Selling Science

Although the idea of government agencies making direct pitches to the public makes me squeamish, there are times when I think we should let them talk about their work in a clear and compelling way to the people who funded it. That’s a way of saying that the NSF, NIH, DOE and other agencies that fund basic science should hire whichever agency (or amateur) created this wonderful video ad for NASA.

It is a nearly perfect advertisement for exploration and discovery, and I hope it sparks a lot of discussion about the goal of NASA funding. NASA should be about doing real science (like the Hubble telescope and the Rover missions) and real exploration in space (i.e. beyond low-earth orbit) instead of dumping more money down the maws of Space Shuttle and ISS projects.

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Science Blogs

There’s an interesting article about Scientists who blog over at The Scientist. I know that the fear of being scooped keeps a lot of professional scientists from showing their cards to their peers before a manuscript is accepted or in press. In fact, I find my blog topics are very rarely about the day-to-day details of what we do in my lab. I’m sure this varies from field to field. (Actually we know this is true; the physics community has happily accepted the arXiv preprint model, while chemists and biologists have much more internalized fears of being scooped.) I would imagine that scientists in corporate settings have even more constraints on what they can reveal about their science in a blog.

Some of what my group does in lab is publicly viewable. The CVS tree for our simulation code is out there for anyone to look at, although they’d be taking their research careers into their own hands if they attempt to use a pre-release version of our code. So what’s the harm in revealing details in a blog? None, I suppose. If a research community all reads the same blogs, they’d be able to figure out attribution chains pretty quickly. Perhaps blogs will become a model for the way that scientific ideas are communicated in the future. There’s certainly a citation mechanism in place for blogging (Trackbacks are even a reverse citation mechanism.) The only mechanism that is truly lacking is anonymous peer review and editorial control. I can be sure that the papers in J. Phys. Chem. for example have passed through a reasonably rigorous peer review and editing process. Sometimes this breaks down and bad papers appear in the literature, but in general. peer review adds immense value to scientific communication. Blogs don’t really have this kind of review process other than as public airing of grievances by another blogger, and the only editorial control is by the reader’s interest (or by what google will digs up for a keyword search).

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Intelligent Design isn’t.

Yoikes. The President says that ‘Intelligent Design’ Should Be Taught. I find it disturbing to hear someone elected to a national political office actually voicing support for ID. Here are some other ‘different schools of thought’ he could also suggest be taught alongside ID:

  • Copernicus could have been right! Kepler’s laws are, after all, only a theory!
  • Heavier bodies just might fall faster than lighter ones. Gravity is, after all, only a theory!
  • Phlogistion-powered vehicles can cure our dependence on foreign oil! Burning by oxidation is, after all, only a theory!
  • Pons and Fleischman should be appointed to the vice-president’s energy task force! Our understanding of nuclear reactions is, after all, only a theory!
  • Learning the Four bodily Humours would greatly simplify medical training! The germ theory of disease is, after all, only a theory!
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PGOPHER

PGOPHER is a general purpose program for simulating and fitting rotational spectra. PGOPHER will handle linear molecules and symmetric and asymmetric tops, including effects due to unpaired electrons and nuclear spin. The program can handle many sorts of transitions, including Raman, multiphoton and forbidden transitions. It can simulate multiple species and states simultaneously, including special effects such as perturbations and state dependent predissociation. Fitting can be to line positions or band contours.
Find PGOPHER at: http://pgopher.chm.bris.ac.uk/

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Cassandra

Cassandra is a open source data viewer based on VTK. Cassandra provides a dynamic interaction with the VTK pipeline and enables to load plugins dynamically in order to perform specific tasks in data manipulation and visualisation.
Find Cassandra at: http://dev.artenum.com/projects/cassandra

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New Software links!

Now that the site redesign is nearly complete, we’ve got a backlog of user-submitted software links:

  • EASY! is a fortran code for constrained or unconstrained optimization (added to our Optimization section).
  • OpenFlower is a C++ CFD code which can handle complex 3D geometries (added to our Fluid Dynamics section).
  • SPINA is a method to calculate constant structure parameters of endocrine feedback control systems from hormone levels obtained in vivo (added to our Medical Sciences section).
  • ROC.KIT is an open-source Macintosh application allowing for automated calculation of ROC (Receiver-Operating-Charateristic) curves (also added to Medical Sciences section).
  • OpenScientist (we particularly like the name) is an integration of open source products working together to do scientific visualization and data analysis ; in particular for high energy physics (added to our Physics section).
  • GENtle is software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more (added to our BioInformatics section).
  • PGOPHER is a general purpose program for simulating and fitting rotational spectra (added to our Spectroscopy section).
  • Cassandra is an open source data viewer based on VTK that looks remarkably capable. (added to our 3D visualization section).

These all look like great resources. Check them out!

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Where did SAL go?

Back before we opened up shop at openscience.org, we used to browse the Scientific Applications for Linux (SAL) site at Kachinatech. It had some interesting links to programs we didn’t know much about. The old SAL mirrors are still around, but the primary site appears to be gone, replaced with ads for scholarships and fellowships.

Do any of our readers know if the SAL database is still around, and whether it would be possible to filter the open source licensed software so that we can import it into the openscience database?

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Koders

We just discovered this amazing new site, koders.com which lets you search a huge volume of open source software (and not just the scientific software). To demonstrate how useful it is, here’s a sample search for GPL’d software with the string Chebyshev. That’s a pretty darn useful search tool for scientists!

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Posted in Science, Software | 4 Comments

Changes have been made

We’ve switched to entirely new software to run some of the OpenScience site. The blog is now being handled by WordPress and the forums have been switched to PunBB. We’re trying to combat some of the annoying spam, and to make posts, comments, and the forums a bit easier to use. The Software section is still being handled by our homegrown LinkWeaver software (although it has advanced substantially from the version available at the LinkWeaver site).

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GENtle

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
Find GENtle at: http://gentle.magnusmanske.de

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Posted in Bioinformatics | Leave a comment