Sources of Modeling Software

For more information, consult the references listed for each software package, as well as overviews of these and other programs by Mangold and Tsang (1991) and Appel and Reilly (1994). 

Centre d lnformatique Ge ologique Ecole des Mines de Paris 35, rue Saint-Honore  

Department of Geological Sciences 1272 University of Oregon Eugene, Oregon 97404-1272 USA mhreedOoregon.uoregon.edu Reed (1982) 

EQ3/EQ6 inquiries Thomas J. Wolery Mail Stop L-219 Lawrence Livermore National Laboratory P.O. Box 808 Livermore, California 94550 USA 

GEOCHEM-PC inquiries Dr. David R. Parker Department of Soil and Environmental Sciences University of California Riverside, California 92521 USA 

---

Approximately 70% of evaluated companies store a dangerous substance classified as toxic or highly toxic. In approximately 25% of evaluated companies, the toxic substances are treated in such an amoimt and in such a physical form (gas, liquefied gas and highly volatile hquid) to be considered as possible threat for human health in the vicinity of the evaluated source of risk. Figure 2 shows the percentage occurrence of the use of individual software and methods in which acute toxicity limits are used. The versions of modeling software were not distinguished in the evaluation, because they were not always stated in risk analysis documents. The most often used software include TEREX (T-Soft 2000), SAVE II, ROZEX (TLP 2001), EFFECTS (TNO 2003), ALOHA (US ERA 2007) and CEI method (AIChE 1994). 

The IMES software is an MS-DOS application capable of running on a network. Model codes and documentation can be downloaded from the CD-ROM to a hard drive. An MS-DOS interface is included to provide easy access to IMES and to the model directories, althougli such is not required to access the files. This third edition provides an HTML Interface for s iewing the model directories and Internet sources of some the models. 

It is essential that, with the use of evidence-based medicine to inform decisions in health care, the processes used in program development be as transparent as possible. Information about the limited evidence and inherent uncertainty should be disclosed and available for scrutiny, even within the software itself. In fact, in an attempt to maximize transparency, some have advocated open source development and publication of interactive software models [49, 50]. Certainly, details of methodologies, sources, and other techniques employed for development of the underlying models must be acknowledged. However, the proprietary nature of many of these programs must be taken into consideration and measures put into place to ensure confidentiality. Requested publication of all NIH-sponsored research online (in PubMed) [51] within a reasonable time frame after journal acceptance will help to ensure that these data are available in the public domain in short order. 

The following is a list, current at the time of publication, of sources of some of the most popular geochemical modeling software programs and packages. Some of the packages are available for download at no cost, whereas others may be licensed for a fee. 

Existing procedures, standards documents, software, and user manuals. When these exist, they should be consulted. But keep in mind that procedures as written often do not reflect the actual operations. User manuals for existing systems are a rich source of information. They act as a key input to reverse-engineering an abstract model of a system and therefore of a business. 

Most crystallographic programs arose in academic labs from the vision of their author and the help of a small number of collaborators. The authors maintain various levels of access to their source code. The open source model is an alternative. According to the Open Source Initiative (www.opensource.org) The basic idea behind open source is very simple When programmers can read, redistribute, and modify the source code for a piece of software, the software evolves. People improve it, people adapt it, people fix bugs. And this can happen at a speed that, if one is used to the slow pace of conventional software development, seems astonishing... ... 

Furthermore, the models have to be reproducible. The model should give the same result when used by different users in different locations. This fact may lead to a preference toward easier models. Depending on the method for QS AR, some steps may be critical for reproducibility. Indeed, some approaches require manual optimization of the tridimensional structure of the chemical, e.g., in the case of tridimensional descriptors. In other cases, stochastic processes are used. Some more complex models done by skilled operators, such as docking, can be critical. Another source of variability is the software version or brand, even for simple bidimensional descriptors. 

The sources of renewable energy are natural processes, and weather plays an important role in nature. Because the operation of complex weather stations and weather-modeling software packages is beyond the scope of this book, the systems described here are often used on solar, ocean, and wind-farm-type power plants. 

The EPA uses QSARs to predict a large number of ecological effects, as well as for environmental fate within the PMN process. The EPA s website (www.epa.gov) provides a valuable source of further information on all these predictive methods, as well as a database and aquatic toxicity values and detailed information on how the models have been validated. Many of the predictive models have been brought together into the EPISUITE software (see Table 19.2 for a listing of the models available). This includes the OPPT s models used for the prediction of physical and chemical properties for new chemical substances. The EPISUITE software is downloadable free of charge (www.epa.gov/oppt/exposure/docs/episuitedl.htm). This provides not only an excellent resource for the development of QSARs, but also a transparent mechanism for the assessment of PMNs. 

An updated, greatly enlarged compendium of software for molecular modeling appears as the Appendix. Programs that run on personal computers, minicomputers, workstations, mainframes, and supercomputers are listed together with some of their features. Telephone numbers and addresses of the vendors and/or developers are provided. To our knowledge, this is the most complete listing of sources of software for computational chemistry anywhere. 

In 1988 the Design Institute for Physical Property Data of the American Institute of Chemical Engineers established Project 881 to develop a Handbook of Polymer Solution Thermodynamics. In the area of polymer solutions, the stated purposes were (1) provide an evaluated depository of data, (2) evaluate and extend current models for polymers in both organic and aqueous, solvents, (3) develop improved models, and (4) provide a standard source of these results in a computer data bank and a how-to handbook with accompanying computer software. During the four years of this project most of these objectives have been met and the results are presented in this Handbook. 

A second smaller source of data on software usage is another database file available from the Chemical Abstracts Service. The file CJWILEY covers the full text of polymer journals (Table 3) published by John Wiley Sons. CJWILEY lists 8775 articles published in the seven-year period 1987—1993. Unfortunately, CJWILEY does not include Wiley s Journal of Computational Chemistry. By comparing findings from CJWILEY to the CJACS results, however, one can ascertain whether there are different patterns for modeling polymers versus modeling molecules in general. 

The third source of information on software usage is even smaller, but highly relevant. It is MMCC Results, which is a new, topical newsletter with abstracts of selected articles on molecular modeling.For the two years 1992 and 1993, there were slightly fewer than 2000 articles covered from a wide... 

---