Welcome to DLipid Page.
DLipid is a Java and Matlab application for lipid flux analysis and dynamic simulations. The application uses time-course mass spectrometry data to automatically construct remodeling network and infer dynamic system using B-Spline algorithm.
DLipid is composed of two well-defined sub applications: FluxAnalysis and DynamicSimulation.
How to use it?
This application can be used in linux, mac, and windows.
To use this tool, you must first download and unpack DLipid.
$ tar -zxvf DLipid.tar.gz $ unzip DLipid.zip
You will also need to install Matlab.
Step 1: Construct correlation network and simulation
$ cd DLipid/bin $ java -jar DLipid.jar <inputFile> <minTh> [-m] [-n]
$ java -jar DLipid.jar ../DATA/18_0-18_1.txt 0.3
Notice: The default input folder is "../DATA/". If only a filename is given, the application interprets it as "../DATA/filename".
time1 time2 . . . specie1 mean std mean std specie2 mean std mean std . . .
B) minTh : -- Significance score threshold for FluxNetwork application. -- Must be positive.
-mFLOAT : Maximum threshold. If this value is specified, multiple runs of simulations will be performed using thresholds from minTh to this number at step size 0.1.
- -nINT: Iteration number in B-Spline algorithm, default is 1000. The algorithm will stop at next-closest iteration where the error is min within last four iterations. The algorithm will also stop when error change is less than 0.0001 between subsequent steps.
$ java -jar DLipid.jar ../DATA/18_0-18_1.txt 0.3 -m0.5 -n1500
Then you will see Matlab application starts after a few seconds. You can quit Matlab after calculations finish.
Step 2: Retrieve correlation network and simulation results.
Go to output folder.
If only a filename is given in Step 1, default output folder is "../RESULTS/$inputFile_prefix/". Otherwise an output folder "$inputFilePath/$inputFile_prefix/" will be created.
If you excite the first example command at Step 1, you will see the following files in the output folder.
"log_18_0-18_10.3.txt": stores parameter values and information from dynamic simulations.
"sim_18_0-18_10.3.jpg": shows the fit of simulation to observed kinetics.
"18_0-18_10.1.graphml": is a xml format file of inferred flux network. See Graphml File Extension for more detail.
"18_0-18_10.3.sif": is a sif format file of reaction network. Specification:
source1 parameter1 target1 source2 parameter2 target2 ...
LipidGraphical: A graphical interface for flux analysis.
This application allows vitalization of .grahpml network files.
$ java -jar FluxAnalysisGUI.jar
This application allows simulation with user-defined .sif reaction network file.
$ cd bin $ matlab
> main_remodeling_sim('../DATA/18_0-18_1.txt', '../RESULTS/18_0-18_1/18_0-18_10.3.sif');
Copyright © 2012 Chuang Lab Boston College.