Computing and Software
Scientific computing
Programming
Other resources
 ACD/Labs freeware,
including ChemSketch
 Amber
 ARPACK:
a collection of routines for the iterative solution of large
eigenvalue problems
 Atlas:
automatically tuned BLAS library
 AUTO
 Bardware (Bard
Ermentrout's home page)
 BioModels
Database, a database of models in SMBL
format
 BioNetGen: software for rulebased
modeling
 BioRender: an online drawing
application for biomolecular graphics
 BioSimulators, a registry
of biomulation tools, allows models to be simulated or analyzed
using various
tools through their web site

BIOVIA Draw, a chemical structure drawing program. This
program is free for academics (including students). Contact
information must be provided to download the software.
 C3.ca
 Chaste (Cancer,
Heart And Soft Tissue Environment): a multiscale simulation
environment for biological systems
 ChemAxon, a company that makes
a suite of cheminformatics software, including MarvinSketch, a
chemical drawing program. The software is free for
academics, with some minor restrictions.
 CoNtRol: software
for analyzing chemical reaction networks, and
documentation
 Chemical Reaction Network
Toolbox (CRNT), software based on the research of
Martin Feinberg's group
 Compute Canada
 CompuCell3D
 Copasi: a biochemical
systems simulator with many features

DDEBIFTOOL
 Dizzy
(Edinburgh version): (bio)chemical kinetics simulation and
analysis tool
 FreeFem: A
free system for the finite element solution of partial
differential equations
 GAMESS,
a free ab initio chemistry program
 Gaussian
 GLPK,
the GNU Linear Programming Kit
 GraTeLPy,
software for the graphtheoretical analysis of chemical reaction
networks based on the work of Maya Mincheva and collaborators
 High Performance Computing for
Mac OS X
 IBM Open Visualization Data
Explorer
 Knut, a program
that performs continuation and bifurcation analysis for
delaydifferential equations
 Laboratory of
Biosystem Dynamics software,
including SGSSim and its descendent SGNS2
 LAPACK

LASSPTools
 Macs in Chemistry
 MapleSoft
 MatCont,
a numerical bifurcation package that runs in Matlab
 MathWorks, makers of Matlab
 Matlab
 Matrix Template Library
 Morpheus, a modeling
environment for multicellular systems
 NCAR Graphics
 Netlib
 Numerical Objects
 Numerical Recipes
 ObjectOriented Numerics
resource page
 Octave, a Matlab workalike
 PhysiCell, a simulator for cell
aggregates including growth, division and cell death
 Plot Digitizer
 Sage, a free, generalpurpose
mathematical software package
 Scilab
 Scientific
Computing and Imaging Institute Software: a collection of software
written at the University of Utah
 Singular, a computer
algebra system for polynomial computations
 Sire, a molecular simulation framework
and associated apps

StatPlus:mac LE, a free statistical analysis package for
the Mac that works with Excel
 StochPy, a Python
package for stochastic modeling of chemical and biochemical systems
 StochSS, a software environment
for generating, running and analyzing the results of stochastic
simulations
 TISEAN:
a set of programs for nonlinear time series analysis
 VisualPDE,
a webbased software system for studying the phenomenology of
reactiondiffusion systems interactively
 VMD, a molecular
visualization system
 WestGrid
 AppleSerialNumberInfo.com,
a web utility for decoding Apple computer serial numbers
 Cyberduck, a very powerful
file transfer utility that supports multiple protocols,
available for both Mac and Windows
 Cygwin
 Dropbox, a system for
synchronizing files across computers, including a copy kept on a
central server
 File extensions
 Fink: a system for
grabbing Unix software precompiled for the Mac
 Free Software Foundation
 GanttProject
 Gnuplot
 Homebrew: a system for
installing Unix software on the Mac
 HTML
 JabRef, a reference
manager based on BibTeX
 Jumpcut, a clipboard
manager for Mac OS X
 Lunapic, an online picture
editor
 Mac OS X free software
directory
 MacPorts: a system for
installing Unix software on the Mac
 PostScript
 Publish or
Perish, software for citation analysis based on open databases
 Scientific posters
 TeX
 Ubuntu, a standard and very
robust Linux distribution

WCopyfind, a Windows program for making pairwise comparisons between
documents (oriented towards plagiarism detection)
 WebPlotDigitizer,
a webbased tool for extracting points from a graph
 WinFIG: An XFiglike
program for Windows
 WIRIS, makers of MathType
 XnView
 Xpdf, an opensource pdf viewer
and associated tools for manipulating pdf files
 XQuartz,
a replacement for the XWindows installation that comes standard
on the Mac