Relax – Molecular dynamics by NMR data analysis

RelaxEdward 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 biomolecules through the analysis of experimental NMR data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model or ensemble analysis and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, and the investigation of stereochemistry.

Do.abl.es

Do.abl.es

Do.abl.es

Do you want to know you can 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 Fitzpatrick sends word of a cool collection of open access scientific protocols called Do.abl.es.  For the uninitiated, protocols are the recipes that scientists use to carry out experiments in a reproducible way.  The list of protocols posted to Do.abl.es to date has a number of interesting and important biochemistry and biology experiments.

There’s also a neat companion site called Install.abl.es which concentrates on many of the same things we do – the use of open source software in the sciences.

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


Overture
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 the response of metallic nanostructures to electromagnetic fields) that have difficult boundary conditions in complex geometries.   Overture is an object-oriented code framework for solving partial differential equations (PDEs). It provides a portable, flexible software development environment for applications that involve the simulation of physical processes in complex moving geometry . It is implemented as a collection of C++ libraries that enable the use of finite difference and finite volume methods at a level that hides the details of the associated data structures. Overture is designed for solving problems on a structured grid or a collection of structured grids. In particular, it can use curvilinear grids, adaptive mesh refinement, and the composite overlapping grid method to represent problems involving complex domains with moving components. There are also utilities for   building grids on CAD geometries and for building hybrid grids that can be used with applications that use unstructured grids.

SASSIE – Create atomistic models from Small Angle scattering data

SASSIEHere’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 neutron scattering (SANS) experiments.  SASSIE is the work of Joseph Curtis and Susan Krueger from the NIST Center for Neutron Research.  You can use SASSIE to generate and manipulate large numbers of structures and to calculate the SANS, SAXS, and neutron reflectivity profiles from atomistic structures that result from molecular dynamics (MD) or Monte Carlo (MC) simulations.

“Bridge” or “glue” software increases the functionality of other software by making the data formats from one package usable as input to another.  In SASSIE’s case, the molecular dynamics package being used is NAMD (from the Theoretical and Computational Biophysics Group at UIUC), along with scattering calculators Cryson and Crysol.  The Hydropro package is used for calculating hydrodynamic properties.  (Note that Cryson, Crysol, and Hydropro are not open source programs.  Boo.)

SASSIE isn’t quite a full-bore open source project yet.  I was able to download the source here (159 MB download), but there’s a registration barrier in the way on the SASSIE trac site.  I’m not sure why the small-angle scattering community locks up their code like this.  It discourages re-use, and doesn’t provide any extra benefit to the authors of the code or the home institution.  Likewise, Cryson and Crysol both appear to have an academic and research license (again, not open source).

SASSIE looks interesting.  I’m not in the small-angle scattering community, but I really like the bridge between atomistic simulation and experiment, and the code looks like it has some very useful pieces that could be reused in interesting ways.

Jmol goes JavaScript

JmolAbout 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 most delighted me is the Jmol applet, which allows the program to be embedded in web pages.   The Jmol applet transformed Jmol from a niche application into a way of broadly disseminating and interacting with chemical structures.  It has become the de facto standard for showing protein structures at the RCSB Protein Data Bank, as well as in a number of chemistry journals.

The problem with Java applets is that many new tablet and phone web browsers don’t support them (and it looks like Java applets are being slowly disabled on Mac browsers as well).  Java has always been an elegant but relatively heavy-weight solution to dynamic content, but I think its time as a widely-used language for web content is coming to a close.

So, how do you interact with chemical structures without Java or Flash?

The Jmol team has been hard at work converting the Jmol source so that the same source code that produces the Jmol applet can also be run through Java2Script to create the entire Jmol applet in JavaScript.   The new beast is called JSmol and has almost all of the functionality of Jmol itself (file IO, scripting, etc.)    Bob Hanson’s demo pages give a taste of this work.

This is amazing work.  The same Java code is compiled to create the Jmol applet, a WebGL version of JSmol, and the HTML5 version of JSmol that can run on my phone. Almost all of Jmol is there – the ability to display orbitals, crystals, and van der Waals surfaces.  Some menu interaction is still missing, but if the goal is to display and interact with a chemically meaningful structure on a web page,  JSmol looks like a great solution.

The credit for this work largely goes to a number of people:  The GLmol interface was written by Takanori Nakane.  Java2Script was written by Zhou Renjian.  The Jmol code conversion to JavaScript was done by the current Doctor Who,  Bob Hanson.

Octopus – A cool open source TDDFT code

OctopusI just found out about Octopus, a quantum mechanics package that does time-dependent density functional theory (TDDFT) calculations using pseudopotential approximations.

It works in parallel using MPI and OpenMP and scales to tens of thousands of processors. It also has support for graphical processing units (GPUs) through OpenCL.

The Octopus code can be browsed freely, and it has been released under the GPL.

Particularly cool is the ability to use the time dependent electron localization function (TDELF) to look at orbitals dynamically during a chemical reaction.

Why aren’t voting machines required to be Open Source?

If ever there was a need for the transparency that open source software brings it is in the realm of voting machine technology.    This story makes that point crystal clear.   There may or may not be shenanigans going on in Ohio.  The point is that we have no way of knowing what the patches on those Ohio voting machines actually do, and no faith in the code reading, debugging, and auditing ability of elected officials.   If we want to be confident in the workings of our democracy, closed-source voting machines should be banned.

For that matter, why aren’t voting systems required to leave a physical paper trail so that we can check up on the tabulating algorithms?

Open source fonts

Adobe released an open source font today called Source Sans Pro.   It looks super clean and nearly perfect for user interfaces.  Right now it comes in six weights, but a monowidth version is coming soon.  (I’m most excited about this, as the sample of the monowidth font on the Adobe blog post is gorgeous).    Adobe did this right – they have made all source files used in the production of the fonts available for download at SourceForge.

Maybe we’ll get more scientists using Source Sans Pro instead of releasing their important results in Comic Sans.

Data visualization and Digital Research tools

Two new collections of tools that may be of interest to the OpenScience community.  Not everything on these lists is Open Source, but many of the visualization and research tools look to be very useful.   Hat tip to Eric Lease Morgan (@ericleasemorgan) for pointing these out:

  1. http://selection.datavisualization.ch – A collection of tools that the people behind Datavisualization.ch, work with on a daily basis and recommend. This is not a list of everything out there, but instead a thoughtfully curated selection of our favourite tools that will make your life easier creating meaningful and beautiful data visualizations.
  2. Bamboo DiRT is a tool, service, and collection registry of digital research tools for scholarly use. Developed by Project Bamboo, Bamboo DiRT makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mind mapping software.

PLoS ONE News and Blog Round-Up

Researchers find a possible cure for the common cold and more – in this week’s media digest.

Human Pathogen Shown to Cause Disease in the Threatened Eklhorn Coral Acropora palmata was covered by The NewsHour, The New York Times, NPR, and CNN.

CNET, Hindustan Times, and Okezone covered Automatic Prediction of Facial Trait Judgments: Appearance vs. Structural Models.

The paper, Predator Cat Odors Activate Sexual Arousal Pathways in Brains of Toxoplasma gondii Infected Rats, received coverage from The New York Times, Scientific American, TIME’s Healthland, and The Loom.

Broad-Spectrum Antiviral Therapeutics received media coverage from Voice of America, LA Times, and Forbes.

Large Recovery of Fish Biomass in a No-Take Marine Reserve was covered by National Geographic (nice slideshow too), The Christian Science Monitor, Nature News, and KGTV San Diego. The image above, is taken from Figure 4 of this manuscript.

80 Beats covered the article, Artificial Skin – Culturing of Different Skin Cell Lines for Generating an Artificial Skin Substitute on Cross-Weaved Spider Silk Fibres. So did Treehugger.

The article entitled, Scientists Want More Children received media coverage from The Wall Street Journal, TIME’s Ecocentric, Science Career Blog, and Inside Higher Ed.

Elevated Non-Esterified Fatty Acid Concentrations during Bovine Oocyte Maturation Compromise Early Embryo Physiology was covered by Reuters, The Guardian, and The Press Association.