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fastFVA #560

Merged
merged 209 commits into from
Jun 16, 2017
+2,859 −18
Merged

fastFVA #560

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a44ac41
fastFVA version from MSP/fastFVA
laurentheirendt Mar 14, 2016
60eb169
Updated Readme file for support of ILOG CPLEX on Linux Ubuntu.
laurentheirendt Mar 14, 2016
dbd3d71
Minor modifications for CPLEX support on Linux.
laurentheirendt Mar 15, 2016
ab48e72
Fixed several warning messages in the fastFVA.
laurentheirendt Mar 16, 2016
ac11f68
Added support for timing of the C-Script for debugging purposes.
laurentheirendt Mar 16, 2016
a98e992
Added support for time markers to check performance of c - script.
laurentheirendt Mar 17, 2016
a77ab53
Bugs removed for MEX file generation on win64.
laurentheirendt Mar 18, 2016
95880c3
Bug removal and minor modifications in running scripts.
laurentheirendt Mar 19, 2016
78f5c9e
Minor changes.
laurentheirendt Mar 20, 2016
cdca840
Minor changes in main scripts to run numerical experiments.
laurentheirendt Mar 23, 2016
7e7358a
Minor modifications to fastFVA (matrixAS)
laurentheirendt Apr 1, 2016
8b60135
Changes to several folders; mainly tree restructuring
laurentheirendt Apr 6, 2016
59aebf4
Added file to automatically run multiple models with various CPLEX pa…
laurentheirendt Apr 12, 2016
c4a4995
Minor changes to fastFVA.m
laurentheirendt Apr 12, 2016
bb1d300
Minor changes for parameter changes in cplexFAC.c
laurentheirendt Apr 12, 2016
b2b32a8
Restructuring and rearranging files
laurentheirendt Apr 12, 2016
c206762
Renaming of files and moving GLPK interface to a designated folder
laurentheirendt Apr 12, 2016
4086d60
Reverting cplexFVAc.c back to default settings
laurentheirendt Apr 13, 2016
9077f6e
Minor changes to cplexFVAc.c
laurentheirendt Apr 13, 2016
6214423
Restructuring
laurentheirendt Apr 13, 2016
45d443d
First commit of fastFVAex.m
laurentheirendt Apr 13, 2016
3fb2b03
Minor changes to fastFVA files
laurentheirendt Apr 13, 2016
f70925a
Restructuring of files - fastFVA
laurentheirendt Apr 13, 2016
be1cfa2
Renaming of certain files
laurentheirendt Apr 13, 2016
c05e40d
Changes to cplexFVAc.c for clarity and compiler options
laurentheirendt Apr 14, 2016
da21002
Changes to the runExps script
laurentheirendt Apr 14, 2016
a6a0225
Changes to the runExps script
laurentheirendt Apr 14, 2016
856ef07
Support for running multiple experiments with multiple models, matric…
laurentheirendt Apr 14, 2016
19b5665
Added a variable of numThread to track CPLEX execution
laurentheirendt Apr 14, 2016
6a49fd6
Support for the output of a CPLEX log file for a certain thread i
laurentheirendt Apr 14, 2016
f82a4d0
Minor changes to fastFVA
laurentheirendt Apr 14, 2016
d3dac0f
Timestamps for individual threads and reporting improvements; robustn…
laurentheirendt Apr 15, 2016
ac5359e
Removal of drivers
laurentheirendt Apr 15, 2016
99a6d56
Preparations for setting CPLEX parameters dynamically
laurentheirendt Apr 15, 2016
6fedccc
Progress monitoring in driver for fastFVA
laurentheirendt Apr 15, 2016
80a210a
Changes to the interaction with the user, debugging capabilities impr…
laurentheirendt Apr 15, 2016
8d8ddf5
Script for cleaning the files, better user integration
laurentheirendt Apr 18, 2016
15e8446
Additional comments and headers
laurentheirendt Apr 18, 2016
14fd283
Minor changes
laurentheirendt Apr 18, 2016
39d7a5d
Changes in driver
laurentheirendt Apr 19, 2016
9db081c
Preparation for interactively setting CPLEX parameters
laurentheirendt Apr 19, 2016
a17caab
Definition of function to set CPLEX parameter based on external input
laurentheirendt Apr 19, 2016
2f88700
Setting CPLEX parameters from arrays using CPLEX identifiers
laurentheirendt Apr 19, 2016
7e4ec78
Minor changes and cleanup
laurentheirendt Apr 19, 2016
99eb1dc
CPLEX parameter set adopted from public COBRA
laurentheirendt Apr 19, 2016
f942c77
Integration for setting CPLEX parameters in MATLAB
laurentheirendt Apr 19, 2016
b7d6cd7
Minor changes
laurentheirendt Apr 20, 2016
dc6d066
Changes to MEX wrapper to load the CPLEX parameters dynamically from …
laurentheirendt Apr 20, 2016
4ebf171
Retrieving all CPLEX parameters done - preparation for setting the CP…
laurentheirendt Apr 20, 2016
1ba3377
Changes to setting parameters dynamically
laurentheirendt Apr 20, 2016
91f1e13
Dynamic setting of parameters partially working
laurentheirendt Apr 21, 2016
66a1be4
Setting of all integer parameter implemented
laurentheirendt Apr 21, 2016
658bce4
Setting of double/float parameters implemented
laurentheirendt Apr 21, 2016
b1f6a9e
All parameters can be now dynamically set & minor modifications to ou…
laurentheirendt Apr 21, 2016
a136269
Minor changes to parameters
laurentheirendt Apr 21, 2016
641b504
Simplex method choice and minor changes to code
laurentheirendt Apr 21, 2016
ad8d7a7
Minor changes
laurentheirendt Apr 21, 2016
ede10a4
Bugs removed; parameter setting of CPLEX algorithm choice
laurentheirendt Apr 22, 2016
9bfa653
Minor changes to fastFVA
laurentheirendt Apr 22, 2016
ae1683b
Update to calculate singular values differently
laurentheirendt Apr 22, 2016
092a30c
changes of fastFVAex in fastFVA implemented
laurentheirendt Apr 26, 2016
4e49d04
Minor changes
laurentheirendt Apr 27, 2016
ef83006
Sequential version of fastFVAex debugged
laurentheirendt Apr 27, 2016
467a692
Parallel version debugged
laurentheirendt Apr 27, 2016
786509a
Reorganisation of files and minor changes
laurentheirendt Apr 27, 2016
a299e05
Minor changes and removal of files
laurentheirendt Apr 27, 2016
e7ed363
Changes to FBA and bounds FBA driver
laurentheirendt Apr 27, 2016
16932b1
Reorganizing folder structure and files
laurentheirendt Apr 28, 2016
f0ff5cc
Reorganizing folder structure and files - 2
laurentheirendt Apr 28, 2016
b0faaca
Changes to the FVA driver
laurentheirendt Apr 28, 2016
bbc5e3b
Comments in fastFVA
laurentheirendt Apr 28, 2016
562115d
Changes to the drivers for FBA and FVA; minor changes to fastFVA
laurentheirendt Apr 28, 2016
84e17d1
Minor changes
laurentheirendt Apr 29, 2016
f201a30
Removal of bug removal - not considering all reactions in FVA due to …
laurentheirendt Apr 29, 2016
d20b73b
Removal of bug for serial version
laurentheirendt Apr 29, 2016
e96376f
Added results and logFiles
laurentheirendt May 2, 2016
4fb07f8
Changes to fastFVA driver
laurentheirendt May 2, 2016
ec3e0a2
Changes to driver
laurentheirendt May 2, 2016
1c0abf1
Minor changes
laurentheirendt May 2, 2016
738cf77
Added a simple FVA driver. Bugs in fastFVA removed.
laurentheirendt May 2, 2016
b2a22a8
Changes to fastFVA for extra outputs
laurentheirendt May 3, 2016
20f42c6
Pushing MSP version of cplexFVAc.c
laurentheirendt May 3, 2016
a32e80c
New output arguments in C-code
laurentheirendt May 3, 2016
5094939
Changes to output arguments of fastFVA. Bugs removed.
laurentheirendt May 3, 2016
663f5be
Corrected the output of fastFVA
laurentheirendt May 3, 2016
7050870
Changes to fastFVA and the simpleDriver for FVA
laurentheirendt May 3, 2016
4a7e7f7
Final changes to simple Driver for FVA
laurentheirendt May 3, 2016
95976b7
Removal of MSP version of fastFVA
laurentheirendt May 3, 2016
81ed234
Additional datasets and characteristics
laurentheirendt May 3, 2016
6673ed6
Changes to fastFVA - how extra output arguments are handled
laurentheirendt May 13, 2016
ea16204
Model Column Density Sorting
laurentheirendt May 14, 2016
4782736
Classification in fastFVA
laurentheirendt May 16, 2016
f30321b
New splitting strategies
laurentheirendt May 18, 2016
640334e
Minor changes
laurentheirendt May 28, 2016
8973806
New splitting strategies implemented in fastFVA
laurentheirendt May 28, 2016
617f2ce
Preparation of storage for extra Fluxes of very large models
laurentheirendt May 28, 2016
c7497fc
Minor modifications and individual node drivers
laurentheirendt May 28, 2016
426741e
Changes to driver and draft of minimum working example for fastFVA
laurentheirendt Jun 15, 2016
0946b3d
Changes to cobradriver and fba in Julia
laurentheirendt Jun 28, 2016
1a8f59b
Change of default solver
laurentheirendt Jul 5, 2016
84eb37e
Minor changes to readme.md from fastFVA
laurentheirendt Jul 5, 2016
618fed5
How to install gcc on Windows
laurentheirendt Jul 5, 2016
d73223e
Renamed CPLEXParamSet to CPLEXParamSetFVA
laurentheirendt Jul 8, 2016
2fc04c2
added comment about saving very large matrices
marouenbg Jul 8, 2016
083615c
macOS compatibility for fastFVA
laurentheirendt Jul 12, 2016
6632886
WINDOWS 64 compatibility for fastFVA
laurentheirendt Jul 15, 2016
d74612d
Extended compatibility for WINDOWS support
laurentheirendt Jul 19, 2016
d95100b
Fixing repo structure and new compiled MEX file for WIN
laurentheirendt Jul 19, 2016
1ed4ea4
deleted progress.txt file
laurentheirendt Jul 19, 2016
6187707
Changing rights of access for deletion of files
laurentheirendt Jul 19, 2016
b258706
Fixing bugs and validation of fastFVA
laurentheirendt Jul 21, 2016
3676eec
Changes to README in fastFVA
laurentheirendt Jul 21, 2016
b0ed9ac
Changes to README in fastFVA - Usage
laurentheirendt Jul 21, 2016
ac8ae8c
Minor changes to README and drivers
laurentheirendt Jul 21, 2016
644323f
minor changes readme
laurentheirendt Jul 21, 2016
fb179cf
Notes in README
laurentheirendt Jul 21, 2016
3e8f0e1
Warning message for unsorted input reaction vector
laurentheirendt Jul 22, 2016
17c7021
Updated installation
laurentheirendt Jul 22, 2016
c575e40
fvamin/fvamax optional outputs. Gives error if included by default.
Jul 25, 2016
05be659
Changes to fastFVA.m
laurentheirendt Jul 29, 2016
c67c98f
Preparation for input of rxnsOptMode for selectiveFVA optimization
laurentheirendt Jul 29, 2016
cee6be1
Feature of selective min/max
laurentheirendt Jul 29, 2016
74e5b8b
Changes and testing of rxnsOptMode
laurentheirendt Aug 1, 2016
4ed6326
Debugging of new selectiveFVA feature
laurentheirendt Aug 1, 2016
e014ca2
Fixing bugs with selectiveFVA feature and serial version
laurentheirendt Aug 1, 2016
b663de8
Fixing bug of not properly outputting status
laurentheirendt Aug 1, 2016
cd026d7
Expliciting printing the status returned by CPLEX for each reaction
laurentheirendt Aug 1, 2016
849fa5e
Changes to save solution status of each reaction
laurentheirendt Aug 1, 2016
66805d0
Changes to retrieve the solution status for each reaction & debugging
laurentheirendt Aug 1, 2016
943eaf8
Debugging origStat feature
laurentheirendt Aug 1, 2016
dc8d16f
Debugging origstat feature
laurentheirendt Aug 1, 2016
050cbc6
Bugs fixed for origstat
laurentheirendt Aug 2, 2016
d7551e7
Fixing variable nargout sizes - linux version
laurentheirendt Aug 23, 2016
b2719f5
Print warning message for incorrect number of output arguments
laurentheirendt Aug 23, 2016
6b20535
Minor changes
laurentheirendt Aug 23, 2016
592a196
Implementation of optional user interaction
laurentheirendt Aug 31, 2016
941d46a
Minor changes to paramset
laurentheirendt Aug 31, 2016
dccd4b4
Debugging and benchmarking
laurentheirendt Sep 13, 2016
cb2aa34
Fixing bugs for status retrieval
laurentheirendt Sep 14, 2016
e6a0032
Changing the status of the solutions
laurentheirendt Sep 14, 2016
4cb936d
Updated mex file for macOS (2)
laurentheirendt Sep 14, 2016
1489d4e
Merge branch 'master' of https://git-r3lab.uni.lu/MSP/pCOBRA
laurentheirendt Sep 14, 2016
657bd4e
Validated version
laurentheirendt Sep 14, 2016
f243620
Updated README
laurentheirendt Oct 4, 2016
70dc3e3
Revised README for R2016b compatibility
laurentheirendt Oct 18, 2016
a03ecf4
Fixing bugs for issue 11
laurentheirendt Oct 19, 2016
ea8170e
Removal of debugging lines
laurentheirendt Oct 19, 2016
51ec818
Fixed serial; parallel in progress
laurentheirendt Oct 19, 2016
fd79869
Fixing bug of issue 11 in parallel version
laurentheirendt Oct 20, 2016
a0024b0
Updated README
laurentheirendt Oct 21, 2016
c40b637
Changes to paths and new gitignore
laurentheirendt Nov 26, 2016
fe5f10d
Updated README for fastFVA
laurentheirendt Jan 13, 2017
4106e53
Merge branch 'perfEval' into 'master'
laurentheirendt Mar 1, 2017
d67d7a6
set the file name as a global varaible in fastFVA
marouenbg May 19, 2017
d94f797
took out global variable and used argument instead
marouenbg May 22, 2017
143fa2c
Moving parforprogress and test for transfer
laurentheirendt Jun 12, 2017
1c4b1c3
Moving files for transfer
laurentheirendt Jun 13, 2017
a4b6308
Merge remote-tracking branch 'fastFVA/master' into add-fastFVA-3
laurentheirendt Jun 13, 2017
885f745
Moving fastFVA into place
laurentheirendt Jun 7, 2017
abf12f7
Changing permissions
laurentheirendt Jun 7, 2017
5d9b482
Changing permissions of gitignore
laurentheirendt Jun 13, 2017
2ae431a
Moving scripts for fastFVAmex
laurentheirendt Jun 7, 2017
a249ca1
Integration of MEX compilation
laurentheirendt Jun 8, 2017
a852cb3
Integration of generateMexFile
laurentheirendt Jun 8, 2017
767aab9
Draft version of detectCPLEXversion
laurentheirendt Jun 8, 2017
e348706
Change for tmp folder in gitignore
laurentheirendt Jun 8, 2017
739d2cb
changes in fastFVA and readme
laurentheirendt Jun 8, 2017
7526ccc
Moving exampleFVA to test
laurentheirendt Jun 13, 2017
0777874
Renaming detectCPLEXversion function
laurentheirendt Jun 8, 2017
e087e4b
Moving detect CPLEX version
laurentheirendt Jun 8, 2017
7c7de6f
Change for empty root CPLEX path
laurentheirendt Jun 8, 2017
446ac9f
Renaming generateMex driver
laurentheirendt Jun 8, 2017
b6035af
WIP: debugging
laurentheirendt Jun 8, 2017
de98db9
Function constructor based on generated string
laurentheirendt Jun 9, 2017
c130684
Moving files into place
laurentheirendt Jun 9, 2017
6f70ee6
changes to testfastfva
laurentheirendt Jun 12, 2017
e94886b
Moving parfor progress into place
laurentheirendt Jun 13, 2017
711bd7a
Integration of test for fastFVA
laurentheirendt Jun 13, 2017
21f66c0
Removing CPLEXParamSet for FVA
laurentheirendt Jun 13, 2017
ac093e7
Changes to fastFVA
laurentheirendt Jun 13, 2017
7032118
CI integrated test for fastFVA
laurentheirendt Jun 13, 2017
e91d9df
Removing parfor progress files (duplicate)
laurentheirendt Jun 13, 2017
ada85d9
Minor changes to fastFVA
laurentheirendt Jun 14, 2017
f2f71c5
Fix for fastFVAex and strategy > 0
laurentheirendt Jun 14, 2017
cca724d
Adding .tmp folder in path if exists
laurentheirendt Jun 14, 2017
75afab1
Minor changes to test and fastFVA
laurentheirendt Jun 14, 2017
95c5d95
Linting of fastFVA and test functions for fastFVA
laurentheirendt Jun 14, 2017
11a926f
Documentation formatting
laurentheirendt Jun 14, 2017
4af5ddb
Documentation of fastFVA
laurentheirendt Jun 14, 2017
9cd1ea2
Additional linting
laurentheirendt Jun 14, 2017
1164bc2
Additional linting
laurentheirendt Jun 14, 2017
5c9cb0b
Renaming setWorkerCount and moving to base
laurentheirendt Jun 14, 2017
832018c
Minor changes and linting of setWorkerCount
laurentheirendt Jun 14, 2017
7acb7bb
CI integration of cleanFiles
laurentheirendt Jun 14, 2017
7b9b3aa
Changes to cleanFiles arguments
laurentheirendt Jun 14, 2017
f4cd936
Renaming cleanFiles
laurentheirendt Jun 14, 2017
c64b66b
Fix for log files directory and removal of results folder
laurentheirendt Jun 14, 2017
e2152d3
Serial test for fastFVA
laurentheirendt Jun 14, 2017
b81fbe5
Minor changes for robustness
laurentheirendt Jun 14, 2017
79152ac
Changes for Windows
laurentheirendt Jun 14, 2017
43cc254
New SHA1 for COBRA.binary
laurentheirendt Jun 14, 2017
400b0cb
Check of binaries within fastFVA
laurentheirendt Jun 15, 2017
5cf4e12
Revised documentation
laurentheirendt Jun 15, 2017
cfb0141
Fix for link
laurentheirendt Jun 15, 2017
e805e0c
fix for paths in which the tilde is present.
syarra Jun 16, 2017
996e666
remove txt files from evaluating cplex version
syarra Jun 16, 2017
3468370
create .tmp folder if not already there.
syarra Jun 16, 2017
0130106
Fix for optPercentage = 100
laurentheirendt Jun 16, 2017
6fa43d9
New binaries
laurentheirendt Jun 16, 2017
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New SHA1 for COBRA.binary
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@laurentheirendt
laurentheirendt committed Jun 14, 2017
commit 43cc254df0d6331b620f1029f93c24b53db841b3
2 changes: 1 addition & 1 deletion binary
Open in desktop
Submodule binary updated 3 files
+ − glnxa64/bin/fastFVA/cplexFVA1271.mexa64
+ − maci64/bin/fastFVA/cplexFVA1271.mexmaci64
+ − win64/bin/fastFVA/cplexFVA1271.mexw64