New Software: Reference Tools, Atomic Physics, and Engineering

Some new software to point out today:

• In the Tools section, we have a new link to cb2bib a tool for rapidly extracting unformatted bibliographic references from email alerts, journal web pages, and PDF files.
• In the Atomic & Molecular Physics section we have a new link to FELLA, which stands for Free Electron Laser Atomic, Molecular, and Optical Physics Program Package. FELLA is a joint project of Christian Buth from LSU and Robin Santra at Argonne National Laboratory.
• In the Engineering section, we have two new links, one for View3D, a command-line tool for evaluating radiation view factors for scenes with complex 2D and 3D geometry, and one for OSIV a program that performs cross-correlation analysis of particle image velocimetry (PIV) images.

Check them out, and as always, be sure to suggest your favorite open source scientific software!

Earmarks for Science

At the debate last night, John McCain brought up (twice!) for special scorn an example of spending on earmarks. His target? The “overhead projector for a planetarium”. It wasn’t the first time he’s brought up this earmark request up either. Bad Astronomy had a good post on how McCain’s comments on planetaria make him “literally antiscience”. The projector in question is hardly your run-of-the-mill overhead projector. The Adler planetarium in Chicago has a “Sky Theater” or a hemi-spherical dome on which it can project just about anything if you have the right equipment. Notre Dame (where I teach) has a very similar set-up in our digital visualization theater. The projectors we use were modeled on the current system at the Hayden planetarium, and just to give you some scope, we have a 50-foot high domed ceiling for a hexagon array of chairs that seats 136 students. The system is run with 10 computers, 8 of which do nothing but render 3D objects and transform them for hemispherical projections. It was a million dollar facility that goes a long way toward making all aspects of science visible to our students. In fact, as earmarks go, the planetarium projector at the Adler is a lot less offensive than some other projects (notably a certain bridge in Alaska).

In the past, McCain has also targeted for scorn an expenditure to study the “DNA of bears in Montana”. To be fair, other earmarks have also been his target: The Woodstock museum, and the bridge to nowhere (at least until he picked a running mate who was in favor of that same bridge) have also been the targets of McCain’s anti-pork ire. But last night, he seemed to express a special loathing for earmarks for science.

Now, a good case can be made (and should be made) that using earmarks to fund basic science research or science outreach is just bad policy. In fact, I’d be happier if the budgets for science-related earmarks were turned over to the NSF in order to fund peer-reviewed and merit-based proposals. But if the earmarks are the only way to fund science outreach projects like the Adler’s planetarium, then count me in. It is certainly a better use of money than David Vitter’s proposed earmark of $100,000 for a group that promotes “creation science”. In fact a list of examples of religious earmarks pointed out by Americans United for the Separation of Church and State are all worse than the Adler planetarium project.

Exhibit: make your data web-accessible

David Karger’s lab at MIT has developed some neat web software called exhibit, which is designed to let non-ultra-sophisticated individuals publish data in ways that make it immediately accessible and interactive for people encountering it on the web. With exhibit, a scientist with a lot of data doesn’t need to manage a database (mysql, etc.) and program a front end for it. Instead, they can put a data file (as simple as a spreadsheet) and a presentation file (written in basic html) on their web site and they’re done. There are a couple of great examples including an interactive elements table that one of Karger’s undergraduates put together.

Exhibit is a three-tier web application framework written in Javascript, which you can include like you would include Google Maps. The integration with Google maps is quite impressive. One can imagine using it to display geographic or other spatial data. In fact, here’s an exhibit of Danish monthly weather records since 1874. And here’s a great example of exhibit being used to display a bibliography for the MIT haystack group.

Other useful related projects are Timeplot and Timeline for placing interactive time data on a web page.

New Software: Data Mining

Some new software is in our Knowledge Discovery and Data Mining section. I can remember a time when “data mining” was a bit of an epithet in science (like “fishing expedition”), but now it has become an established way of finding links and connectivities in large data sets. Three new open source data mining programs appeared on our radar recently:

• KNIME, pronounced [naim], is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models.
• RapidMiner (formerly YALE) - not much detail is known about this package
• Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.

Researching Open Science

I don’t know how I missed this before, but there’s a really interesting article from 2006 up at the Harvard Business School “Working Knowledge” site. It details some of Karim Lakhani’s results from a paper called ‘The Value of Openness in Scientific Problem Solving‘. The paper itself is actual detailed research on different methods of scientific problem solving that is really worth a read for anyone in the Open Science movement. They went looking to see if “Broadcast Search” (i.e. telling the world what problem you are working on) is an effective means of problem solving. My favorite part of the paper:

Our most counter-intuitive finding was the positive and significant impact of the self-assessed distance between the problem and the solver’s field of expertise on the probability of creating a winning solution. This finding implies that the farther the solvers assessed the problem as being from their own field of expertise, the more likely they were to create a winning submission. We reason that the significance of this effect may be due to the ability of “outsiders” from relatively distant fields to see problems with fresh eyes and apply solutions that are novel to the problem domain but well known and understood by them.

Cool Radiohead interactive video

So, I like Radiohead. A lot. Kid A has been in permanent rotation in my music collection for a couple of years now. But their new video for House of Cards is something else entirely. It was generated from 3-D data of Thom Yorke’s face collected via a Geometric Informatics scanning system which uses structured light to capture 3D images at close proximity. There’s an official video, but the best part is the completely interactive data viewer. Try it yourself!

Automated out-of-plane finder?

The code I’ve been working on has some cool features. If you give it a list of atoms and bonds, it automatically figures out bend and dihedral interactions using simple graph concepts. That is, if the molecule has a bond between atoms i and j and another bond between atoms j and k, you can easily deduce that there’s a bend interaction between i, j, and k. Similar three-bond ideas can be used to automatically determine dihedral interactions: Find bonds i-j, j-k, and k-l, then you can deduce the torsion for i-j-k-l.

For out-of-plane bends or improper torsions at the sp2 sites, there’s no simple graph theory way to determine an out-of-plane interaction. You actually need to know something about the chemical identity of the central atom. At least, I think this is the case. I’d love to be proven wrong, because keeping track of valences and bond counts is beyond the level of coding I wanted to include.

FooCamp? BarCamp?

One of the more interesting aspects of the New Communication Channels workshop was something called the “SciBarCamp” that was organized by Jen Dodd. I’d never been at a meeting which used this format before, and I was a bit dubious when I first heard about it, but it worked well with the group that was at this meeting. Here’s how it functions:

• After a morning of more traditional talks, everyone files in to a large room. Each participant gets a sheet of paper on which they write their name, and the name of a workshop that they are interested in leading.
• Each of these sheets of paper gets tacked up to a board in the middle of the room, and people mill around looking at all of the proposed workshop titles. If you see a workshop that looks interesting, you vote for that workshop by bubbling in a circle on the sheet of paper.
• The conference organizer can combine workshops if they look similar (in our case, a bunch of Wiki-related workshops were combined).
• After about half an hour, the most popular workshops are selected and scheduled in particular rooms and time slots.
• If your workshop was popular enough, you then have to lead it!
• People can vote with their feet too; if a workshop is boring, you are encouraged to walk out and find one that isn’t (although in practice, few people actually did this).

Controversy was pretty much at a minimum because we were all converts to doing open science in one form or another (open source, open data, open access, open notebook). But we certainly got groups of people in each workshop who were guaranteed to be interested in the topic under discussion. After all, they’d voted for that workshop topic!

In order to make this work, you need a really good organizer to explain things up front. Scientists can be socially awkward and unwilling to try new formats, but this worked out well. I hope we start to see more of this kind of thing at smaller meetings.

Cool finds at the NCCB2008 workshop

Some of the cooler online resources that have been discussed at the NCCB2008 workshop:

• OpenWetWare
• The international genetically engineered machines competition (IGEM)
• Registry of Standard Biological Parts
• Nature Precedings
  
• Proteopedia
• The Open Protein Structure Annotation Network (TOPSAN)
• SciVee.tv
• FriendFeed

New Communication Channels for Biology Workshop

I’m going to be giving a talk at the “New Communication Channels for Biology” Workshop run by the CalIT2 folks at UCSD. The workshop is Thursday and Friday, and there are going to be some interesting folks like Michael Nielsen, Hilary Spencer, Jean-Claude Bradley, Aaron Fulkerson, Michael Gribsikov, and a bunch more. It should be pretty interesting!