MacResearch

COSMOtherm now available on Mac
COSMOtherm is a program for the quantitative calculation of solvation mixture thermodynamics based on quantum chemistry.

A recent publication caught my eye

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott, Arthur J. Olson *
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California

The WWDC Core Plot code-a-thon is now less than a week away. Beginning next Tuesday at midday in San Francisco, the coding marathon will begin, and it will end at midday Friday.

The Core Plot team has been working very hard the last few weeks to make sure everything is ready. The project wiki now includes introductory documents and procedures to help developers new to the framework find their way. It also includes information about what you need to do in order to contribute to the code-a-thon. Those attending WWDC and planning to partake are advised to do a bit of background reading before coming, in order to get up and running quicker.

Those that have not been lucky enough to get a ticket to WWDC are not left out: The source code repository used for the code-a-thon is publicly accessible, and all the information you need to contribute can be found on the wiki. You can contribute even if you are not physically present at WWDC. We are going to be using IRC throughout for discussions (#coreplot on server irc.oftc.net), so it will be like you are actually there.

PLplot (seehttp://plplot.sourceforge.net) is a cross-platform software package for creating scientific plots that has been in continuous development since its inception 17 years ago. On May 23, 2009 the PLplot developers quietly celebrated our ten thousandth commit since our initial software repository was populated back in May 1992.

The there are multiple OS X users among the developers and the Mac is a first-class citizen in the PLplot world.

Today I came across the RoamBi App for iPhone and was admittedly impressed with its visualization capabilities. Apparently you can upload spreadsheet-based data to their web application and visualize it in a remote, interactive manner using the iPhone application. I had never heard of RoamBi before the iPhone app came on to my radar, but it appears they are primarily targeting their product to business users.

Although I haven't come across any scientific examples on the RoamBi site, it's not hard to imagine at least a few simple uses for such a service in science. For example, I often find myself referencing data from papers I previously published and often find myself trying to recreate the chart in the air using odd gesticulations, or through back-of-the-napkin scribbles. I think it would be great if I could upload barcharts and other data from previous papers that I could display and interact with on my iPhone on-demand. Can you think of any other scientific utility for a RoamBi like visualization application for iPhone.

Version 1.30 of Vibration, the vibration spectrum analyzer for the iPhone was just released on the iTunes App Store. Version 1.30 contains a number of new features which greatly increase the functionality of the application.

Author: Drew McCormack

MacWorld.com has reprinted a piece from InfoWorld by Neil McAllister. The basic premise of McAllister’s article is that while technologies that promise greater parallel performance, like Snow Leopard’s Grand Central, are useful on web servers, they will do nothing to change our experience on the Desktop, and will be considered by most developers too difficult to bother adopting.

A native Mac GIS (Geographical Information System) application called Cartographica 1.0 was recently released. For more information, please see http://www.macgis.com/.

Author: Drew McCormack

For those of you who have been wondering about what Apple's mystery WWDC Science Coding Project will be, I am now able to spill the beans. I'm sure some have already connected the dots, but for those who haven't figured it out yet, Apple's WWDC code-a-thon is centered around the new open source Core Plot framework.

The Core Plot project began back in January after a post I made here on MacResearch as a 'call to arms' to build a decent open source plotting alternative for Apple systems. There are some options already available, such as SM2DGraphView and my own Narrative framework, but these are getting long in the tooth and are reasonably basic. There is also the very capable DataGraph framework, which is a commercial offering, but one drawback of all of these solutions is that they were developed before the iPhone, and do not support what has become a very important platform for developers.

Apple has posted a page on their WWDC web site targeting scientists. The page touts WWDC as a great place to learn how to develop scientific apps for the iPhone, and learn about new high-performance technologies in Snow Leopard such as OpenCL and Grand Central Dispatch. But perhaps most interesting of all is a mysterious 'Science Coding Project'. According to the page

WWDC will feature a Science Coding Project for anyone interested in showing off what they’ve learned at the sessions with a fun, hands-on project. Come to the Coding Project area during session breaks to work with your peers on implementing the latest Mac OS X technologies to increase the performance and power of our open source project. You’ll get a chance to contribute your own coding expertise and implement your newly-found insights in a hands-on environment.

Hmm, intriguing. Wonder which open source project they have in mind ... something of particular use to scientists perhaps.