The OpenScience Project | Open source scientific software

Chemicool Periodic Table

Posted on August 14, 2006 by Dan Gezelter

Chemistry periodic table (periodic chart) of the elements. Information about hydrogen, oxygen, silver, carbon, aluminum…plus forum, dictionary and tools.
Find Chemicool Periodic Table at: http://www.chemicool.com/

Posted in Periodic Tables | Leave a comment

Software Carpentry Course

Posted on August 11, 2006 by Dan Gezelter

Greg Wilson pointed me to a new version of the Sofware Carpentry course at (www.swc.scipy.org); it’s all open source, and they’re actively looking for corrections and contributions.

Reading through the online course materials, I can say that it is a fantastic resource. The new version covers topics like revision control using svn, relational databases, object-oriented programming, debugging, and just about every other topic that scientists-in-training should be learning.

Go check it out!

Posted in education, Science, Software | 1 Comment

A Theory about Questions in Paper Titles

Posted on August 10, 2006 by Dan Gezelter

I have this hypothesis about scientific papers: If the title of the paper contains a question, the paper answers the question with a “no”.

My own examples:

I’m sure there are plenty of counter-examples, but just leafing through the piles of papers and issues of “Science” on my desk, this seems to be a genuine predilection of scientific writers. You pose a hypothetical question, then you demolish it.

[tags]science, papers, questions[/tags]

Posted in Fun, Science | Leave a comment

Sally Forth and Me…

Posted on August 10, 2006 by Dan Gezelter

About these comics:
Sally Forth 8/8/06
Sally Forth 8/9/06

Ces Marciuliano (the writer of Sally Forth) and I shared adjoining dorm rooms when we were undergrads. He’s been dropping his friends’ names in his strips since he took over the gig from Greg Howard, and for a while, I was known as “Ol’ Man Gezelter”. After he killed off my character this spring, he promised to bring me back (this time with my wife and daughter). Carey seems reasonably happy that she’s been cast as a leggy, blonde pediatric surgeon, and I’m quite fond of the extra hair and the leg extensions that have been given to me. I’ll have to thank the illustrator.

However, we do seem destined to be the smug next door neighbors that the Forths will come to loathe. Given Ted’s mob connections, his memories of past abuse, and mental illness, this doesn’t look like it will end well. The day will come when we ignore Ted and Sally’s parenting advice, and later that evening Carey will have to hole up in the safe room waiting for Ted’s mafia friends to leave, Ted will put on one false eyelash, a white suit, black bowler, and will personally attack me with a golf club while belting out “Singing in the Rain” at the top of his lungs. And then we’ll find out that Hillary is really Tyler Durden and Keyser Soze all rolled up into one twisted mess. Sally will keep smirking right through the entire episode.

It can’t end well, I tell you!

[tags]Sally Forth, web comics, psychotic cartoons[/tags]

Posted in Fun | 5 Comments

XMD

Posted on August 2, 2006 by Dan Gezelter

XMD is a GPL’ed Molecular Dynamics program written in C. It supports the following potentials: pair, EAM, Tersoff and Stillinger-Weber, and implements a large variety of commands to help simplify simulation.
Find XMD at: http://xmd.sf.net

Posted in Molecular Dynamics | Leave a comment

Crystal orbital algebraic diagrammatic construction

Posted on July 29, 2006 by Dan Gezelter

The CO-ADC program suite has been designed to calculate band structures of semiconducting and insulating crystals. Thereby, the electron correlations are accounted for on ab initio level using the crystal orbital algebraic diagrammatic construction (CO-ADC) scheme. The software comprises an independent band Lanczos code for real- symmetric, complex-symmetric, and complex-Hermitian matrices.
Find Crystal orbital algebraic diagrammatic construction at: http://planet.pks.mpg.de/trac/co-adc

Posted in Condensed Matter | Leave a comment

Fun with Bessel Functions

Posted on July 26, 2006 by Dan Gezelter

Almost everyone has seen that wonderful first picture of a “Quantum Corral” from the now-famous paper by Crommie, Lutz and Eigler (Confinement of electrons to quantum corrals on a metal surface. Science 262, 218-220 (1993)). The surface states of the electrons on the copper substrate were coralled by a cylindrical barrier made out of iron adatoms. And waves confined to a nearly-circular box have Bessel functions as a good basis set. The second picture is a new device that uses waves to print standing patterns on water surfaces. It is a neat collaboration between Akishima Laboratories and professor Shigeru Naito of Osaka University. The device consists of 50 water wave generators encircling a cylindrical tank 1.6 meters in diameter and 30 cm deep. Once again, the cylindrical geometry makes Bessel functions a natural basis set for expanding the standing-wave pictures that are drawn on the surface. Once the Bessel function components are known, the drivers at the edge of the tank can be made to work in unison to excite that pattern.

Neat!

Found via Pink Tentacle.

[tags]bessel functions, quantum corrals, water[/tags]

Posted in Fun, Science | Leave a comment

Design Patterns for Scientific Software

Posted on July 24, 2006 by Dan Gezelter

Class Hierarchy I’ve been reading a really interesting paper out of a group that’s just across campus from me. The paper is called Design Patterns for Generic Object-Oriented Scientific Software and it comes out of the Izaguirre Group.

Design patterns have a long history in the object-oriented software community. The idea originally came from an amazing book on architecture and urban planning (A Pattern Language by Christopher Alexander), but was transformed into a major area of software design by the famous “Gang of Four” book (Design Patterns: Elements of Reusable Object-Oriented Software by Erich Gamma, Richard Helm, Ralph Johnson, and John Vlissides). In this book, they outline some of the fundamental roles various software objects can play (and these are now quite famous: Factory Methods, Singletons, Composites, Iterators, etc.)

I’ve only seen a few people floating ideas for design patterns for scientific software. Cickovski, Matthey, and Izaguirre suggest a few in their paper, and I’ve seen some others suggested as a pattern language for parallel programming. So, to add to the discussion, here are my candidates:

Fundamental Objects
- Particle (e.g. atoms, planets, etc.)
- Mesh (e.g. representations of wavefunctions, continuum fluids, etc.)
Interaction Patterns
- Particle-particle (i.e. the Double Loop)
- Particle-mesh
- Mesh-mesh
- Multi-level Grid
- Multiple Space (i.e. real vs. inverse space interactions)
Propagator Patterns
- Synchronous Propagator
  - Regular Stepping
  - Adaptive Stepping
  - Multiple Stepping
- Asynchronous Propagator
- Event-Driven Propagator
- Markov Chain Propagator
Analysis Patterns
- Ensemble Average
- Correlation Functions
  - Autocorrelation (single property, multiple time)
  - Cross correlation (multiple property, multiple time)
- Overlap-related Analysis Patterns
Linear System Pattern
- Inversion
- Diagonalization
- Singular Value Decomposition
Transformational Patterns
- Spectral
- coordinate
Time-saving Patterns
- Neighbor Lists
- Cutoffs / Switching functions
- Interpolation

This list is very chem-centric. I’m sure I’m leaving out other very important and common object structures from other fields. So, what would you add? If a code library was constructed which implemented the skeletal patterns in C++, would the scientific community use it?

[tags]design patterns, scientific software[/tags]

Posted in Science, Software | 1 Comment

Worm-like chains

Posted on July 24, 2006 by Dan Gezelter

BioCurious has a really great review / research article on wormlike chains and the differences in the force-extension relationships between freely-jointed chains and wormlike chains. It is worth a read!

[tags]biophysics, DNA[/tags]

Posted in Science | Leave a comment

New Software links

Posted on July 23, 2006 by Dan Gezelter

We’ve got two new links today in the software section. iBabel is a Mac front-end to a bunch of cheminformatics tools (i.e. Babel, Jmol, JChemPaint, SMARTS-based substructure searching, etc.). It can be found in our Molecule Viewers and Editors section.

catool is a GPL tool for the analysis of internal combustion engine pressure data. It can be found in the Engineering section.

[tags]Open Source, science, software[/tags]

Posted in Software | Leave a comment

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