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?
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.
If ever there was a need for the transparency that open source software brings it is in the realm of voting machine technology. This story makes that point crystal clear. There may or may not be shenanigans going on in Ohio. The point is that we have no way of knowing what the patches on those Ohio voting machines actually do, and no faith in the code reading, debugging, and auditing ability of elected officials. If we want to be confident in the workings of our democracy, closed-source voting machines should be banned.
For that matter, why aren’t voting systems required to leave a physical paper trail so that we can check up on the tabulating algorithms?
Adobe released an open source font today called Source Sans Pro. It looks super clean and nearly perfect for user interfaces. Right now it comes in six weights, but a monowidth version is coming soon. (I’m most excited about this, as the sample of the monowidth font on the Adobe blog post is gorgeous). Adobe did this right – they have made all source files used in the production of the fonts available for download at SourceForge.
Maybe we’ll get more scientists using Source Sans Pro instead of releasing their important results in Comic Sans.
Two new collections of tools that may be of interest to the OpenScience community. Not everything on these lists is Open Source, but many of the visualization and research tools look to be very useful. Hat tip to Eric Lease Morgan (@ericleasemorgan) for pointing these out:
http://selection.datavisualization.ch – A collection of tools that the people behind Datavisualization.ch, work with on a daily basis and recommend. This is not a list of everything out there, but instead a thoughtfully curated selection of our favourite tools that will make your life easier creating meaningful and beautiful data visualizations.
Bamboo DiRT is a tool, service, and collection registry of digital research tools for scholarly use. Developed by Project Bamboo, Bamboo DiRT makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mind mapping software.
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.
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.)
Geoff Hutchinson just pointed us to the new blog over at Kitware (the makers of VTK). I’ve found VTK enormously helpful in the past (particularly the source to vtkMath.cxx) and I’m glad they’ve made the commitment to Open Source.