About 10 years ago, I turned the Jmol project over to a series of fantastic lead developers (Jmol programmers regenerate in different bodies just like Doctor Who does).  Since then, the aspect of the new work on Jmol that has most delighted me is the Jmol applet, which allows the program to be embedded in web pages.   The Jmol applet transformed Jmol from a niche application into a way of broadly disseminating and interacting with chemical structures.  It has become the de facto standard for showing protein structures at the RCSB Protein Data Bank, as well as in a number of chemistry journals.

The problem with Java applets is that many new tablet and phone web browsers don’t support them (and it looks like Java applets are being slowly disabled on Mac browsers as well).  Java has always been an elegant but relatively heavy-weight solution to dynamic content, but I think its time as a widely-used language for web content is coming to a close.

So, how do you interact with chemical structures without Java or Flash?

The Jmol team has been hard at work converting the Jmol source so that the same source code that produces the Jmol applet can also be run through Java2Script to create the entire Jmol applet in JavaScript.   The new beast is called JSmol and has almost all of the functionality of Jmol itself (file IO, scripting, etc.)    Bob Hanson’s demo pages give a taste of this work.

This is amazing work.  The same Java code is compiled to create the Jmol applet, a WebGL version of JSmol, and the HTML5 version of JSmol that can run on my phone. Almost all of Jmol is there – the ability to display orbitals, crystals, and van der Waals surfaces.  Some menu interaction is still missing, but if the goal is to display and interact with a chemically meaningful structure on a web page,  JSmol looks like a great solution.

The credit for this work largely goes to a number of people:  The GLmol interface was written by Takanori Nakane.  Java2Script was written by Zhou Renjian.  The Jmol code conversion to JavaScript was done by the current Doctor Who,  Bob Hanson.

I just found out about Octopus, a quantum mechanics package that does time-dependent density functional theory (TDDFT) calculations using pseudopotential approximations.

It works in parallel using MPI and OpenMP and scales to tens of thousands of processors. It also has support for graphical processing units (GPUs) through OpenCL.

The Octopus code can be browsed freely, and it has been released under the GPL.

Particularly cool is the ability to use the time dependent electron localization function (TDELF) to look at orbitals dynamically during a chemical reaction.

Today marks (roughly) the tenth birthday of a fantastically successful open science project called the Chemical Development Kit (CDK).  At the time the skeleton of the project was set down on my office whiteboard, I was still the lead developer of Jmol, and Egon Willighagen and Christoph Steinbeck had contributed code to the Jmol project. Christoph’s pet code was a neat 2-d structure editor called JChemPaint, and Egon was working largely on the Chemical Markup Language (CML), although his code contributions were showing up nearly everywhere. Egon and Christoph were in the US for a “Chemistry and the Internet” conference and made a side trip by train to visit me so we could figure out how to unify these projects and to make a more general and reusable set of chemical objects.

The CDK waterfall whiteboard

The CDK design session was a fun weekend. In retrospect, they were some of the purest days of collaborative creativity I’ve ever experienced. We spent many hours and a lot of coffee hashing out some of the basic classes of CDK. The final picture of the whiteboard shows a classic waterfall diagram of what we were going to implement.

I’m the first to admit that my contributions to CDK were minimal. Egon & Chris ran with the design, expanded and improved it, implemented all the missing pieces, and released it to the world. It has become an important piece of scientific software, particularly in the bioinformatics community. Beyond Egon & Chris, Rajarshi Guha has been one of the prime developers of the software.

CDK is, by all objective standards a fantastic success story of open source scientific software. It has a large and vibrant user community, active developers, and a number of people (including myself) who browse the code just to see how it does something difficult. Egon has written a thoughtful piece on where CDK should go from here.

Happy Birthday CDK!

One of the biggest issues you face when you first start doing molecular dynamics (MD) simulations is how to create an initial geometry that won’t blow up in the first few time steps. Repulsive forces are very steep if the atoms are too close to each other, and if you are trying to simulate a condensed phase (liquid, solid, or interfacial) system, it can be hard to know how to make a sensible initial structure.

Packmol is a cool program that appears to solve this problem. It creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers. It works with PDB and XYZ files and appears to be available under the GPL. Very, very cool!

We just discovered a very cool open source program for analyzing scanning probe microscopy (SPM) data files. There a number of incompatible and proprietary file formats for surface microscopies (AFM, MFM, STM, SNOM/NSOM) and getting data out from a microscope for further processing (including baseline leveling, profile analysis, and statistical analysis) can be a difficult task. Gwyddion is a Gtk+ based package that runs on Linux, Mac OS X (with MacPorts) and Windows and appears to do nearly everything that some expensive commercial packages (and some free closed-source packages) can do. Some of our colleagues were very happy to discover this piece of wizardry!

A very nice aarticle by Darrel Ince has just been posted over at the Guardian. It deals with the climate-gate email theft and the quality of academic science code has just been . An excerpt:

Computer code is also at the heart of a scientific issue. One of the key features of science is deniability: if you erect a theory and someone produces evidence that it is wrong, then it falls. This is how science works: by openness, by publishing minute details of an experiment, some mathematical equations or a simulation; by doing this you embrace deniability. This does not seem to have happened in climate research. Many researchers have refused to release their computer programs — even though they are still in existence and not subject to commercial agreements. An example is Professor Mann’s initial refusal to give up the code that was used to construct the 1999 “hockey stick” model that demonstrated that human-made global warming is a unique artefact of the last few decades. (He did finally release it in 2005.)