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TCA_cycle
TCA_cycle
 
 
syn7002_ll-n
syn7002_ll-n
 
 
test
test
 
 
.gitattributes
.gitattributes
 
 
INST_FLUX_documentation.pdf
INST_FLUX_documentation.pdf
 
 
INST_emu.m
INST_emu.m
 
 
INST_emu_par.m
INST_emu_par.m
 
 
INST_fun.m
INST_fun.m
 
 
INST_grad.m
INST_grad.m
 
 
INST_sqerror.m
INST_sqerror.m
 
 
INST_sqerror_grad.m
INST_sqerror_grad.m
 
 
INSTdfode.m
INSTdfode.m
 
 
INSTdfode_mex.c
INSTdfode_mex.c
 
 
INSTdvode.m
INSTdvode.m
 
 
INSTdvode_mex.c
INSTdvode_mex.c
 
 
INSTdxode.m
INSTdxode.m
 
 
INSTdxode_mex.c
INSTdxode_mex.c
 
 
INSTfjac.m
INSTfjac.m
 
 
INSTode.m
INSTode.m
 
 
INSTode_mex.c
INSTode_mex.c
 
 
README.md
README.md
 
 
abundance.csv
abundance.csv
 
 
calc_ci_samp.m
calc_ci_samp.m
 
 
calc_conf_int.m
calc_conf_int.m
 
 
calc_corr_matrix.m
calc_corr_matrix.m
 
 
calc_sim_mid.m
calc_sim_mid.m
 
 
chebycenter.m
chebycenter.m
 
 
conf_int_fun.m
conf_int_fun.m
 
 
corr_matrix_row.m
corr_matrix_row.m
 
 
cprnd.m
cprnd.m
 
 
dec2binvec.m
dec2binvec.m
 
 
eval_kfpsol.c
eval_kfpsol.c
 
 
eval_kfpsol.h
eval_kfpsol.h
 
 
forward_simulation.m
forward_simulation.m
 
 
generate_emumodel.m
generate_emumodel.m
 
 
load_abundances.m
load_abundances.m
 
 
load_compositions.m
load_compositions.m
 
 
plot_result.m
plot_result.m
 
 
plot_result_forward_sim.m
plot_result_forward_sim.m
 
 
process_results.m
process_results.m
 
 
read_conc.m
read_conc.m
 
 
read_conc_forward_sim.m
read_conc_forward_sim.m
 
 
read_ldata.m
read_ldata.m
 
 
read_ldata_forward_sim.m
read_ldata_forward_sim.m
 
 
sample_polytope.m
sample_polytope.m
 
 
setup.m
setup.m
 
 
simulate_demumodel.m
simulate_demumodel.m
 
 
simulate_emumodel.m
simulate_emumodel.m
 
 
write_results.m
write_results.m
 
 
write_results_conf_int.m
write_results_conf_int.m
 
 

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INST-Flux is a Matlab based software package that can infer flux distributions based on experimental labeling data.

The framework used is the EMU framework for INST-MFA (Young et al, 2008, Biotechnology and Bioengineering, Vol. 99, No. 3), with a different optimization algorithm, namely the built-in Matlab interior point method.

INST-FLUX requires the Matlab optimization toolbox, as well as the Matlab SDK compiler.

Installation:

To install INST-FLUX, after downloading the software, in the parent directory INST-FLUX run the command:

setup

the following command should terminate without any errors.

INST_emu('test')

For information on input files as well as directions on use please see the file "INST_Flux_documentation.pdf" in the parent directory.

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