This is where I play around with various packages. Most of them are in some way related to the needs of a theoretical biophysics research group.
Feedback and bug reports are welcome!

ANN is a library written in C++, which supports data structures and
algorithms for both exact and approximate nearest neighbor searching
in arbitrarily high dimensions.

In the nearest neighbor problem a set of data points in d-dimensional
space is given. These points are preprocessed into a data structure,
so that given any query point q, the nearest or generally k nearest
points of P to q can be reported efficiently. The distance between two
points can be defined in many ways. ANN assumes that distances are
measured using any class of distance functions called Minkowski
metrics. These include the well known Euclidean distance, Manhattan
distance, and max distance.

Based on our own experience, ANN performs quite efficiently for point
sets ranging in size from thousands to hundreds of thousands, and in
dimensions as high as 20. (For applications in significantly higher
dimensions, the results are rather spotty, but you might try it
anyway.)

The library implements a number of different data structures, based on
kd-trees and box-decomposition trees, and employs a couple of
different search strategies.

The library also comes with test programs for measuring the quality of
performance of ANN on any particular data sets, as well as programs
for visualizing the structure of the geometric data structures.

Authors:
---------
David M. Mount
Sunil Arya

CCP4 exists to produce and support a world-leading, integrated suite
of programs that allows researchers to determine macromolecular
structures by X-ray crystallography, and other biophysical techniques.
CCP4 aims to develop and support the development of cutting edge
approaches to experimental determination and analysis of protein
structure, and integrate these approaches into the suite. CCP4 is a
community based resource that supports the widest possible researcher
community, embracing academic, not for profit, and for profit
research. CCP4 aims to play a key role in the education and training
of scientists in experimental structural biology. It encourages the
wide dissemination of new ideas, techniques and practice.

This package contains an LGPL-licensed subset of the full CCP4 suite.

There are currently two major pressures on crystallographic computing:

* Increased automation to increase throughput in line with genomics applications.

* Increased data complexity, as data from more sources is
combined and carried through the whole calculation to solve
more difficult problems.

The Clipper project is an initiative to address these
pressures.

The aim of the project is to produce a set of object-oriented
libraries for the organisation of crystallographic data and
the performance of crystallographic computation. The libraries
are designed as a framework for new crystallographic software,
which will allow the full power of modern programming
techniques to be exploited by the developer. This will lead to
greater functionality from simpler code which will be easier
to develop and debug.

Author:
Kevin Cowtan

Coot is for macromolecular model building, model completion and
validation, particularly suitable for protein modelling using X-ray
data.

Coot displays maps and models and allows model manipulations such as
idealization, real space refinement, manual rotation/translation,
rigid-body fitting, ligand search, solvation, mutations, rotamers,
Ramachandran plots, skeletonization...
Author: Paul Emsley

GROMACS is a versatile and extremely well optimized package to perform
molecular dynamics computer simulations and subsequent trajectory
analysis. It is developed for biomolecules like proteins, but the
extremely high performance means it is used also in several other
field like polymer chemistry and solid state physics. This version has
the dynamic libs and executables; to hack new utility programs you
also need the headers and static libs in gromacs-dev.

This version has been modified for use with pymacs.

The old version of the Qt Assistant has been removed from Qt 4.7.
This package brings it back for those application that still
depend on it.

MEAD is a set of software objects for the purpose of modeling the
electrostatics of molecules using a semi-macroscopic picture in which
the solvent and the molecular interior have different dielectric
constants, the boundary between the different dielectric regions is
dependent on the detailed atomic structure of the molecule, and the
electrostatic potential is determined by the Poisson-Boltzmann
equation. This version of MEAD includes modeling of a membrane as a
low dielectric slab, possibly with a water-filled channel through a
protein in the membrane.

MEAD is written in C++, which is a significant departure from most
molecular software, which is more commonly written in Fortran or
(recently) C. My purpose in choosing C++ was to explore the
object-oriented programming style that C++ facilitates and to make a
software system that other people could borrow pieces from and make
extensions to in a convenient way.

MEAD is free software. You can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation; either version 1, or (at your option) any later
version. For more details, see the README, INSTALLATION and COPYING
files inside the distribution. If you use MEAD in a scientific
publication, please cite the papers, Bashford92 and ISCOPE97.

Author:
---------
Donald Bashford
don.bashford@stjude.org

Hartwell Center
Saint Jude Children's Research Hospital
Memphis, TN

A library for storage and manipulation of macromolecular models.

Author: Eugene Krissinel

Pmw is a toolkit for building high-level compound widgets in Python
using the Tkinter module.

It consists of a set of base classes and a library of flexible and
extensible megawidgets built on this foundation. These megawidgets
include notebooks, comboboxes, selection widgets, paned widgets,
scrolled widgets and dialog windows.

Authors:
--------
Greg McFarlane

TODO: Give a detailed description.

PyMOL is a molecular graphics system targetted at medium to large
biomolecules like proteins. It can generate high-quality
publication-ready molecular graphics images and animations.

Features include:

* Visualization of molecules, molecular trajectories and surfaces
of crystallography data or orbitals
* Molecular builder and sculptor
* Internal raytracer and movie generator
* Fully extensible and scriptable via a python interface

File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile,
ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

Authors:
--------
Warren L. DeLano

This plugin provides tConcoord support from within PyMol.

Author: Daniel Seeliger

A Python module for estimation of entropy and information theoretic
quantities using cutting edge bias correction methods.

If you use results of this software in any publication, please cite:

Ince, R. A. A., Petersen, R. S., Swan, D. C., Panzeri, S., 2009
"Python for Information Theoretic Analysis of Neural Data",
Frontiers in Neuroinformatics (Under Review)

QTeXEngine was written as an add-on to QtiPlot, in order to enable the
export of 2D plots to TeX. All drawing capabilities of the QPainter
class used in QtiPlot are supported by QTeXEngine.
QTeXEngine can generate TeX code using either Pgf or TikZ syntax.

Authors:
--------
Ion Vasilief

Scientists often need to use data analysis and plotting software. The
purpose of this project is to develop an open source platform
independent alternative to proprietary scientific software like
Origin, SigmaPlot, Regressi or Igor Pro. QtiPlot can be successfully
used for teaching as well as for complex data analysis and
visualisation and is being used in companies, high schools,
universities and reseach institutes all over the world.
Author:
--------
Ion Vasilief

Wordom is a (simple) command line utility conceived to spare the user
some time in manipulating and converting dcd, xtc, pdb, crd and xyz
files. Wordom is also a versatile program for a broad range of types
of analysis of molecular dynamics trajectories. Original tools in
Wordom include a module for the calculation of order parameters to
monitor polypeptide aggregation and a procedure to evaluate
significance of sampling for principal component analysis. As a plus,
it's easy to use in shell scripts. Due to its simplicity, it is very
easy and straightforward to add your own analysis module. Basically,
all you have to do is write the algorithm. The data are made available
by the existing wordom i/o modules.

Authors:
M. Seeber, M. Cecchini, F. Rao, G. Settanni and A. Caflisch;
Wordom: a program for efficient analysis of molecular dynamics
simulations;
Bioinformatics, 2007, 23(19):2625-2627

DrawChem is a two-dimensional molecule drawing program for Unix
operating systems. It is similar in functionality to other molecule
drawing programs such as ChemDraw (TM, CambridgeSoft). It can read
and write MDL Molfiles and CML files to allow sharing between
XDrawChem and other chemistry applications.

Author:
-------
Mostly written by Bryan Herger, bherger@users.sourceforge.net

CCP4 exists to produce and support a world-leading, integrated suite
of programs that allows researchers to determine macromolecular
structures by X-ray crystallography, and other biophysical techniques.
CCP4 aims to develop and support the development of cutting edge
approaches to experimental determination and analysis of protein
structure, and integrate these approaches into the suite. CCP4 is a
community based resource that supports the widest possible researcher
community, embracing academic, not for profit, and for profit
research. CCP4 aims to play a key role in the education and training
of scientists in experimental structural biology. It encourages the
wide dissemination of new ideas, techniques and practice.

This package contains an LGPL-licensed subset of the full CCP4 suite.

GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification.

Nagios is a program that will monitor hosts and services on your
network. It has the ability to email or page you when a problem arises
and when a problem is resolved. Nagios is written in C and is designed
to run under Linux (and some other *NIX variants) as a background
process, intermittently running checks on various services that you
specify.

The actual service checks are performed by separate "plugin" programs
which return the status of the checks to Nagios. The plugins are
available at http://nagios-plugins.org/.

This package provides core programs for Nagios. The web interface,
documentation, and development files are built as separate packages.