(2011-nov) MotifSuite figure : webdesign.png
(2012-June) MotifSuite Home page
USE APPLICATIONS :
----------application pages :
(2012-June), CreateBackgroundModel
(2012-June), MotifSampler
(2012-June), MotifRanking
(2012-June), FuzzyClustering
(2012-June), MotifComparison
(2012-June), MotifLocator.
----------check application version (on application page and (2) on standalones page)
(2013-April), submitVersionCheck.php
----------executive and send results
(2013-April), submitApplicationresult.php
(2012-June), follow_jobstatus.php (UG only)
(2012-June), reportjobidstatus.php (UG only)
----------standalone use :
(2012-June), standalones.php (UG/KUL version in ~/command_design/)
(2011-nov), submitemail.php
(2012-June), how to compile all FuzzyClustering executables Compile Guideline
----------[record times used] : contents of ../logging/
multiple files with date-recording : to record the times an application is 'Run' (submitted), 'Download' (standalones), 'Guide' (guidelines), 'Access' (application page clicked) and which users actually run the applications.
(2013-March), MotifSuiteUsage.pl : script to summarize usage-statistics (to be run manually from commandline)
----------[MotifSuite installation information]
(2013-March), config.php : centralized information used throughout MotifSuite
GUIDELINES :
----------help pages :
(2012-June), MotifSuite Guidelines
(2012-June), CreateBackgroundModel Guidelines
(2012-June), MotifSampler Guidelines
(2012-June), Extra MotifSampler Guidelines
(2012-June), MotifSampler prior Pr(x) (parameter -p)
(2012-June), MotifRanking Guidelines
(2012-June), FuzzyClustering Guidelines
(2012-June), MotifComparison Guidelines
(2012-June), MotifLocator Guidelines
(2012-June), MotifSuite Step by Step approach
(2012-June), Case Study MotifSampler
(2012-June), Case Study MotifRanking
(2012-June), Case Study FuzzyClustering
(2012-June), E.coli benchmark
----------format description pages :
(2012-June), backgroundmodel format
(2012-June), Fasta format
(2012-June), PWM format
(2012-June), instances format
FOLDERS :
----------static database information :
(2011-April), ~/bg-thijs/ : precompiled background models
(2011-April), ~/motifcomparison-motif-databases/ : Jasper/Regulon/Transfac PWM databases
----------interactive uploadfiles and resultfiles storage :
~/createbackgroundmodel_uploads/Results/ : lifetime 7 days
~/motifsampler_uploads/Results/ : lifetime 7 days
~/motifranking_uploads/Results/ : lifetime 7 days
~/fuzzyclustering_uploads/Results/ : lifetime 7 days
~/motifcomparison_uploads/Results/ : lifetime 7 days
~/motiflocator_uploads/Results/ : lifetime 7 days
~/standalone_uploads/Results/ : 32bit & 64bit, executables updated every upload
----------illustrative examples, in ~/example_data/
Fasta file : EvgA.fnacopy
output CreateBackgroundModel : EcoliK12_2.bg, EvgA_2.bg
output MotifSampler : oEvgA_MS.txt, oEvgA_MS.mtrx
output MotifRanking : oEvgA_MR.txt, oEvgA_MR.mtrx
output MotifFuzzyClustering : oEvgA_FC.txt, oEvgA_FC.mtrx
input FuzzyClustering : dirichlet.default
output MotifComparison : oEvgA_MCkl.txt, oEvgA_MCblic.txt
output MotifLocator : oEvgA_ML.txt
input MotifLocator : lEvgA_ML.txt
----------linked figures, stored as .png in ~/images/
supporting/original drawings in ~/images/pdf-folder/ and ~/images/svg-folder/
----------old file versions - kept for archiving in ~/old/
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