Recent changes to Home

Home modified by arne

arne — Mon, 06 Jan 2014 09:46:36 -0000

--- v12
+++ v13
@@ -1,6 +1,6 @@
 Welcome to FluxModules Wiki!

-Here, you find a brief overview on the content of the project.
+Here, you find a brief overview on the content of the project. This project contains essentially the supplementary material for a (not yet published) paper in the RECOMB 2014 proceedings (reference will follow as soon as available).

 Source Code
 ===========
@@ -26,6 +26,10 @@
 It is not really intended for other uses.
 * *makeSummary.m* - runs all the afore mentioned methods and creates a latex file with summary information

+
+Mathematical Proofs
+===================
+The proofs from the paper you can find in the [files](http://sourceforge.net/projects/fluxmodules/files/proofs.pdf/download).

 Examples

Home modified by arne

arne — Sat, 04 Jan 2014 17:36:59 -0000

--- v11
+++ v12
@@ -51,6 +51,7 @@
 ==================

 SBML files of the metabolic networks used for the example computation can be found
+
 * in the [BiGG database](http://bigg.ucsd.edu/)
 * Human Recon 2 at [Biomodels Database](https://www.ebi.ac.uk/biomodels-main/MODEL1109130000)
 * E. coli iJO1366 at [PMC](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261703/bin/msb201165-s3.xml)

Home modified by arne

arne — Sat, 04 Jan 2014 17:36:27 -0000

--- v10
+++ v11
@@ -46,5 +46,14 @@
 [Home/attachment/network.pdf]
 * a pdf giving summary informtion on the modules. [Home/attachment/network_summary.pdf]

+
+Metabolic Networks
+==================
+
+SBML files of the metabolic networks used for the example computation can be found
+* in the [BiGG database](http://bigg.ucsd.edu/)
+* Human Recon 2 at [Biomodels Database](https://www.ebi.ac.uk/biomodels-main/MODEL1109130000)
+* E. coli iJO1366 at [PMC](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261703/bin/msb201165-s3.xml)
+
 [[members limit=20]]
 [[download_button]]

Home modified by arne

arne — Sat, 04 Jan 2014 17:23:41 -0000

--- v9
+++ v10
@@ -44,7 +44,7 @@
 [[img src=V2.png alt="Module V2 of Ecoli iAF1260"]]
 * a figure showing the interactions of the modules 
 [Home/attachment/network.pdf]
-* a pdf giving summary informtion on the modules.
+* a pdf giving summary informtion on the modules. [Home/attachment/network_summary.pdf]

 [[members limit=20]]
 [[download_button]]

Home modified by arne

arne — Sat, 04 Jan 2014 17:22:07 -0000

--- v8
+++ v9
@@ -42,7 +42,8 @@
     - *time.txt* runtime in seconds
 * figures of the computed modules (unless the modules are too big), for example: 
 [[img src=V2.png alt="Module V2 of Ecoli iAF1260"]]
-* a figure showing the interactions of the modules
+* a figure showing the interactions of the modules 
+[Home/attachment/network.pdf]
 * a pdf giving summary informtion on the modules.

 [[members limit=20]]

Home modified by arne

arne — Sat, 04 Jan 2014 17:17:04 -0000

--- v7
+++ v8
@@ -40,8 +40,8 @@
     - *variability.txt* minimal and maximal flux values (in the order as in the network)
 * run time
     - *time.txt* runtime in seconds
-* figures of the computed modules (unless the modules are too big),
-    - for example: [[img src=V2.png alt=Module V2 of Ecoli iAF1260]]
+* figures of the computed modules (unless the modules are too big), for example: 
+[[img src=V2.png alt="Module V2 of Ecoli iAF1260"]]
 * a figure showing the interactions of the modules
 * a pdf giving summary informtion on the modules.

Home modified by arne

arne — Sat, 04 Jan 2014 17:15:41 -0000

Home modified by arne

arne — Sat, 04 Jan 2014 17:08:59 -0000

--- v5
+++ v6
@@ -41,6 +41,7 @@
 * run time
     - *time.txt* runtime in seconds
 * figures of the computed modules (unless the modules are too big),
+    - for example: [[img src=V2.png alt=Module V2 of Ecoli iAF1260]]
 * a figure showing the interactions of the modules
 * a pdf giving summary informtion on the modules.

Home modified by arne

arne — Sat, 04 Jan 2014 17:00:12 -0000

--- v4
+++ v5
@@ -22,9 +22,9 @@

 General Summary Generation
 --------------------------
-For reproducability we also supply the matlab code that we used to generate the results in the supplementary material. 
+For reproduceability we also supply the matlab code that we used to generate the results in the supplementary material. 
 It is not really intended for other uses.
-* *makeSummary.m* - runs all the afore mentioned methods and creates a latex file with summaryinformation
+* *makeSummary.m* - runs all the afore mentioned methods and creates a latex file with summary information

@@ -33,12 +33,13 @@

 We also uploaded some [examples](https://sourceforge.net/projects/fluxmodules/files/examples/) so that you can see what kind of results can be obtained.
 For each example network there is a .zip file, which contains 
+
 * the results in text-form, 
-    * *flux.txt* a feasible flux distribution (here, we only analyze the optimal flux space, so this is actually an optimal feasible flux distribution)
-    * *modules.txt* the names of the reactions in the modules (one line for each module)
-    * *variability.txt* minimal and maximal flux values (in the order as in the network)
+    - *flux.txt* a feasible flux distribution (here, we only analyze the optimal flux space, so this is actually an optimal feasible flux distribution)
+    - *modules.txt* the names of the reactions in the modules (one line for each module)
+    - *variability.txt* minimal and maximal flux values (in the order as in the network)
 * run time
-    * *time.txt* runtime in seconds
+    - *time.txt* runtime in seconds
 * figures of the computed modules (unless the modules are too big),
 * a figure showing the interactions of the modules
 * a pdf giving summary informtion on the modules.

Home modified by arne

arne — Sat, 04 Jan 2014 16:58:16 -0000

--- v3
+++ v4
@@ -34,11 +34,11 @@
 We also uploaded some [examples](https://sourceforge.net/projects/fluxmodules/files/examples/) so that you can see what kind of results can be obtained.
 For each example network there is a .zip file, which contains 
 * the results in text-form, 
-    - *flux.txt* a feasible flux distribution (here, we only analyze the optimal flux space, so this is actually an optimal feasible flux distribution)
-    - *modules.txt* the names of the reactions in the modules (one line for each module)
-    - *variability.txt* minimal and maximal flux values (in the order as in the network)
+    * *flux.txt* a feasible flux distribution (here, we only analyze the optimal flux space, so this is actually an optimal feasible flux distribution)
+    * *modules.txt* the names of the reactions in the modules (one line for each module)
+    * *variability.txt* minimal and maximal flux values (in the order as in the network)
 * run time
-    - *time.txt* runtime in seconds
+    * *time.txt* runtime in seconds
 * figures of the computed modules (unless the modules are too big),
 * a figure showing the interactions of the modules
 * a pdf giving summary informtion on the modules.