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 rule-based
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.
- 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
- CompuCell3D
- Copasi: a biochemical
systems simulator with many features
-
DDE-BIFTOOL
- Digital Research Alliance of
Canada
- 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 graph-theoretical analysis of chemical reaction
networks based on the work of Maya Mincheva and collaborators
- High Performance Computing for
Mac OS X
- Knut, a program
that performs continuation and bifurcation analysis for
delay-differential equations
- LAPACK
-
LASSPTools
- Macs in Chemistry
- MapleSoft
- MatCont,
a numerical bifurcation package that runs in Matlab
- MathWorks, makers of Matlab
- Matlab
- Morpheus, a modeling
environment for multicellular systems
- NCAR Graphics
- Netlib
- Numerical Recipes
- Object-Oriented Numerics
resource page
- Octave, a Matlab work-alike
- PhysiCell, a simulator for cell
aggregates including growth, division and cell death
- Plot Digitizer
-
Ribeiro lab software, focusing mostly on the simulation
of genetic control systems, but also including some image analysis
software
- Sage, a free, general-purpose
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
- VisualPDE,
a web-based software system for studying the phenomenology of
reaction-diffusion systems interactively
- VMD, a molecular
visualization system
- 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 web-based tool for extracting points from a graph
- WinFIG: An XFig-like
program for Windows
- WIRIS, makers of MathType
- XnView
- Xpdf, an open-source pdf viewer
and associated tools for manipulating pdf files
- XQuartz,
a replacement for the XWindows installation that comes standard
on the Mac