The DNA and Natural Algorithms Group:

All software installed on our cluster should have links here. Comments should be added for *where* it is, how one might start using it, etc. Should we restrict access to within Caltech? If you ask to have new software installed, you're responsible for adding an entry here, to help other students become aware of what's available.

• A few web-based servers we commonly use.
  • Zuker et al's RNA mfold and DNA mfold servers.
  • ViennaRNA RNA and DNA folding server.
• Of course we use LaTeX a lot.
  • A good manual for how to include graphics in latex. epslatex.pdf
• Software packages that we actively use for research. These are all in /research/bin (and build trees in /research/stow)
  • Python is a scripting language with object-oriented flavor, and a strong open source community. Math (MATLAB-like) commands and graphics are in packages such as "NumPy" and "NumArray" and "SciPy". [Note: "python" uses Python 2.2.1 as included in Red Hat; "python2", "python2.2", and "python2.3" are also available.]
  • R is a language used by many hard-core folks in the statistics community. It also competes with MATLAB.
  • Open RasMol (rasmol.sh) for viewing molecular models. Other RasMol sites include this and this.
  • NAMOT version 2.2.0 for building molecular models of complex DNA structures. SourceForge hosts the open source Namot development and Namot mailing list for development issues.
    NAMOT now has a a python interface. To use it, python must find the libraries -- this requires an environment variable:
    setenv PYTHONPATH "/research/lib:/research/libexec"
    Then, in python, "import pynamot".
    Documentation for NAMOT is primarily in the help files, which can be accessed by the pull-down menu. But some recent commands are documented only in /research/src/namot-2.2.0-pre4/newrelease/ and /research/src/namot-2.2.0-pre4/docs/, while there are many helpful examples in /research/src/namot-2.2.0-pre4/tests/. For example, .../docs/numrules attempts to explain the ever-frustrating renumbering of molecular groups when link and nick operations occur. The wise will learn the new commands "group tag" and "helix tag" to avoid renumbering headaches.
  • PyMol version 0.97 is excellent for rendering and examining molecular structures. A manual is on the PyMol web page. It is built on top of python, but you just run "pymol" rather than using "import" from an existing python session. (The latter can actually be done also; see the many helpful hints here.
  • ViennaRNA package for prediction of RNA and DNA secondary structures: minimum free energy, partition functions, and design. This is also a C library of functions. Documentation can be found at the same site.
  • Kinfold (not fully installed yet) program for stochastic kinetic folding of RNA; outgrowth of the ViennaRNA package, by C. Flamm et al.
  • RNAmovies for making movies of secondary structure changes in RNA.
  • O protein crystallographic package. Also see O-linux versions.
  • VOIDOO for calculating the cavity volume of pockets in proteins, using a rolling disk algorithm. Also, FLOOD and MAPROP.
  • Swiss PDB Viewer (spdbv.sh) for viewing molecular models.
• Home-grown software... we need "users manuals" for these, and they probably need to be cleaned up, and various archival versions should be available. The software should be already installed on the cluster, so no downloads here (if we want to make it public, we'd want another page anyway). Most of the software below either severely needs to be cleaned up, or is still in the process of being written. One reason for having this list is to encourage people to ask the authors to tell them about the code.
  • DNAdesign MATLAB and C code, tools for working with DNA sequences, specifying structures, and stochastic sequence design. Includes spuriousC and spuriousD. Out growth of DNAdesign (but much faster), for designing DNA sequences. Authors: Erik Winfree and Dave Zhang.
  • AFMhacks MATLAB code for quick & dirty reading and futzing with DI AFM images. Author: Erik Winfree (The Alex package is better, but more complex.)
  • xgrow stochastic tile assembly simulater Author: Erik Winfree and friends
  • Ksim. Stochastic kinetic simulator, a modification of Kinfold above, to handle temperature changes and DNA polymerase action. A general resource page is available here Author: Joseph Schaeffer (and Kinfold authors)
• Commercial or enabling software installed on our cluster. These are all in /software/bin (and build trees in /software/stow)
  • tcl scripting language
  • Matlab numerical computation system
  • Mathematica symbolic mathematics systems
  • ssh and scp for secure remote shell logins and secure remote file copy
  • xfig simple graphics figure editor
  • rsync for (optionally secure) fast remote file copy
  • cvs (concurrent versions system) for multiple-author source code control Joe Schaeffer wrote a how-to for our cluster: (cvsdoc text file; cvsdoc.ps).
  • stow for versioning control in the main /research filesystem. Click here for the HOWTO.
  • ghostview (=gv) postscript and pdf viewer
  • tetex Latex technical document formatting system; cit_thesis and chicago-bibtex packages
  • VMware for running Windows under Linux as a virtual machine, or visa-versa (not yet installed on all our computers)
  • LICQ, an ICQ chat clone. More info on www.licq.org. Please go to System:System Functions:Authorization required to make it more secure. You may also want to check System:Options:Miscellaneous:Paranoia.
  • StarOffice, Sun's full featured office suite. Run /software/stow/office52/program/soffice. [Soon the /software/bin/soffice script should just work.] First run /software/stow/office52/program/setup. Do a worksation install instead of a full install. The registration information is optional; name, email, etc will be added to things as a convenience, as in MS Office. Staroffice will be installed as ~/office52/soffice.
• Computer system administration and information.

Erik Winfree, 10/26/01, 1/3/05