SimThyr, a numerical simulator of thyrotropic feedback control for education and research

Posted on February 11, 2013 by Dan Gezelter

SimThyr is a simulation program for the pituitary thyroid feedback control that is based on a parametrically isomorphic model of the overall system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.
Find SimThyr, a numerical simulator of thyrotropic feedback control for education and research at: http://simthyr.sourceforge.net

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Posted in Medical Sciences, Physiology | Leave a comment

The Up-Goer Five Research Challenge

Posted on January 17, 2013 by Dan Gezelter

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: Explain your research using only the 1000 most common English words. Here’s a tool to keep you honest: http://splasho.nfshost.com/upgoer5/  The idea was inspired by Randall Munroe’s wonderful Up Goer Five explanation of the Saturn V moon rocket.

And here’s my attempt:

The things we use every day are made of very tiny bits. When we put lots of those bits together we get matter. Matter changes how it acts when it gets hot or cold, or when you press on it. We want to know what happens when you get some of the matter hot. Do the bits of hot matter move to where the cold matter is? Does the hot matter touch the cold matter and make the cold matter hot? We use a computer to make pretend bits of matter. We use the computer to study how the hot matter makes cold matter hot.

The task is much harder than you think.   Here’s a collection curated by Patrick Donohue (a PhD candidate in lunar petrology right here at Notre Dame):  Common words, uncommon jobs

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Posted in education, Fun, Science | 2 Comments

DuMuX

Posted on January 10, 2013 by Dan Gezelter

DuMuX, DUNE for multi-{phase, component, scale, physics, …} flow and transport in porous media, is a free and open-source simulator for flow and transport processes in porous media. It is based on the Distributed and Unified Numerics Environment DUNE, dune-project.org. Its main intention is to provide a sustainable and consistent framework for the implementation and application of model concepts, constitutive relations, discretizations, and solvers. It has been successfully applied to CO2 storage scenarios, environmental remediation problems, transport of therapeutic agents through biological tissue, and subsurface-atmosphere coupling. DuMuX is part of the OPM (Open Porous Media) initiative, opm-project.org.
Find DuMuX at: http://dumux.org

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mMass – Open Source Mass Spectrometry Tool

Posted on November 24, 2012 by Dan Gezelter

mMass is designed to be feature rich, yet still easy to use. Stay focused on your data interpretation, not on the software. *Supports multiple formats (mZML, mzXML, mzData, MGF, ASCII and copy-Past from clipboard) *Various data processing tools avalaible (Proteomics, calibration, peak picking deconvolution, in-silico digestion and many more) *Platform Independent: No matter what operating system you are using, mMass works on MS Windows, Apple’s Mac OS X and Linux platforms as well. Multiple Formats: mMass supports all of the modern open formats like mzML, mzXML, mzData, MGF, ASCII and even copy n’ paste from clipboard.
Find mMass – Open Source Mass Spectrometry Tool at: http://www.mmass.org/

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Posted in Analytical | Leave a comment

OpenChrom

Posted on November 24, 2012 by Dan Gezelter

OpenChrom is an open source software for chromatography and mass spectrometry based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF. Moreover, it offers a nice graphical user interface and is available for various operating systems, e.g. Windows, Linux, Solaris and Mac OS X. A basis set of methods to detect baselines, peaks and to integrate peaks in a chromatogram are implemented. Preprocessing steps, e.g. to remove certain mass fragments (m/z) such as nitrogen (28) or water (18), are supported by applying filter on the chromatogram or mass spectrum. Extensions are welcome, as OpenChrom is open source and uses a flexible approach, which allows others to implement their own methods, algorithms, filters, detectors or integrators. Therefore, OpenChrom shall be an efficiently system to process chromatographic and mass spectrometric data using an extensible and flexible plugin approach. OpenChrom is distributed under the Eclipse Public License 1.0 (EPL). Third-party libraries are separated into single bundles and are released under various OSI compatible licenses.
Find OpenChrom at: http://www.openchrom.net/main/content/index.php

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

Posted on November 16, 2012 by Dan Gezelter


OvertureThis 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.

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SASSIE – Create atomistic models from Small Angle scattering data

Posted on November 8, 2012 by Dan Gezelter

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.

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Posted in Science, Software | 1 Comment

Jmol goes JavaScript

Posted on November 7, 2012 by Dan Gezelter

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.

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Posted in open science, Science, Software | Leave a comment

Octopus – A cool open source TDDFT code

Posted on November 6, 2012 by Dan Gezelter

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.

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Posted in open science, Science, Software | 3 Comments

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

Posted on November 5, 2012 by Dan Gezelter

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?

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Posted in Policy, Software | Leave a comment