Anonymous FTP

While serious research of the behavior of CA systems demands the use of dedicated hardware, the often high cost of such hardware sometimes prevents its acquisition, particularly by young researchers and graduate students just entering this field of study. It is therefore important to realize that there are many excellent software-only solutions that can often be used very effectively for research. While the list provided below is by no means exhaustive, it gives some idea of the kind of packages that are currently available either commercially or via anonymous ftp over the Internet. 

Cellsim s universe consists of a 512 x 512 array. The program itself is completely menu-driven and includes these features (1) 256-state computed-function rules, in addition to lookup-tables, on both the Sun and CM (2) creation of look-up tables using Langton s lambda parameter (see section 3.2) (3) the ability to save images in Sun raster format and (4) the ability to generate lookup tables with standalone C code. Cellsim can be obtained via anonymous ftp on the Internet to think.com. 

Chemical Physics Preprint Database. This database [81] is a fully automated electronic archive and distribution server intended to provide a means for rapid and efficient preprint distribution within the international theoretical chemical physics community. A preprint is a copy of a paper that has been submitted for publication. This database has been designed to be a useful and freely available tool for education and research. It allows investigators to submit and retrieve electronic copies of preprints via the Internet. Access for retrieval and listing of papers in the database is possible through WWW servers, anonymous ftp, or e-mail. Currently research papers are submitted to the databases via e-mail. This project is a joint effort by the Department of Chemistry at Brown University and the Theoretical Chemistry and Molecular Physics Group at the Los Alamos National Laboratory. The homepage of Chemical Physics Preprint Database is http // www.chem.brown.edu/chem-ph.html. (For a more... 

JPL Publication 97-4, Chemical Kinetics and Photochemical Data for Use in Stratospheric Modeling, Evaluation Number 12, by W. B. DeMore et al., January 15, 1997. Files may be downloaded from http // remus.jpl.nasa.gov/jpl97/ or may be copied via anonymous FTP from the Internet host remus.jpl.nasa.gov under /jmb/jpl97. 

Sarle, W.S. In Proceedings of the Nineteenth Annual SAS Users Group International Conference (1994) Cary, NC. Available as /pub/sugil9/neural/neurall.ps via anonymous ftp from ftp.sas.com... 

It can be seen from these simple examples that computing the P-polynomial of any complicated oriented link will be quite cumbersome. However, there are a number of excellent computer programs which will compute all of the link polynomials for any oriented link which can be drawn with up to about 50 crossings (for example, the program KNOTTHEORY by COMPUTER written by M. Ochiai, and available through anonymous ftp [7]). 

M. Ochiai, Knot Theory by Computer, version 3.60, info available by anonymous FTP at ttftp.ics.nara-wu.ac.jp). 

The Insitute for Genomic Research (TIGR) provides a collection of curated databases containing DNA and protein sequences, gene expressions, cellular roles, protein families, and taxonomic data for microbes, plants, and humans. Anonymous FTP access to sequence data is also provided. 

The EMBL in Heidelberg provides a multitude of services that can be hclprful Ah the molecular modeler. DSSF, HSSFt FSSP, FDBFINDER, PDBREPORT, and PDB SELECT are derived protein databases. They are based on data from the Protein Data Bank of 3D structures and the Swissprot database of LD protein sequences. The data and related software can be obtained vis anonymous FTP or, mote easily these days, via the WWW. 

R. F. Smith and T. F. Smith, Protein Eng. 5, 35 (1992). This UNIX-based package is available from the authors, or by anonymous ftp from mbcrr.harvard.edu (in subdirectory MBCRR-Package). 

R. J. Harrison, Int. J. Quantum Chem., 40, 847 (1991). Portable Tools and Applications for Parallel Computers. TCGMSG is available by anonymous ftp from ftp.tcg.anl.gov or by sending electronic mail to rj harrison pnl.gov. 

R. A. Kendall, unpublished work, 1993. The source code for the Hartree-Fock modified Amdahl s law application is available from anonymous ftp at ftp.pnl.gov. It may be necessary to send electronic mail to ftpadmin pnl.gov to get access from your site. 

A. Beguelin, J. Dongarra, A. Geist, R. Manchek, and V. Sunderam, Oak Ridge National Laboratory Technical Report, TM-11826, 1991. A User s Guide to PVM Parallel Virtual Machine. PVM is available by electronic mail and anonymous ftp from netlib ornl.gov. 

User s Guide to the P4 Parallel Programming System. P4 is set of portable parallel programming routines being distributed by Ewing Lusk of the Mathematics and Computer Science division at Argonne. P4 is available by anonymous ftp from info.mcs.anl.gov and by electronic mail from netlib ornl.gov. 

PCN and many other packages are available using anonymous ftp from info.mcs.anl.gov. 

Computer-Aided Composition of Atomic Orbitals. Molecular orbital calculations with extended Hiickel method, orbital plots, and Walsh diagrams. Also available via anonymous ftp from cacao.issecc.fi.cnr.it (149.139.10.2). PCs. 

Molecular graphics of structures imported from molecular modeling packages, rotation. A demonstration version is available via anonymous ftp from ftp.uni-linz.ac.at. Macintosh. 

Statistical analysis using spreadsheet format experimental design. Macintosh. Anonymous ftp at ftp.sas.com. SAS statistical and data management system on IBM mainframes, VAX, PCs (Windows), Sun, HP, and IBM UNIX workstations. 

Molecular dynamics and minimization of proteins locally enhanced sampling and free energy calculations along reaction paths by perturbation or thermodynamic integration. Stardent, Silicon Graphics, IBM, and HP workstations, moil-view for visualization of shaded spheres and sticks on Silicon Graphics. Available by anonymous ftp from 128.248.186.70. 

Modular FORTRAN programs for performing general ab initio, multireference single and double excitation configuration interaction (Cl), averaged coupled-pair functional, and linearized coupled-cluster method calculations. Available via anonymous ftp from ftp.tcg.anl.gov (146.137.200.2). Cray and other versions. 

VIBRATE (normal modes), VOID (protein packing), and mdXvu (visualization of AMBER trajectory files). QCPE has also accepted the responsibility to distribute semicommercial academic software, such as MM2, MM3, MOPAC 93, POLYRATE, PEFF, and COMPARE-CONFORMER. Most programs in library are in FORTRAN and are available as source code. Current catalogs and information are available by anonymous ftp from qcpe6.chem.indiana.edu (129.79.74.206). Many of the programs run on several hardware platforms, including DEC VAX, IBM, Silicon Graphics, Stardent, Sun, Fujitsu, and Cray. 

Molecular graphics of molecular models and MD trajectories. Available via anonymous ftp from perutz.scripps.edu (137.131.152.27). Sun, DEC, and Stardent. 

Fax 612-625-6817, e-mail gopher boombox.micro.umn.edu Internet client/server for a distributed information delivery system. Client program for workstations is available by anonymous ftp from boombox.micro.umn.edu (132.84.132.2). UNIX workstations VAX, IBM, Macintosh, PCs. 

Communication of text and graphics files between computers using World-Wide-Webb (WWW) servers. UNIX, PC, and Macintosh versions available via NCSA anonymous ftp from ftp.ncsa.uiuc.edu (141.142.20.50). Alternative anonymous ftp sources for Mosaic include sunsite.unc.edu (all versions), ftp.sunet.se (all versions), and ftp.Iuth.se (Macintosh version). Alvis (Alpha Shape Visualizer) for construction and rendering of objects from x,y,z coordinates in 3D space. Poly view for graphics rendering. Silicon Graphics. 

Tel 44-081-966-3567, fax 44-081-966-4476, e-mail ras32425 ggr.co.uk Molecular graphics visualization tool for proteins and nucleic acids. Available by anonymous ftp from ftp.dcs.ed.ac.uk (129.215.160.5) in directory /home/ ftp/pub/rasmol. Sun, Digital Alpha, IBM RS/6000, and Silicon Graphics. Macintosh version RasMac is available from ftp.dcs.ed.ac.uk in /home/ftp/ pub/rasmol/rasmac.sit.hqx. 

Tel. 206-543-1421, fax 206-543-1524, e-mail merritt xray.bchem.washington.edu Raster rendering of proteins and other molecules in stick, ball-and-stick, spacefilling, and ribbon representations. Available via anonymous ftp from stanzi.bchem.washington.edu (128.95.12.38). Silicon Graphics and Sun. 

Scientific visualization and animation program that can be applied to molecules. Available via anonymous ftp from ftp.scri.fsu.ed. Silicon Graphics and IBM RS/6000 workstations with Z-buffer capability. 

FTP is a method of transferring files across the Internet. In may cases the files are made available for anonymous FTP access, i.e. you do not need previously arranged passwords. Log in as anonymous and give your e-mail address as the password. Use your web browser to locate the file you want and then use its FTP software to transfer it to your computer. 

The thermodynamic data bases of most geochemical models are only occasionally corrected and updated. Updated data bases for the Geochemist s Workbench (Bethke 1994, 1996) and EQ3/6 (Wolery 1992a, 1992b) may be obtained by anonymous ftp from ftp //s32.es.llnl.gov/johnson where they are located in the files gwb and eq36. For further information contact Jim Johnson at his e-mail address jviJohnson llnl.gov. 

We use a software package called xvseq to analyse scanning array images that is run on a SUN Solaris workstation (available by anonymous ftp at (ftp //bioch.ox.ac.uk/pub/xseq.tar.gz)). The progranmie reads and displays im-... 

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