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The OpenScience Project

Open source scientific software


New Software: Reference Tools, Atomic Physics, and EngineeringDecember 2 2008

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
Earmarks for ScienceOctober 8 2008

skytheater.jpg 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

Exhibit: make your data web-accessibleSeptember 18 2008

Exhibit Logo 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 b

New Software: Data MiningAugust 7 2008

Scientific Software 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 develop
Researching Open ScienceJuly 31 2008

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.