### Categories

- Conferences (3)
- education (10)
- Fun (58)
- Meta (12)
- Open Access (10)
- Open Data (13)
- open science (34)
- Policy (49)
- Science (135)
- Software (634)
- Acoustics (3)
- Engineering (1)
- Physical (1)
- Speech Communication (2)
- Structural (1)

- Anthropology and Archaeology (3)
- Artificial Life (9)
- Astronomy (21)
- Aviation and Aeronautics (2)
- Chemistry (131)
- Analytical (4)
- Atmospheric (1)
- Biochemistry (6)
- Biophysical (3)
- Chemical Information (3)
- Crystallography (2)
- Electrochemistry (1)
- Molecule Viewers and Editors (39)
- Organic (2)
- Synthesis (1)

- Periodic Tables (3)
- Physical (1)
- Kinetics (1)

- Polymers (1)
- Spectroscopy (9)
- NMR (5)

- Surfaces (1)
- Theoretical and Computational (45)

- Cognitive Science (3)
- Neural Networks (2)

- Complex Systems (2)
- Computer Science (22)
- Algorithms And Computational Theory (2)
- Artificial Intelligence (4)
- Data Communication (4)
- Information Retrieval (1)
- Knowledge Discovery and Data Mining (3)
- Languages (1)
- Fortran (1)

- Measurement and Evaluation (1)
- Simulation and Modeling (2)
- Software Engineering (2)
- Symbolic and Algebraic Manipulation (1)

- Earth Sciences (19)
- Geology and Geophysics (5)
- Hydrology (5)
- Meteorology (1)
- Oceanography (3)

- Energy (3)
- Engineering (24)
- Forensics (2)
- Geography (12)
- Information Technology (1)
- Life Sciences (60)
- Bioinformatics (34)
- Ecology (5)
- Evolution and Population Genetics (3)
- Statistical (1)
- Theoretical (1)

- Genetics (9)
- Population (1)

- Medical Sciences (7)
- Physiology (2)

- Linguistics (2)
- Mathematics (108)
- Abstract Algebra (9)
- Combinatorics (1)
- Differential Equations (17)
- Fluid Dynamics (7)
- Ordinary (3)
- Partial (7)

- Dynamical Systems (4)
- Education (1)
- Geometry (3)
- Linear Algebra (26)
- Number Theory (6)
- Numerical Methods (5)
- Optimization (12)
- Probability (1)
- Set Theory (1)
- Statistics (8)
- Topology (1)

- Measurements and Units (3)
- Nanotechnology (2)
- Physics (30)
- Astrophysics (1)
- Atomic and Molecular (1)
- Computational (2)
- Condensed Matter (4)
- Dynamics (2)
- Fluid (1)

- High Energy (4)
- Magnetism (1)
- Materials (1)
- Nuclear (4)
- Optics (5)
- Plasma (1)

- Required Reading and Other Sites (25)
- Space (3)
- Tools (56)
- Numerical Libraries (8)
- Random Number Generators (2)
- Visualization (18)
- 2D Plotting (8)
- 3D Plotting (2)

- Acoustics (3)
- Uncategorized (4)

# Category Archives: Science

## Not a kickstarter for science, a prize clearinghouse

Yesterday’s post on the reversible random number generators received some interesting reactions from my colleagues. They were uniformly impressed with the solution to what everyone thought was a hard problem, but surprisingly, most of the scientists I talked to were … Continue reading

## Reversible Random Number Generators

This news comes by way of John Parkhill, my new colleague here at Notre Dame. William G. Hoover (of the Nosé-Hoover Thermostat) and Carol G. Hoover issued a $500 challenge on arXiv to generate a time-reversible random number generator. The … Continue reading

Posted in Science, Software
Tagged langevin equation, pseudo random number, random number generator, time reversibility
3 Comments

## Relax – Molecular dynamics by NMR data analysis

Edward d’Auvergne pointed out the relax program, which looks like a useful way to connect experimental NMR spectra with molecular dynamics simulations. relax is designed for the study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other … Continue reading

Posted in open science, Science, Software
Tagged molecular dynamics simulations, nmr data analysis
Leave a comment

## The Tyranny of Pi day

March 14th is -day in the US (and perhaps day in Europe). The idea of a day devoted to celebrating an important irrational number is wonderful — I’d love to see schools celebrate e-day as well, but February 71st isn’t on … Continue reading

Posted in education, Science
Leave a comment

## Fantastic news on the Open Access front

The White House just posted a new policy memorandum in response to the Open Access petition: Expanding Public Access to the Results of Federally Funded Research. This is great news for Open Science!

Posted in Open Access, open science, Policy, Science
Leave a comment

## Do.abl.es

Do you want to know how to measure DNA contour lengths using ImageJ? Perhaps you want to stain a C. Elegans embryo for imaging? Or possibly, you might want to test whether or not you have gotten an immune response using ELISA? Martin … Continue reading

Posted in Open Access, open science, Science
Tagged biology experiments, c elegans, open source, open source software, protocols, Science, Software
1 Comment

## The Up-Goer Five Research Challenge

I thought this was silly at first, but after struggling to do it for my own research, I now think it can be a profound exercise that scientists should attempt before writing their NSF broader impact statements. Here’s the challenge: … Continue reading

Posted in education, Fun, Science
2 Comments

## Overture – A C++ toolkit for Solving PDEs in Complex Geometries

This looks useful! The partial differential equations (PDEs) we solve in my lab are the equations of motion for atoms in molecular dynamics. These are relatively easy to integrate numerically. Lots of labs work with harder PDE problems (like … Continue reading

## SASSIE – Create atomistic models from Small Angle scattering data

Here’s a neat bit of “bridge” or “glue” software for today – SASSIE is a python-based suite for creating atomistic models of molecular systems in order to compare those models directly to data from small-angle X-ray scattering (SAXS) and small-angle … Continue reading

## Jmol goes JavaScript

About 10 years ago, I turned the Jmol project over to a series of fantastic lead developers (Jmol programmers regenerate in different bodies just like Doctor Who does). Since then, the aspect of the new work on Jmol that has … Continue reading

Posted in open science, Science, Software
Leave a comment