Tag Archives: Open Chemistry

First Open Chemistry Beta Release

We are pleased to announce the first beta release of the Open Chemistry suite of cross platform, open-source, BSD-licensed tools and libraries – Avogadro 2, MoleQueue and MongoChem. They are being released in beta, before all planned features are complete, to get feedback from the community following the open-source mantra of “release early, release often”. We will be making regular releases over the coming months, as well as automatically generating nightly binaries. A Source article from 2011 introduced the project, slides from FOSDEM describe it more recently, and the 0.5.0 release binaries can be downloaded here.

These three desktop applications can each be used independently, but also have the capability of working together. Avogadro 2 is a rewrite of Avogadro that addresses many of the limitations we saw. This includes things such as the rendering code, scalability, scriptability, and increased flexibility, enabling us to effectively address the current and upcoming challenges in computational chemistry and related fields. MoleQueue provides desktop services for executing standalone programs both locally and on remote batch schedulers, such as Sun Grid Engine, PBS and SLURM. MongoChem provides chemically-aware search, storage, and informatics visualization using MongoDB and VTK.

Avogadro 2

Avogadro 2 is a rewrite of Avogadro; please see the recently-published paper for more details on Avogadro 1. Avogadro has been very successful over the years, and we would like to thank all of our contributors and supporters, including the core development team: Geoff Hutchison, Donald Curtis, David Lonie, Tim Vandermeersch, Benoit Jacob, Carsten Niehaus, and Marcus Hanwell. We also recently obtained permission from almost all authors to relicense the existing code under the 3-clause BSD license, which will make migration of code to the new architecture much easier.

Some notable new features of Avogadro 2 include:

  • Scalable data structures capable of addressing the needs of large molecular systems.
  • A flexible file I/O API supporting seamless addition of formats at runtime.
  • A Python-based input generator API, creating an input for a range of quantum codes.
  • A specialized scene graph for supporting scalable molecular rendering.
  • OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
  • Unit tests for core classes, with ongoing work to improve coverage.
  • Binary installers generated nightly.
  • Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.

Avogadro is not yet feature complete, but we invite you to try it out along with the suite of applications as we continue to improve it. The new Avogadro libraries feature much finer granularity; whereas before we provided a single library with all API, there is now a layered API in multiple libraries. The Core and IO libraries have minimal dependencies, with the rendering library adding a dependence on OpenGL, and the Qt libraries adding Qt 4 dependencies. This allows us to reuse the code in many more places than was possible before, with rendering possible on a server

From: http://blog.cryos.net/archives/265-First-Open-Chemistry-Beta-Release.html

FOSDEM: Open Science and Open Chemistry

I will be talking about the Open Chemistry Project at FOSDEM this year in the FOSS for scientists devroom at 12:30pm on Saturday. I will discuss the development of a suite of tools for computational chemists and related disciplines, which includes the development of three desktop applications addressing 3D molecular structure editing, input preparation, output analysis, cheminformatics and integration with high-performance computing resources.

Open Chemistry

On Sunday Bill Hoffman will be speaking in the main track about Open Science, Open Software, and Reproducible Code at 3pm on Sunday. Bill and Alexander Neundorf will also be talking about Modern CMake in the cross desktop devroom on Saturday.

FOSDEM is one of the first conferences I attended (possibly the first, I can’t remember if I went to a science conference before this). It will be great to return after so many years, and hopefully meet old colleagues and a few new ones. Please find me, Bill or Alex if you would like to discuss any of this work with us. I fly out tomorrow, and hope to get over jet lag quickly. Once FOSDEM is over we will be visiting Kitware SAS in Lyon, France for a couple of days (this is my first trip to our new office).

Then I have a few days in England visiting friends and family before heading back to the US.


Source: FULL ARTICLE at Planet KDE

The Roller Coaster of 2012

It has been a long time since I wrote anything on here, I am still alive and kicking! 2012 was another roller coaster of a year, with many good and bad things happening. Louise and I got our green cards early on in the year (massive thanks to my employer), which was great after having lived in the US for over five years now. We started house hunting a few months after that, which was an adventure and a half.

As we were in the process of looking for a house I was promoted to technical leader at Kitware, and I continue to work on our Open Chemistry project. We ended up falling in love with the first house we found, and found a great realtor who took us back there for a second look. We then learned how different buying a house in the US versus England, but after several rounds of negotiations came to an agreement. We had a very long wait for completion, but that all proceeded well in the end.

As we moved out of the place we had been renting for the last three years we found out just how bad some landlords can be about returning security deposits…that is still ongoing and has not been a fun process. We never rented in England, but many friends have assured us that this isn’t that unusual. Our move actually went very smoothly though, and we have some great friends who helped us with some of the heavy lifting. We have been learning what it is like to own a home in the country, with a well, septic, large garden etc. The learning curve has been a little steep at times! We attended two weddings (I was a groomsman in one) with two amazing groups of friends – it was a pleasure to be part of the day for two great friends.

I made a few guest blog posts, which I will link to in another post, and attended some great conferences including the ACS, Semantic Physical Science and Supercomputing. Our Avogadro paper was published, and was recently published in final form (I will write more about this too). I finally cancelled my dedicated server (an old Gentoo box), which I originally took when I was consulting in England, this was very disruptive in the end and I didn’t have a complete backup of all data when it was taken offline. This caused lots of disruption to email (sorry if I never got back to you). I moved to a cloud server with Rackspace in the end, after playing with a few alternatives. I was retired as a Gentoo developer too (totally missed those emails), it was a great experience being a developer and I still value many of the friendships formed during that time. My passion for packaging has wained in recent years, and I tend to use Arch Linux more now (although still love lots of things about Gentoo).

Just before Xmas our ten year old German Shepherd developed a sudden paralysis in his back legs and had to be put down. It was pretty devastating, after having him from when he was 12 weeks old. He joined our little family just after we got our own place in England, he had five great years in England and another five in the US. He was with me for so much of my life (a degree, loss of my brother, marriage, loss of my sister, moving to another country, birth of our first child, getting a “real” job). We had family over for the holidays as we call them over here (Xmas and New Year back home), which was great but we may not have been the best of company after having just lost our dog.

I think I skipped lots of stuff too, but it was quite a year! Hoping for more of a steady ride this year to say the least.


Source: FULL ARTICLE at Planet KDE