Marcus D. Hanwell's Blog

So I had my first experience of Halloween in the US tonight. As I went grocery shopping I saw all the shops with big bowls full of sweets handing them out to passing children. Dozens of children dressed up as various ghoulish characters wandering around with their parents in toe, helping them to carry their swag.

I walked back to my apartment to witness yet more children wandering the streets with their parents and people up and down my street handing out sweets (or candy as it is known over here). I got home to meet a few of my neighbours work colleagues handing out treats on our doorstep. Lots of the houses around here have been decorated for weeks and it amazes me what a big thing Halloweeen is.

I am really going to miss Guy Fawkes Night on the 5th of November - don't think anyone knows about it over here We always had great parties and gatherings on Bonfire night, although currently my social calendar is emptier than it has ever been due to me being very new in town. Hope you have all enjoyed your Halloween and have a great Bonfire night if you celebrate it!

Today we released Avogadro 0.2 which features many improvements since the 0.1 release. It has lots of the new features I worked on during my Google Summer of Code project along with some great work by other contributors such as the bond centric manipulation tool coded by Shahzad Ali, Ross Braithwaite and James Bunt.

Geoffrey Hutchison announced the release earlier today, on what I have been informed is mole day due to the date format used in the US - 10/23 corresponding to the 10^23 of Avogadro's number. So today seemed like an even more fortuitous time to make a release of Avogadro!

Today also marked my first commit to the Gentoo repository in quite some time to add this release to Gentoo's ebuild repository. If you have been waiting for me to add/update packages and I haven't gotten around to it due to life being so busy now would be a good time to poke me. I will also hopefully be completing the ribbon support I have already talked about and that should make it into a release soon but wasn't ready for this release.

We would love to receive feedback on the latest release of Avogadro. These new features will also make their way into Kalzium in KDE 4.1.

I term it as "ribbon" because it really isn't a ribbon. I haven't figured out how to calculate the plane the ribbon lies on and right now it is a series of cylinders drawn from point to point. I hope you will agree that it already looks fairly effective and can certainly show the nature of the secondary structure of biological molecules.

There is still a lot to do such as draw the tube in a more efficient manner as a continuous OpenGL construct and draw each residue separately. It would also be good to be able to draw ribbons but this may take a deeper understanding of ribbons and how they are visualised than I have. If there are any biologists out there who want to help me out then tips, or even better patches, would be great fully received

As I moved continent I guess it is only right I move servers too I have spent most of the weekend backing up, transferring and restoring email, web sites and other assorted services over to a different server I will be sharing access to. Thankfully it is still a Gentoo Linux based server that I will be sharing with my brother-in-law.

The move has taken a lot longer than I anticipated but I think everything is over now. Still some cleaning up tasks to perform. Hopefully this blog hasn't been kicked off planets or spammed them during the move over. If you notice any problems with anything feel free to poke me. Hoping I have finished moving for quite some time now - it isn't much fun and reduces productivity...

What a hectic few months it has been. This year has been really tough on many levels but also very rewarding in other ways. I never really got chance to write up my final thoughts on my Google Summer of Code project and will hopefully get the time to do that soon. Still working on it adding new functionality and fixing bugs where I can.

I completed my thesis over the summer and did my viva which went very well. Managed to hand in the final library copy of my thesis the day after my viva before leaving for a two week diving holiday. Louise won the holiday at the London International Dive Show in March of this year. It was an awesome week away in Curacao and a second week in Bonaire with some amazing diving, although I sprained my ankle really badly at the end of the last week.

Then we returned home for a couple of days before leaving for Pittsburgh via JFK. Got to Pittsburgh on 26 September to start my postdoctoral position at the University of Pittsburgh on 1 October (or October 1 as they say over here). Louise came out with me on the first week and helped me look for a place to live and everything.

Life has been amazingly hectic and I am still feeling very displaced and missing many of the creature comforts I am used to such as money, a car, furniture, good beer... I did get cable, internet and phone on Monday and brought my laptop out with me so things are picking up a little. Hopefully I will be able to write more soon about the dive holiday, my new job, GSoC and continuing work on Avogadro.

For now I am going to hobble to the shops to find some dinner - still not used to eating out alone... Lots of work to get on with that will keep me occupied at least!