Alchem.org

Introduction to PyMOL

Jerome Pansanel — 2010-05-20T13:43:00Z

Documentation. A french tutorial about the PyMOL software is linked to this article. It contains four chapters that detail the usage of PyMOL. The first chapter covers basic usage of PyMOL while later chapters cover intermediate usage like scripting, movies or PyMOL function embedding in Python script. This document is released under the BSD Documentation License.
PyMOL. PyMOL is a molecular visualization system. It's a Free Software created by Warren DeLano. PyMOL has many features, like : (...)

Free Software for Molecular Screening

Jerome Pansanel — 2010-03-19T15:24:05Z

The attached document is an article about Free Software for molecular screening. After a short introduction, it presents software for the following uses:
Chemical library management
Virtual screening
Image processing and analysis
Quantitative data analysis
Study of active compounds
This article is written in French. An English translation will be available soon.

Open Babel and Open Source Database Systems

Jerome Pansanel, Ernst-Georg Schmid — 2008-03-28T12:45:10Z

Introduction. Chemical data can be stored into databases. In the fact, the storage of thousands to millions of compounds in relational database systems, like PostgreSQL, MySQL and Oracle, is frequent. However such systems do not provide functions for handling and converting chemical data. For example, it is not possible to compute the molecular weight of a SMILES string. In order to provide a solution, two complementary projects are under development, Pgchem and Mychem.
Pgchem. (...)

Towards a chemistry-aware desktop: a new Strigi extension

Jerome Pansanel — 2007-05-15T12:11:07Z

Strigi. Strigi is a daemon which uses a very fast and efficient crawler that can index data on your harddrive. Indexing operations are performed without hammering your system, this makes Strigi the fastest and smallest desktop searching program.
Strigi can index different file formats, including the contents of the archive files. A detailed list of the supported file formats is available on this page. Strigi can be run from different OS and window manager. It has been written focusing on (...)

Introduction to the Kalzium software

Jerome Pansanel — 2007-04-21T17:37:18Z

Description. Kalzium is a free software that displays an interactive periodic system of the elements. It's integrated to the K Desktop Environment (KDE). Many informations about each element are available. They can be easily displayed on a graph. The Kalzium software is used worldwide by schools and universities, like the Max-Planck-Institut f�r Kernphysik, the Oxford University and the Sorbonne.
Features. Kalzium has many features:
each element is colored by acidity, physical state, groups, (...)

OptiCat: Optimization and datamining for compound library design

Frederic Clerc — 2006-12-04T11:11:59Z

OptiCat is a platform for building custom metaheuristic algorithms. Opticat is more specially designed for chemists / physicists who are seeking for user-friendly tools for design of experiments and who are neither expert in programming nor in advanced statistics. OptiCat is an Open Source software which can be used according the CeCILL license.
OptiCat is a platform for building custom metaheuristic algorithms.
Using this software, anyone can build its own algorithm easily. Simple drag and (...)

NumPy - Scientific Computing with Python

Jerome Pansanel — 2006-11-20T10:42:38Z

Introduction. NumPy is the fundamental package needed for scientific computing with Python. This package contains:
a powerful N-dimensional array object
sophisticated (broadcasting) functions
basic linear algebra functions
basic Fourier transforms
sophisticated random number capabilities
tools for integrating Fortran code.
a framework to extend the software with C modules
NumPy derives from the old Numeric code base (written by Paul Dubois) and adds the features introduced by (...)

International Free Software Contest

Jerome Pansanel — 2006-06-28T15:03:16Z

International Free Software Contest. The International Free Software Contest, also known as Troph�es du Libre, is a competition that aims to give credit and reward to the work of individuals, companies and intitutions which contribute to development and enhancement of Free and Open Source software all around the world.
Schedule. Here is the schedule for the third edition:
from 9 March 2006 to October 1st 2006: apply !
November 2006: announcement of the nominees
November 2006, the 30th: (...)

Overview of Scientific Linux Distributions

Jerome Pansanel — 2006-05-15T16:15:44Z

Introduction. Most of the GNU/Linux distributions are desktop distribution. Although some distributions (Debian, Gentoo, Ubuntu, ...) are providing many scientific packages, science-oriented distributions have been developped. You will find below the most popular distributions.
Bioknoppix. The Bioknoppix distribution is a customized distribution of Knoppix Linux Live CD. It permits you to have a fully functional Linux OS distribution with open source applications targeted for the molecular (...)

CompLife '06: Computational Life Science Symposium

Jerome Pansanel — 2006-05-10T10:43:57Z

Announcement. The second symposium on Computational Life Science will be held at Cambridge University, 27 - 29 September 2006. This symposium will focus on computational methods for the modelling, analysis and exploration of all aspects of life sciences, ranging from effects on the molecular level to complex interactions networks.
Free Software. As many Free and Open Source software have been released in the last years, a Life Science Free Software Session will be organized. Authors of free (...)