update and tidbits

It’s been a while since I blogged last, time for a brain dump.


The newly elected Edubuntu Council is kicking of the Lucid Lynx cycle. They are scheduling a bunch of focused work days to look at bugs, the wiki, the website, docs, etc. It should be pretty productive and I wish them well on their endeavor to make Edubuntu 10.04 a solid educational OS. Check out the meeting minutes for more info if you’re interested. There is going to be a Bug Day on the 12th and the wonderful HedgeMage has come up with an outstanding redesign of the Edubuntu website (see here and here) .

No Longer a Developer

As much as I have loved working on Ubuntu, real life has been such that I haven’t had time to really keep up with development policies and practices. Ubuntu is a huge project and so it takes a fair amount of effort/time to keep up with. With my chemistry carrier actually going somewhere I don’t see for the foreseeable future that I’ll have enough time to keep up. Since I don’t like the idea of staying in Launchpad groups I’m not actually involved with I decided last week to deactivate from the Ubuntu Core Developers team. Instead, with what little time I have to devote to FLOSS I’m going to be working on small, upstream projects where I don’t have so much to keep up with. Recently I took over the development of Plotdrop (a GNOME frontend to the graphing program, gnuplot) from John Spray. I’ve also been working on a few patches to GChemUtils (awesome set of chemistry GTK libraries and programs) and gnome system tools (specifically on users-admin).


Some people might find this utterly boring so I put it last but I’m a bit of a political junkie. So in 2004 after I moved to Nevada to go to grad school my party won the presidential election but lost the senate race. Now I’ve recently moved to Massachusetts and my party lost the last presidential election and there is a senate race in just a couple weeks. I wonder if the trend (win one, lose one) will hold and we win a crucial senate seat. It’s certainly a long shot in Massachusetts, but who knows, stranger things have happened. 🙂 It’s a least some motivation to get to the polls.

Busy, busy!

The last two months have been quite hectic. I thought I’d give everybody a brief outline of what I’ve been up to:

  • Finished my dissertation, defended it, and received my Ph.D. This is huge news for me. It took me 7 years but I finally got it done. For those that may be interested, my degree is in Chemistry and my dissertation title was, rather blandly, Ultra-Sensitive Detection Methods of the Orientation of Surfaced-Adsorbed Molecules. Basically I “developed” a new analysis technique that would most accurately be called Polarization-Resolved Normal Incidence Cavity Ring-down Spectroscopy (PRNICRDS, yes scientists love acronyms). The purpose was to use it to detect the rotation of an artificial, light-driven, molecular motor less than 1 nanometer in size.
  • I got a job as a postdoctoral research working for the Space Dynamics Lab (run by Utah State University) and contracted to the US Air Force Research Laboratory at the Hanscom Air Force Base near Boston. If that isn’t confusing enough, I work in the Battlespace Environment division of the Space Vehicles directorate. I think this is probably the closest I’ll ever come to being a rocket scientist 🙂 It’s exciting work even though working in the military has it’s own peculiarities.
  • Given my new job, my wife, two pets, and I moved from Reno, NV to Boston. We’ve always been west-coast people so it’s been quite a different experience. Neither one of us had been to New England before and we’d only been west of the Rocky Mountains for family vacations. We love the weather so far but are bracing for the (in)famous New England winter.
  • In between all this I seem to have been able, with help from Colin Watson,  to get the seeds for the new Edubuntu DVD working. This is a pretty big step for Edubuntu as for a few releases now we’ve been just an addon to Ubuntu. This meant our users had to first install Ubuntu and then grab the Edubuntu disk and install the educational packages from there. Additionally, LTSP, which is commonly used in schools labs, was shifted to the Ubuntu Alternate CD. The decision to go to a DVD wasn’t easy though. DVDs are a big download and we have to make sure that we maintain good sync with the Ubuntu installer, kernel, etc. Edubuntu 9.10 will be basically a Beta for Edubuntu 10.04 LTS as we’re trying to get the DVD thing going and revitalize development.

Well, those are the highlights from me, nothing too important but it’s been keeping me busy. I’m looking forward to seeing Karmic released and then focusing on the big push to the next Long Term Support release.

Avogadro rocks!

I’ve been involved a little bit with the Avogadro project. Avogadro is a cross-platform 3D molecular editor. It’s written in C++/Qt4 for people who care and sports a new Python console for people like me who want to have our cake and it it too. Here are the things I like about it:

  • cross-platform – my lab has both Linux and OS X machines. Being able to use the same application on all of them is a big plus
  • auto-optimization – you can turn on an autooptimizer that does does geometry optimizations on the fly as you move atoms around. Not only does this look awesome, it’s also a great teaching tool.
  • Gaussian input – we have an undergrad this summer in our lab and he’s working on some MO calculations using Gaussian. The Avogadro Gaussian input tool was really easy to having start using and he didn’t have to spend time figuring out all the syntax/options.

For a project this young, it’s really coming along nicely.

Chemists can code! sorta …

Anybody who knows me knows that I’m not a programmer, I don’t even play one on TV 😦 .  I’m a PhD Physical Chemistry student and an experimentalist at that. I knew nothing about distro or software development for most of the time I’ve used Linux. A little over a year ago I figured out how to get on freenode hopped on #ubuntu-motu . I was sucked into the MOTU world and have been known as a raging Ubuntu-holic MOTU.  So now that I’ve experienced a little distro development I’ve been itching a little to do some software development.  Well, the short story is through a series of events I found Gnome Chemisty Utils (and it’s author Jean Bréfort) and a group of chemists interested in open standards and open source in the area of chemoinformatics called Blue Obelisk. Now, putting this all together I ended up learning a little C++ and GTK to create a new color scheme for the gchemutils periodic table app that reads in data from the Blue Obelisk Data Repository (BODR). The new scheme “colorizes” the elements by family (noble gases, alkali metals, etc. ). The fruit of my labor, released today as a part of Gnome Chemistry Utils version 0.7.4, is shown in the following screenshot:


So if you happen to be interested in periodic tables (you know you are) then grab BODR 4 and gchemutils 0.7.4 and have fun.

Next step: figure out how to get all this fun stuff in Universe for Feisty!