EasyChem

EasyChem is a program designed to draw chemical molecules, written under Linux and using Gtk+ 2. Focus is on press-quality final drawings, drawing very easily ornaments (non-bonding electron pairs, …) and exporting to EPS/PDF formats with LaTeX fonts (Computer Modern).
Find EasyChem at: http://easychem.sourceforge.net/

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Posted in Molecule Viewers and Editors | Leave a comment

Opium: Pseudopotential generation project

Opium is a pseudopotential generation tool for planewave pseudopotential calculations in condensed matter. At present, it supports generation of pseudopotential formats suitable for CASTEP, ABINIT, PWSCF, Bh, and FHI98md.
Find Opium: Pseudopotential generation project at: http://opium.sourceforge.net/

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nemesis

nemesis is an open source, experimental, C++ finite element code, freely distributed under the terms of the GNU Public License.
Find nemesis at: http://www.nemesis-project.org

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Math::MatrixReal

Math::MatrixReal is a nifty perl module for doing just about anything you could want with an NxN matrix, or vector of real numbers.
Find Math::MatrixReal at: http://leto.net/code/Math-MatrixReal/

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Dear Apple: open the iPhone!

My Dream iPhone CalculatorMy new iPhone is just about the most amazing piece of technology I’ve ever used. There’s just one problem: I hate hate hate the calculator. Apple’s normal desktop calculator on OS X is remarkably functional. It has the standard scientific functions, a programmer’s mode, and best of all, there’s an RPN mode, which is essential for those of us who grew up with HP scientific calculators and therefore can’t figure why one would even want to use a “normal” calculator.

I guess I was expecting Apple to just port the desktop calculator to the iPhone. Instead, we’ve got a visually beautiful, but essentially useless, four function widget. I know it is a visual tribute to Dieter Rams‘s design of 1970’s-era Braun desktop calculators, and I can appreciate simple and elegant design as much as any Apple fanboy. That’s what has me so annoyed; I love the look, but I need sin, cos, yx, sqrt, log, ex, DRG to RAD, and all the other functions of a scientific calculator.

I know there are a couple of good web-based scientific calculators designed for the iPhone: Belfry’s scicalc is one, iPhav has created MiniCalc, there’s a fake HP-35, and a pared-down barebones version, but as great as those are, the lag to load up a web app when using EDGE is just too long. Apple, if you want to make us nerds truly happy, keep your tribute to Dieter Rams when the iPhone is upright, and when someone rotates their phone while in the calculator, have it switch automagically to a HP-15C emulator. (The 15C had a lovely brushed metal finish, and your own engineers can tell you that the 15C was the best calculator ever made.)

There’s also news that the iPhone calculator app also has a relatively serious interface bug.

More importantly, my problems with the calculator wouldn’t be a big deal if third-party applications could run on the iPhone. (Legally, that is. Without jailbreak and iPhoneInterface, and plist editing and assembling a toolchain.) I’d happily start writing a replacement calculator myself if the SDK were available. So Apple, while you guys have done some truly astonishing engineering, can I humbly request that you open the iPhone to third party developers? Please?

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Posted in Uncategorized | 9 Comments

AGM Build

A molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. Features: * Geometry editing * Lattice building * Building of chain molecules (for example proteins) * Chains with predetermined conformations * Charges and atom types according to selected Force Field
Find AGM Build at: http://www.agilemolecule.com/Products.html

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jMATLAB

jMATLAB is an Eclispe based interpreter interface to linear algebra libraries. It is based on the notion of MATLAB. It provides MATLAB like scripting language for quick programming. It also provides ability to write toolboxes using java based plug-ins. Interface to GNUPLOT provides access to powerful plotting capabilities.
Find jMATLAB at: http://sourceforge.net/projects/jmatlab/

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Cool new software

Scientific Software A whole bunch of new software to highlight today:

In our Engineering section, we have two new packages: OOFEM is an object oriented, parallel, multiphysics finite element code system for solving mechanical, transport and fluid mechanics problems, and ASCEND is a generalized modelling environment for engineering and science problems. It offers: an object-oriented model description language for describing your system, an interactive user interface that allows you to solve your model and explore the effect of changing the model parameters, and a scripting environment that allows you to automate your more complex simulation problems.

Our Molecule Viewers and Editors section sees the addition of Avogadro, a new molecular editor built on OpenBabel that looks like it will be great (although I can’t find a download link to try it out).

I’m really excited to see CP2K show up in our Theoretical & Computational Chemistry section. CP2K is performs atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

PhyloSort is a neat Java code that sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units. Look for it in our Bioinformatics section.

And the newest link is to massXpert, a follow on package by the author of polyXmass. massXpert simulates and analyzes mass spectrometry data obtained on linear (bio-)polymers. Both massXpert and polyXmass can be found in our Analytical Chemistry section.

Check them out and keep those suggestions coming!

[tags]open source, science, software[/tags]

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Posted in Science, Software | 2 Comments

massXpert

This massXpert package aims to give mass spectrometrists a software package to simulate and analyze data obtained on linear (bio-)polymers. Users are empowered to define their polymer chemistry at a rather fine detail level. The new polymer chemistry definitions are then used by polymer sequences that are created to make the simulations.
Find massXpert at: http://www.massxpert.org

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Heat Capacity of Water

Heating a Water Balloon It is no secret to my students, family and friends that I’m now completely obsessed by the odd properties of water, including the anomalously high heat capacity. Here’s a neat parlor trick involving this water anomaly that is masterfully explained by Robert Krampf in one of his many great Science Experiment videos: Heating a Balloon.

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Posted in education, Fun, Science | 2 Comments