UNIX Shell, PERL, PHP, Python, Ruby, R, AppleScript, Automator Actions, Matlab/Octave
For TeXShop and Skim: Script to open TeXShop at a particular line
Description:
I was e-mailed a request for this. Some people want to use Skim as their TeXShop previewer. However, they want to be able to use Skim's PDFSync compatibility to open TeXShop at a particular line. This script allows them to do this (NOTE: This 1.01 version has been updated. Try the -h option for details or see the web page).
Author's Email:
ted@tedpavlic.com
Author's Full Name:
Ted Pavlic
Author's Homepage:
http://phaseportrait.blogspot.com/2007/07/using-skim-pdfsync-and-texshop.html
Script File:
texshop.gz (1.25 KB)
NCSAstore.pl
Description:
This is a script to put on the end of your NCSA batch files, to do parallel uploads to mass storage at the end of your runs. It should be possible to adjust this script to work with other supercomputers too.
Sample usage is
# Designate storage directory on MSS
set STORAGE_DIR="Runs/Flash25/bhl/exe01"
# Make the file list
\ls -1 --hide-control-chars *hdf* *log flash.dat > files.txt
Author's Email:
rge21@pas.rochester.edu
Author's Full Name:
Richard Edgar
Author's Homepage:
http://www.pas.rochester.edu/~rge21/computing/programs/ncsastore/index.shtml
Script File:
NCSAstore.pl (2.8 KB)
Script for inverse PDF/DVI searches to Vim
Description:
"Inverse" or "backward" PDF (via PDFSync) and DVI searches allow an author to click on text in a document produced by LaTeX and have the actual LaTeX source get opened and the cursor positioned at the corresponding line. This is supported by several PDF/DVI viewers and text editors in OS X. However, it is not really practical to do with Vim.
I've created this UNIX script to make inverse searches easy to do in Vim. See the "Author's Homepage" URL (or the first few commented lines of the script) for usage information. (UPDATE: There was a typo in version 1.0 uploaded to site. This is now fixed in v1.01 uploaded to site)
Author's Email:
ted@tedpavlic.com
Author's Full Name:
Ted Pavlic
Author's Homepage:
http://phaseportrait.blogspot.com/2007/07/pdfsync-inverse-searches-on-vim-for-os.html
Script File:
gvim-pdfsync.gz (871 bytes)
simpdftexnodel: A simpdftex that is compatible with Skim 0.5+ autorefreshes from disk.
Description:
The simpdftex that comes with most LaTeX distributions is not compatible with the auto-refresh features of Skim version 0.5 and up.
This simpdftexnodel (where "nodel" is short for "no delete") is compatible with Skim.
Author's Email:
ted@tedpavlic.com
Author's Full Name:
Ted Pavlic
Author's Homepage:
http://phaseportrait.blogspot.com/2007/07/skim-automatic-refreshes-and-simpdftex.html
Script File:
simpdftexnodel.gz (7.63 KB)
UNIX script for opening (and refreshing) file in Skim
Description:
Allows a file to be opened from the shell by Skim. This is convenient for some text editors (e.g., Vim, GVim, Emacs, iTeXMac) used to produce, for example, LaTeX documents. (NOTE: Updated 1.03 version has lots of PDFSync support and other AppleScript hooks. Also will figure out file name when you omit extension)
Author's Email:
pavlic.3@osu.edu
Author's Full Name:
Ted Pavlic
Author's Homepage:
http://phaseportrait.blogspot.com/2007/07/script-to-open-file-in-skim-from.html
Script File:
skim.gz (1.88 KB)
UNIX script for opening (and refreshing) file in TeXniscope
Description:
Allows a file to be opened from the shell by TeXniscope. This is convenient for some text editors (e.g., Vim, GVim, Emacs, iTeXMac) used to produce, for example, LaTeX documents. (NOTE: Updated version has PDFSync support and other AppleScript hooks. See web page or -h option for more information)
Author's Email:
pavlic.3@osu.edu
Author's Full Name:
Ted Pavlic
Author's Homepage:
http://phaseportrait.blogspot.com/2007/07/script-to-open-file-in-texniscope-from.html
Script File:
texniscope.gz (1.84 KB)
ANOVA for study of algorithmic components
Description:
To study the performance of a parallel ACO algorithm with various components (interconnection topology, migration frequency, number of CPUs) I wrote this R script to perform an ANOVA on the experimental results.
Hope it could be a start point for others with similar needs.
Author's Email:
mmanfrin@iridia.ulb.ac.be
Author's Full Name:
Max Manfrin
Author's Homepage:
http://iridia.ulb.ac.be/~mmanfrin/
Script File:
ANOVA-30-10000-small.zip (80.77 KB)
Ruby Bioinformatics code(very basic)
Description:
This code is ported from the Python code in "Beginning Python for Bioinformatics" by Patrick O'Brien. This code has not been heavily tested(only lightly tested), so use at your own risk.
Author's Homepage:
http://gavmacprogramming.wordpress.com/2007/03/29/exploring-bioinformatics-with-ruby/
Script File:
bioinformatics_april.zip (11.8 KB)
multi_chemprops.scpt
Description:
This script takes as input a file containing SMILES strings and calculates a variety of chemical properties using ChemDraw.
Author's Email:
swain@mac.com
Author's Homepage:
http://www.macinchem.org/
Script File:
multi_chemprops.scpt.zip (9.17 KB)
Chem_Props_Mac.scpt
Description:
This is the script from the Applescript tutorial 3. Takes as an input a file containg SMILES string and compound name, uses Chemdraw to calculate properties and adds them to the file.
Author's Email:
swain@mac.com
Author's Homepage:
http://www.macinchem.org/
Script File:
Chem_Props_Mac.scpt.zip (8.02 KB)
