DICE: Discovering Informative Co-occurring
Elements The software package that can be
downloaded below provides a pipeline that integrates DICE with several
accessory tools for identification and validation of co-occurring elements and
for subsequent application in interaction prediction. You are granted a royalty-free non-transferable right
to use the software and accompanying documentation included in this
downloadable package strictly for academic research and education purposes. If
you intend to use the software for any other purpose, please contact Dr. Reza Salavati. Windows Download the DICE package from here: DICE.zip (11,808 KB). Extract the package and it will be ready to
use. Execute DICE-GUI.jar; a user interface will then allow you to select the
analyses that you want and to determine the input files and parameters. In
the last page, press Run to start the job in a separate window that can be
closed at any time in order to terminate the job. A log viewer window will
also appear where you can see the progress of the job by pressing the Refresh
button. You can also inspect the job folder by pressing the Output button. The
progress log is saved in a .log file in the job folder in case you wish to view
it in another text viewer. After the job is finished, two postscript files
(.ps) will be created in the GraPE folder, containing graphical
representations of the results. Alternatively, you can run a job by
manually creating a properly named and formatted XML file and calling
DICE.EXE directly. Execute DICE.EXE as follows: \>DICE.EXE
–job [jobname] –root [rootfolder] The parameter ‘jobname’ should contain no spaces.
A folder with the same name should exist in the “jobs” folder, in which an
XML file with the same name should contain the information about how to run
the job. A sample job is included with DICE package. If you want to actually
run that sample job, you should first download and extract the precompiled
human data package (see below). The parameter ‘rootfolder’ should point to
the root directory of DICE, where DICE.EXE is located. For example, if you
have extracted this package in the C drive, this parameter should be C:\DICE.
Note that ‘rootfolder’ cannot have spaces. If the active directory is the
same as rootfolder, you can omit this parameter. Linux The Linux version of DICE is being
developed and will be available soon. Data files These data files should be extracted in the
“data” folder where DICE package is extracted. PhyloProfile.zip
(6,307 KB) If you want the DICE to perform
phylogenetic profiling, you should create a folder named “PhyloProfile” in
the “data” folder, and create a file named “files.list” in which the paths
and the names of the protein sequence files for different organisms is
indicated. The protein sequence files should have been already parsed using
“formatdb.exe” from NCBI BLAST package. The paths should be with respect to
the root folder of DICE. This compressed package only provides an example
containing protein sequences for five organisms. Extract the package in the
“data” folder and DICE will be able to do phylogenetic profiling based on
these five genomes. PDB.zip
(59,782 KB) If you are using DICE to find protein
motifs and you want DICE to check for occurrences of these motifs in protein
interaction interfaces, download this file and extract it in the “data”
folder. DICE searches for “data\PDB\files.tab” in order to locate the PDB
files and their associated information. H.sapiens.zip
(34,767 KB) This is a precompiled package for analysis
of biological networks in human. S.cerevisiae.zip
(21,454 KB) This is a precompiled package for analysis
of biological networks in yeast. Last updated on 3/23/2010 10:27:47 AM |
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