[R-pkgs] New package: CHNOSZ
jmdick at asu.edu
Sat Apr 25 01:33:22 CEST 2009
Dear R users,
A new package, CHNOSZ (version 0.8), is available on CRAN.
CHNOSZ is a package for thermodynamic calculations and analysis.
Functions are available for calculating the standard Gibbs energies and
other thermodynamic properties, and chemical affinities, of reactions
between species contained in the thermodynamic database. The database
includes standard thermodynamic properties and equations of state
parameters for a variety of minerals and inorganic and organic aqueous
species. The relative abundances of species in equilibrium can be drawn
on activity diagrams as a function of temperature, pressure and/or
chemical activities of basis species.
The documentation includes many examples taken from the literature, as
well as calculations of the metastability relationships in systems of
proteins. The protein examples were developed to explore the chemical
features of thermophilic adaptation, subcellular localization, proteomic
stress response, and microbial diversity. Calculation of the standard
Gibbs energies of proteins is based on a published group additivity
algorithm and is further supported in this package by the inclusion of
data files for the amino acid compositions of selected proteins and of
proteins in yeast and E. coli.
A paper describing some applications of the package can be found in
The project website highlights many of the example calculations. There
is also an Rpad script available for download that presents basic
functionality of the program in a browser interface. The website is
This release offers major enhancements over previous versions available
on the project website. Chemical affinities of formation reactions can
be calculated as a function of more than two variables, parallel
processing of some computations is optionally carried out using the
mclapply function of the multicore package, amino acid compositions of
proteins can be read from FASTA files, protein stress response and
richness calculations were added to the examples, and a mass transfer
algorithm for reaction path modeling has been introduced.
Feedback about the package is appreciated.
Jeffrey M. Dick
NSF Postdoctoral Fellow
School of Earth and Space Exploration
Arizona State University
Tempe, AZ 85287-1404
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