I just realized that I don’t have any links in our Programming Languages section, so I’ve added a link to GFortran, the gcc front-end for Fortran 95 (which is not the same as g95). I haven’t yet tried to compile our mixed C++/F95 code with GFortran, but it looks like it is worth a look!
[tags]compilers, fortran, open source[/tags]
Gfortran is the name of the GNU Fortran 95 project, developing a free Fortran 95 compiler for GCC, the GNU Compiler Collection. The gfortran development effort uses an open development environment in order to attract a larger team of developers and to ensure that gfortran can work on multiple architectures and diverse environments.
Find GFortran at: http://gcc.gnu.org/wiki/GFortran
I’m not really sure what SimTK.org is all about yet, but they do look like they have some interesting things in the works. Of particular interest to me is the Molecular Dynamics Language and the Simbody multibody dynamics toolset.
Check out the list of projects!
It has been a slow week in South Bend, and this afternoon over lunch at Lula’s, I came across a fantastic article on the Dover School Board trial that was in the December 5th edition of the New Yorker. It doesn’t appear on the web anywhere, but the online-only edition contains a Q & A with the Margaret Talbot as well as a 1925 New Yorker article on the Scopes Monkey Trial and Dayton, Tennessee. The Talbot article is gripping and well-written, and gives a great glimpse into a trial that will set precedent for many years to come. I particularly like this description of the courtroom proceedings:
Yet the trial that Jones oversaw, which took place in a functional courtroom trimmed with teal and white panels, turned out to be rather like the biology class you wish you could have taken. Lawyers spent six weeks posing questions like “What is science?” and “Who was Charles Darwin?”
Update: the article does appear on the web over at The New America Foundation.
[tags]evolution, magazines, lunch[/tags]
From MSNBC.com, here’s the headline: Judge rules against ‘intelligent design’. And here’s an excerpt from the decision:
To be sure, Darwin’s theory of evolution is imperfect. However, the fact that a scientific theory cannot yet render an explanation on every point should not be used as a pretext to thrust an untestable alternative hypothesis grounded in religion into the science classroom or to misrepresent well-established scientific propositions.
The citizens of the Dover area were poorly served by the members of the Board who voted for the ID Policy. It is ironic that several of these individuals, who so staunchly and proudly touted their religious convictions in public, would time and again lie to cover their tracks and disguise the real purpose behind the ID Policy.
With that said, we do not question that many of the leading advocates of ID have bona fide and deeply held beliefs which drive their scholarly endeavors. Nor do we controvert that ID should continue to be studied, debated, and discussed. As stated, our conclusion today is that it is unconstitutional to teach ID as an alternative to evolution in a public school science classroom.
Those who disagree with our holding will likely mark it as the product of an activist judge. If so, they will have erred as this is manifestly not an activist Court. Rather, this case came to us as the result of the activism of an ill-informed faction on a school board, aided by a national public interest law firm eager to find a constitutional test case on ID, who in combination drove the Board to adopt an imprudent and ultimately unconstitutional policy. The breathtaking inanity of the Board’s decision is evident when considered against the factual backdrop which has now been fully revealed through this trial. The students, parents, and teachers of the Dover Area School District deserved better than to be dragged into this legal maelstrom, with its resulting utter waste of monetary and personal resources.
That pretty much sums up what most scientists have been saying about the Dover school board decision all along. Bravo, Judge Jones. You are a very wise man.
Found on Pharyngula, of course.
[tags]creationism, intelligent design, science[/tags]
Over in the OpenScience Forums there are two threads which ask some good questions:
Stop by the forums and have your say!
[tags]graphics, science, conferences[/tags]
Greg Wilson has written a great article in American Scientist on the shocking absence of modern software development practices from groups that do science using computers. I know exactly what Greg is talking about. Some of the groups I’ve worked with have had 10 or 20 different versions of a code, each developed by a different graduate student or post-doc. There may be some pedagogical reasons for doing this; my own students usually start with a first-year project that involves re-implementing (and then modifying in some interesting way) the basic liquid simulation code for a small box of Argon. There’s a lot to be said for understanding the gory details of what a piece of scientific code is doing before moving on to a larger and much more complex piece of software.
After my students do that first-year project, they usually start working with the larger group code, and that code is managed with all of the modern tools we can get our hands on. We use CVS for source control, doxygen for automatic generation of class documentation, autoconf for building on multiple architectures, and a mix of IDEs and symbolic debuggers for working out the kinks. We use every buzzword-compliant feature of modern programming languages (including pointers and self-adjusting vectors in Fortran). These tools are used by an astonishingly small fraction of working scientists, however. Greg points to the number of working scientists still editing their code with vi or wordpad, and I’m continually astonished at how many scientists see absolutely nothing wrong with implicit variable names.
Unfortunately, the situations in which we’ve needed excellent coding tools (i.e. debugging our parallel simulations, data passing between different languages) are the places where the open source codes have been missing. There are wonderful symbolic debuggers in the commercial world, but very few open source projects to do what needs to be done.
Greg hasn’t just written an article lamenting the inability of modern scientists to use the tools that are out there. He’s gone and done something about it. He’s created an online course to teach us too-smart-for-our-own-good lunkheads how to use the things that make software development easier.
Here’s an excerpt from the article:
I finally asked a friend who was pursuing a doctorate in particle physics why he insisted on doing everything the hard way. Why not use an integrated development environment with a symbolic debugger? Why not write unit tests? Why not use a version-control system? His answer was, “What’s a version-control system?”
A version-control system, I explained, is a piece of software that monitors changes to files—programs, Web pages, grant proposals and pretty much anything else. It works like the “undo” button on your favorite editor: At any point, you can go back to an older version of the file or see the differences between the way the file was then and the way it is now. You can also determine who else has edited the file or find conflicts between their changes and the ones you’ve just made. Version control is as fundamental to programming as accurate notes about lab procedures are to experimental science. It’s what lets you say, “This is how I produced these results,” rather than, “Um, I think we were using the new algorithm for that graph—I mean, the old new algorithm, not the new new algorithm.”
My friend was intelligent and intimately familiar with the problems of writing large programs—he had inherited more than 100,000 lines of computer code and had already added 20,000 more. Discovering that he didn’t even know what version control meant was like finding a chemist who didn’t realize she needed to clean her test tubes between experiments. It wasn’t a happy conversation for him either. Halfway through my explanation, he sighed and said, “Couldn’t you have told me this three years ago?”
Go read the whole article.
Update: Greg has a blog!
[tags]science, software, programming, tools[/tags]
My new favorite site of the day: United Nuclear’s Chemicals & Exotic Metals which appears to be a page for people doing experiments with home-brewed fireworks, magnetic levitation, and neutron activation experiments. On a single page, they have D2O, Beryllium pellets, and lead sheeting as well as various fireworks coloring agents like BaCO3 and (NH4)2Cr2O7. They also have great warning messages on their magnets:
Beware – you must think ahead when moving these magnets.
If carrying one into another room, carefully plan the route you will be taking. Computers & monitors will be affected in an entire room. Loose metallic objects and other magnets may become airborne and fly considerable distances – and at great speed – to attach themselves to this magnet. If you get caught in between the two, you can get injured.
Two of these magnets close together can create an almost unbelievable magnetic field that can be very dangerous. Of all the unique items we offer for sale, we consider these two items the most dangerous of all. Our normal packing & shipping personnel refuse to package these magnets – our engineers have to do it. This is no joke and we cannot stress it strongly enough – that you must be extremely careful – and know what you’re doing with these magnets. Take Note: Two of the 3″ x 1″ disc magnets can very easily break your arm if they get out of control.
Axially Magnetized (the top & bottom flat faces are the north & south poles).
We can only ship these magnets by ground UPS – they cannot be shipped via air as it will interfere with the aircraft’s navigational equipment.
With warnings like that, I think I must buy one…
[tags]science, toys, boom[/tags]
Nature ran a comic as Nature 438, pp 449-453 (2005). You can read about it here and see the comic here. The comic was drawn by Chuck Wadey and was written by Drew Endy and Isodora Deese from the MIT Synthetic Biology Working Group.
Found via Drawn!
[tags]comics, biology[/tags]
We have a new link today in our Abstract Algebra section for YACAS, which stands for “yet another computer algebra system”. YACAS is an easy to use, general purpose Computer Algebra System, a program for symbolic manipulation of mathematical expressions. It uses its own programming language designed for symbolic as well as arbitrary-precision numerical computations. The system has a library of scripts that implement many of the symbolic algebra operations; new algorithms can be easily added to the library.
[tags]algebra, open source[/tags]
