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Environment

Digital Briefs

New Software and Websites for the Chemical Enterprise

by Janet S. Dodd
August 22, 2005 | A version of this story appeared in Volume 83, Issue 34

Spellex Biotech software enables an ordinary spell-checker to provide correct spelling choices for incorrectly spelled bioscience words. It allows users to look up more than 200,000 bioscience words by phonetic or typographical search without exiting their program. The Spellex Biotech dictionary checks both nonscientific and bioscience words simultaneously. Users can spell-check documents while they type or can spell-check hundreds of pages with a single keystroke. The software covers more than 40 bioscience fields, including agronomy, biochemistry, bioinformatics, biomedical engineering, biophysics, ecology, molecular and genetic biology, microbiology, organic chemistry, taxonomy, toxicology, and pharmacology. Spellex Corp., www.spellex.com

Teranode XDA 2.7 is an informatics platform that automates the entire life cycle of experiment data, including management, integration, analysis, and reporting. It is a model-driven LIMS that transforms experiment designs into automation without programming. Protocol Player converts experiment designs into a guided protocol that includes a checklist of steps, instructions for each step, data entry, and data analytics. Protocol Modeler enables experiment parameters, protocol sequence, data capture, and analytics to be schematically defined for automation by Protocol Player. Teranode, www.teranode.com

Chemkin 4.02 offers reactor networks to simplify complex modeling and visual diagramming options. The software provides detailed understanding of complex chemical kinetics problems, which helps streamline development and optimize yield without unwanted by-products. Process chemists can evaluate trade-offs and rate limitations; automotive engineers can model ignition delay; and gas-turbine combustor designers can target the sources of NOx emissions. With this latest release, users can build reactor networks by dragging and dropping from a customizable palette of reactor modules and clicking to draw connections for mass and heat transfer. Platforms supported are Windows, Linux, IRIX, UNIX, and others. Reaction Design, www.reactiondesign.com

Kintecus V3.82 is a full-featured chemical kinetic, thermodynamic, true equilibrium software with optional data-fitting and normalized sensitivity analysis. The latest version utilizes uncertainty analysis and extensive statistical output. Another important new feature is the capability to calculate model uncertainty. The software runs on Windows 98, 2000, and XP. Vast Technologies Development, www.kintecus.com

Mathematica CalcCenter 3 is much like a scientific calculator for the desktop, but it has more capabilities than Excel or traditional scientific calculators. It is also faster than more expensive products like Mathcad or Maple. A useful feature for chemists and chemical engineers is the many physical constants included in the Units & Constants palette (like Avogadro’s constant and the masses of atomic particles). Also, InstantCalculators for each function prompt users for input and automatically set up the problem. CalcCenter performs symbolic as well as numeric calculations, solves equations, calculates integrals, manipulates matrices, factors polynomials, and analyzes data. The software is available for Windows and Mac OS X. Wolfram Research, www.wolfram.com

Databases

Luna is a database of protein-ligand structural information. It consists of records for each ligand with dependable connectivity information. Ligands, cofactors, and other small molecules from the public Protein Data Bank are available by subscription and are updated monthly. The database contains SMILES and currently about 25,000 entries for about 5,000 distinct ligands bound to macromolecules. Metaphorics, www.metaphorics.com

Online

ADME/Tox Web is a reference data and prediction service on the Web that provides critical ADME/Tox information for both previously reported and new compounds in a straightforward interface. Considered properties include pKa, pH-dependent solubility, passive absorption, active transport, P-glycoprotein efflux and inhibition, cumulative oral bioavailability, Ames test, LD50 in mouse and rat, and six types of organ-specific effects. Chemical structures can be selected from the internal dictionary of nonsystematic names, copied and pasted from most drawing programs, or entered as SMILES codes. Pharma Algorithms, www.ap-algorithms.com/admetox_web.htm

Computational Science & Engineering Online (CSE-Online) allows users to securely connect to any Unix/Linux server, access, analyze, and visualize data in local directories, and access application tools on the server. Users can submit jobs to and retrieve data from remote computers and can access public databases. Version 0.5 capabilities include graphic user interfaces for applications in quantum chemistry (Gaussian and GAMESS), biosimulation (AMBER), kinetics (TheRate), and reaction engineering (CHEMKIN II). CSE-Online also provides visualization tools for analyzing electronic structure calculations and for viewing biomolecules, an interface for the public Protein Data Bank, and general tools. CSE-Online is platform-independent. It is freely accessible at cse-online.net.

Digital Briefs is written by Janet S. Dodd, who can be reached at j_dodd@acs.org.

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