Freeware programs

An interesting tool to document some of these parameters and to evaluate the separation is a computer freeware program available from Gas et al. " The PeakMaster software allows prediction of the behavior of BGEs and analytes. This program contains a large database of products with their pKf and mobility. Though some data may be inaccurate, it affords a global view of the separation. Nevertheless, real separation will provide the final answer on the feasibility of a separation. 

Most comprehensive software programs suitable for protein modeling are commercial packages, some of which are listed in Table 15.2. The application of HyperChem in the biomolecular modeling has been described (Chapter 14) and can be extended to the modeling of protein structures. The aspects of protein modeling will be illustrated with two freeware programs and two online servers. 

A freeware program for Windows, implemented in Kalvados, is used with powder diffraction and crystal structure files. It can read structures from GIF and DFT output files and has a function to calculate bond valence sums for the structure. The user can modify or update (by hand) what Rq values you wish to use. It also has an option to optimize structures based on bond valence sums. 

Note that this program is not exaetly freeware, but it is a site lieense at no eost, whieh means (I think) that you ean t package it and sell it to someone who s not hip enough to get it for himself. 

Computation and practical use are further important concerns, and thus the R package chemometrics has been developed, including data sets used in this book as well as implementations of the methods described. Although some programming skills are required, the use of R has advantages because it is freeware and is continuously updated. Thus interested readers can go through the examples in this book and adapt the procedures to their own problems. Feedback is appreciated and it can lead to extension and improvement of the package. 

Rasmol It was one of the first Protein Databank (PDB) compatible viewers available as freeware. Upgrades have now been stopped, but the program is still widely available. Versions exist for both PC and Mac. 

There are several variographic software packages available including freeware versions commensurate with the above demand for proficiency. All of these can perform the necessary data analysis shown above a few sampling consultant programs include more advanced features as well. 

Most of molecular modeling software programs accept the pdb files (struname.pdb). RasMol, which is one of the most widely used molecular graphics freeware, can be downloaded from http //www.umass.edu/microbio/rasmol/... 

There is a variety of freely available software, which enables one to deconvolute a powder diffraction pattern and determine either or all individual intensities, lattice and peak shape function parameters, and observed structure factors of all possible Bragg reflections. Freeware codes include EXPO, FullProf, GSAS, LHPM-Rietica, and others. In addition to free programs, nearly all manufacturers of commercial powder diffractometers offer software for sale either as a package with the sale of the equipment or as stand-alone products. ... 

Many early PBPK modeling efforts were based on the Simusolv software, and support for this seems not readily available at the present time. More recently the ACSL and Berkeley Madonna (University of California, Berkley, CA) have become more widely used. In addition to these computer software packages, Haddad et al. [35] demonstrated the application of a spreadsheet program to support a PBPK model, and Trent University (Peterborough, Ontario, Canada, updated 2003) made available a spreadsheet program to run PBPK models. Further there are several computer-assisted applications, several as freeware, to perform pharmacokinetic analyses and interpret in vitro enzyme kinetic data (see Chapter 3). 

TRACER.EXE TRACER.HLP 7-8 Program to aid in the digitizing of graphs.3 Freeware written by Marcus Karolewski, karolewski alum.mit.edu, 1999. 

Perl interpreters are available for the Macintosh, Windows, and UNIX operating systems and more often than not is made available as freeware. A number of download sites are listed at the end of this chapter. Because Perl program files are usually compressed to speed downloads, Macintosh users will need to use a utility like UnStuffIt to uncompress the package, whereas Windows users will need WinZip or PKZip. Perl should come as part of the standard software installation on most UNIX-based machines. Typing perl -v at the UNIX prompt will indicate whether the program is indeed installed and, if so, the version number that is available on that machine. 

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