to .doc or .rtf. A critical aspect of any solid academic paper is citing your reference in a bibliography. does have some basic bibliography capabilities, but that’s what they are: basic. Work is underway to fix that, but it’s not expected to get anywhere for a year or so.

After some research, I’ve come across a few promising packages:

Zotero: A Firefox 2.0 extension, public beta started less than 2 weeks ago. No integration with word processors yet, but you can copy and paste a formatted bibliography across, and export and import the actual data. “It lives right where you do your work — in the web browser itself.” As a result, adding references from online searches such as PubMed is as simple as a single click. Every other package needs explicit support added for online searches.
Bibus: Uses’s Python functionality, also integrates with MS Word. The build system sucks — it should use distutils, but instead it’s got some custom Makefile and weird shell scripts and configuration files. Its functionality comes highly recommended, however. Will do PubMed and eTBLAST queries.
Pybliographer: The development version (1.3) integrates into OO.o and LyX. The 1.3-series GUI is alpha-quality and just had its first release. Will do PubMed, Web of Science and CrossRef queries.
bibutils: Command-line filters to convert between a variety of formats, including EndNote (which is currently in use under MS Word). Also handles RIS and BibTex, so that provides for OO.o import and export as well.

Update: As of now, bibutils and Bibus are both available in Portage. Try ’em out.