Marcus D. Hanwell's Blog - KDE

Conferences: Talking Open Science at OSCON, Desktop Summit and Chemical Databases Meeting

marcus@cryos.net (Marcus D. Hanwell) — Sat, 03 Sep 2011 20:37:00 -0400

Over the last two months I have had one of my most hectic travel schedules ever. It started withOSCON, and a panel discussion about "Practicing Open Science". This one was a bit of a surprise, as Bill Hoffman was originally presenting with Will Schroeder and Brian Wylie, from Sandia National Laboratories. As Bill couldn't make it we decided to change the content of my section, and talk about the new open chemistry area that I have been working on for about four years now. Will went first, followed by me and a wrap up from Brian, with a nice flow between Kitware working on open science for over a decade, me growing a new area of open science (now at Kitware) and Brian giving a government perspective on open source and open science. The slides are below and on slideshare if you would like to take a look.

Oscon 2011 Practicing Open Science

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I thoroughly enjoyed OSCON, and would love to attend future events. The toughest thing was deciding which talks to attend as there were often multiple tracks with talks of interest to me. This was also by far the largest and most commercialized open source event I have attended so far, in the beautiful city of Portland, OR. I couldn't stick around for long after the conference as I was flying out to England on the following Tuesday, and on to Berlin, Germany Friday to attend the Desktop Summit. This was my first time in Germany, and I was looking forward to exploring Berlin a little, along with some time to catch up with a few family and friends in England before and after the conference. I talked about "Open Source Visualization of Scientific Data" on the final day of the main conference, and was very pleased to have a large and interested audience. Here I also discussed my work in open chemistry, along with a lot of the other work we do at Kitware in the Scientific Computing group.

Open Source Visualization of Scientific Data

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I stayed for the remainder of the conference, attending my first KDE e.V. meeting, and was joined by Bill Hoffman towards the end of the week. Bill gave a workshop on using CMake, and I helped out with that, along with taking part in several BoF sessions and meetings. It was a very hectic week, very different feel to OSCON with a lot of great presentations, BoFs and hacking sessions. I also had the opportunity to meet up with Alexander Neundorf who was an intern at Kitware for half a year, and several other KDE developers interested in build systems, software process, testing, coverage and related areas.

Then I was back home for just over a week before braving the elements and heading straight for the path of hurricane Irene. I was invited to the 5th Meeting on U.S. Government Chemical Databases and Open Chemistry where I talked about "Chemical Databases and Open Chemistry on the Desktop". This meeting was very focused on chemical databases and the open chemistry I have been working on so hard for the last few years. It was a great experience to be able to see what others are working on, and discuss possible points for future collaboration. There is some amazing work happening in this area, and this meeting helped me gain greater clarity on how my work at Kitware can fit into the larger picture to significantly improve the landscape in open chemistry.

Chemical Databases and Open Chemistry on the Desktop

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Thanks to Kitware for allowing me to attend, and funding my travel/other expenses, and to my wife and son for tolerating my long absences over the last couple of months. An even bigger thank you to my wife, Louise, for letting me off the hook on my first missed wedding anniversary so that I could present at OSCON! I had some great news about funding for the continued development of many of the ideas discussed in the slides, and so hope to have much more to talk about over the coming months (and years). This post is already pretty long, I hope to continue developing this work and promoting open science, especially in chemistry, materials science, physics and the bio areas. There are lots of other amazing people working in these areas too, and I feel like we are getting to a point where we can create real change to improve the outlook in scientific research.

Talking About Open Source Visualization of Scientific Data at the Desktop Summit

marcus@cryos.net (Marcus D. Hanwell) — Thu, 04 Aug 2011 20:20:00 -0400

I have begun my journey to the Desktop Summit, making the flight over from the US to Manchester yesterday. A short stay in Sheffield, and catch up with family before heading out to get my flight to Berlin tomorrow. I will be talking about the work I have done both at and before joining Kitware with the title "Open Source Visualization of Scientific Data". I plan to talk about a range of work from my Google Summer of Code project on Kalzium back in 2007, through to some of the exciting work at Kitware in VTK, ParaView and Titan looking at the challenges of large data, remote visualization and how to integrate the web and smartphones/tablets into the scientific data visualization workflow.

Bill Hoffman is also planning to attend, and we will be running a workshop introducing CMake on Thursday. This is my first Desktop Summit, although Bill and I have both attended previous aKademy and Camp KDE meetings. I should be in on time to attend the pre-registration event, and will not be leaving until Saturday. Looking forward to a great summit, catching up with some old friends and making some new ones. Now, I think I should try to get some sleep before my flight tomorrow!

Talking at OSCON 2011 about Open Science

marcus@cryos.net (Marcus D. Hanwell) — Tue, 26 Jul 2011 14:30:00 -0400

I am currently on a plane bound for Portland, Oregon enjoying the in-plane wi-fi. Will Schroeder, Brian Wylie and I will be talking about "Practicing Open Science" on Friday in the government track. I am standing in for Bill Hoffman who unfortunately could not make it, and will be discussing the work I have been doing to grow open chemistry both at Kitware and outside of Kitware with many amazing collaborators scattered around the world. I am really excited to have the opportunity to talk at OSCON, and would be happy to meet up and discuss this work if you are at OSCON. Will and Brian are both very passionate about open science too, they will both give their unique perspectives on practicing open science. I will be there from this evening and don't fly out until early Saturday morning.

I am very much looking forward to OSCON, and the major difficulty I have had is choosing between the talks that are all happening at the same time. In some cases there are two or three I would like to see in any given slot. I am hoping to attend the KDE release party tomorrow too, please join us there if you would like to celebrate with us.

Avogadro 1.0.3 Released

marcus@cryos.net (Marcus D. Hanwell) — Mon, 25 Apr 2011 12:58:39 -0400

I am pleased to be able to announce the availability of Avogadro 1.0.3! What happened to Avogadro 1.0.2 I hear you ask...shortly after tagging Michael reported an issue with i18n building/installations. So 1.0.3 contains a couple of very small build system fixes, but see the 1.0.2 release notes for details of most of the fixes.

As always, we appreciate your feedback. There are still a few issues outstanding, but many things were fixed. These binaries are also built against much newer versions of Qt and Open Babel where significant improvements have also been made. There may be one or two more releases of the 1.0 line if necessary (I have streamlined the release process with a view to making more releases), but I would like to focus our efforts on an unstable release for 1.1. Once 1.1 is stable, a 1.2.0 release will be cut and branched. There are lots of new features in master that we would love more feedback on.

Blue Obelisk Award

marcus@cryos.net (Marcus D. Hanwell) — Wed, 13 Apr 2011 13:22:45 -0400

At the recent ACS Spring meeting I attended the Blue Obelisk dinner, where I was honored to receive a Blue Obelisk award, pictured below, for my contributions to Open Data, Open Standards and Open Source. This is largely due to the work I have done on Avogadro, Open Babel and other open source chemistry tools.

This was one of the biggest dinners I have had the opportunity to attend, and I got to meet many of the people I have worked with (or used their work), along with several people I had not had the opportunity to work with yet, but hope to in the future. We presented the work we had been doing on Quixote project at the chemical information symposium on chemistry and the internet, after attending the first Quixote meeting the previous week (thank you to Hartree Centre for inviting me to speak there, and sponsoring the event).

These are exciting times, thank you very much to Peter Murray-Rust for presenting me with the award, and all of the support he has shown, along with his relentless passion for open science. I have only been a part of this for a few years, but Peter has been working on opening up chemistry for decades now.

CMake External Projects: Building Project Dependencies

marcus@cryos.net (Marcus D. Hanwell) — Sat, 05 Mar 2011 16:41:21 -0500

Historically projects have attempted to minimize their dependency list, and often bundle in small third party libraries in an attempt to make things easier for new developers/users to compile their code. In the Avogadro project we have bundled a few really small libraries, but on the whole have maintained a dependency list and tried to keep it smaller. As I work on new code, I see opportunities to break off bits of functionality, such as with OpenQube, but don't want to add yet another thing a new user or developer must download, compile and install somewhere.

Linux packagers, myself included, dislike the practice of bundling in libraries. It means that instead of patching one libxml2, we get to patch one plus the three or four in our tree that have been bundled (often with different version, some local patches). The problem is less pronounced on Linux where package managers are ubiquitous and we are able to provide a list of packages to install, but even there we might be developing against versions not yet in the main distribution repository. This is one of the reasons I have always favored rolling release distributions over the periodic.

CMake's external project module helps us to deal with this issue in quite an elegant fashion. Coupled with meta repositories to bring several source trees together, CMake is able to direct the build of several projects, passing locations between projects and expressing dependencies between the projects being built. This means that something like Open Babel can build zlib and libxml2 before building the main Open Babel library. External projects and CMake allow us to download the source, create the build trees and even direct the build of non-CMake based projects like libxml2.

I have a prototype of this that I just put up to build the core of Avogadro, its working name is Avogadro Squared as I was feeling geeky that day and had no good names. One thing you should note is that everything in there is an external project, and Avogadro is the last one to be built (it depends on all of the other projects). It requires minimal changes to the projects it contains, it uses git submodules for some of the source, and CMake's download and tar functionality for zlib and libxml2. I will be adding options to simply use system versions of the libraries it can build, but Linux distributions etc can continue using the Avogadro repository directly.

As a new developer or user I can checkout the meta repository, have git download the submodules and CMake download the source tarballs. I can then build the entire project, and then continue to work in the Avogadro subdirectory of the build tree after that. That build tree is almost identical to the one I would have ended up with had I not used the meta repository, except it points to the dependencies I just built. I can then use vim, and IDE or whatever I choose to work on the inner projects. This works across Linux, Mac and Windows to get new users and developers up and running very quickly while only loosely coupling the dependencies to the Avogadro project.

I have worked on other larger projects, such as Titan and ParaView that are using this approach to a greater or lesser extent. Titan can actually built Qt, Boost, VTK, protobuf, Trilinos and a host of other dependencies before building the Titan libraries and applications. I think Avogadro Squared is an example of just how minimal a meta repository can be, although I will be extending it with more dependencies it really is just a glue repository.

Volume Rendering in Avogadro

marcus@cryos.net (Marcus D. Hanwell) — Sat, 15 Jan 2011 22:23:43 -0500

Since joining Kitware I have had limited spare time to work on Avogadro, and for various reasons my spare time has been more limited than usual too. Since the new year I have been able to start spending more time working on Avogadro, and open source chemistry in general, thanks to an SBIR phase I proposal that was funded last year with the US Army Corps of Engineers. This is exciting for a number of reasons, including the fact that I have the opportunity to prototype exciting new features for chemistry visualization, workflow and data management.

One of the new bits of work I have been doing is to use some of the advanced visualization techniques in VTK such as GPU accelerated volume rendering. Now the code is still pretty rough, and is more a proof of concept. I wrote a simple external Avogadro extension that links to and uses VTK to render the first volume found in the current Avogadro molecule. All of the parameters are currently fixed, I am hoping to get the time to add in more options along with some integration of the Avogadro rendered molecule in the VTK render window. You can view the code here, please bear in mind it is at a very early stage.

I have also been working on several other things such as splitting out the quantum calculation code from the Avogadro plugins, and putting it in a small library. I have called the library OpenQube, right now it only has the base functionality that was in Avogadro but I will be extending it with more features, regression tests and I am hoping due to the decoupled nature and liberal BSD license it will encourage wider collaboration in this field.

There is also the Quixote project which I am very excited about. Meaningfully storing the results of quantum calculations, annotating them and retrieving them within an open framework. This is a growing problem in todays world, and I am working on extensions to Avogadro to allow it to fully exploit the semantic chemical web. This includes some of the previous work to access the PDB and other public resources as well as private databases within groups and organizations.

I think this is going to be a very exciting year for Avogadro, and open source chemistry in general.

Returning From Hibernation...

marcus@cryos.net (Marcus D. Hanwell) — Sun, 23 May 2010 17:46:23 -0400

Wow, I just looked and I haven't written a thing since January! For those of you who might have been worried, or just wondered what I was up to...here is a quick run down. I am going to start with a little advice, combining starting a new family with moving from academia to industry and moving house it tough I have been really focused on work, home and one big conference, and kinda shut down otherwise.

I hope to remedy that in the coming months, and have started by doing some development for Avogadro and Open Babel. I also got Kalzium in KDE trunk ported to use the system Avogadro library, with some help from Pino Toscano. So KDE 4.5 will feature a Kalzium using the system installed Avogadro, this prompted a couple of bug fixes in Avogadro. So after that I tagged and released a much delayed Avogadro 1.0.1 with several bug fixes.

Way back in March Kitware was kind enough to send me out to the March ACS meeting, where I presented a talk on VTK, ParaView and its use in chemistry. I also gave a talk on Avogadro, and its use as a framework in chemistry visualization, which Geoff followed up with a talk on some applications of the Avogadro framework in his research.

The ACS conference deserves a full post of its own, but I feel like it has been so long I will just summarize a few of my thoughts. There were some other really interesting talks on visualization, and how it can be applied in chemistry. I got a general feeling that commercial software still has too much of a stranglehold, and hope to see that change as we develop powerful open source platforms that can be shared by all. There is a definite need for this in chemistry, and I am doing everything I can to seek some funding to further that cause, failing that I will continue to do what I can in my spare time.

I was honored to meet members of the Blue Obelisk for the first time. Saw some great talks about open science, open data, open standards and open access. I especially enjoyed meeting and seeing Peter Murray-Rust talk for the first time, I found that I share many of his ideals. I think we differ in some places, but life would be boring if that were not the case!

Our son, William, is nearly one year old already! He might be a big part of the reason why I have been inactive. The kinds of sleep deprivation torture you go through with children are indescribable He is thankfully sleeping quite well now, and even took his first two steps yesterday.

We had our first visitors in our new home - friends from Pittsburgh and Washington DC all came up for a weekend. I fired up our new BBQ, an enormous American style with offset fire box. Made some amazing ribs, and shared some of the home brew I made - a portable porter, and an English brown ale (first two batches). We are just getting ready for a trip to Pittsburgh, and then William's first birthday (planning a small party at our place).

Then there is work, lots of exciting things are happening there. I taught my first course at Kitware, going through ParaView plugins. The new CMake book came out (I am one of the contributors to the new edition), and the new VTK book came out at around the same time. Kitware is hiring, so please let me know if you are interested in applying. We have some really interesting projects to work on, most of my time is spent on something called Titan. Last Friday I also pumped the tyres up on my bike, and rode into work for "Bike to Work Day".

I have skipped loads of stuff, but already wrote more than I intended. I will see if I can be a little more disciplined and write more frequently. My current problem is finding time to fit everything in, but I have a new strategy I am working on in order to do better. Life after the big 30 is certainly different. I feel energized again, and hope to be writing about more fun and interesting stuff I am doing over the coming months.