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Index
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__init__ (module)
__init__() (pl.create.newproj.NewProj method)
(pl.pe.parest.ParEst method)
(pl.pipeline.Pipeline method)
(pl.ps1.parscan1.ParScan1 method)
(pl.ps2.parscan2.ParScan2 method)
(pl.sim.sim.Sim method)
(simul.copasi.copasi.Copasi method)
(simul.pl_simul.PLSimul method)
(simul.python.python.Python method)
(simul.simul.Simul method)
_get_input_files() (simul.simul.Simul method)
_get_model_group() (simul.simul.Simul method)
_get_params_list() (simul.copasi.copasi.Copasi method)
(simul.simul.Simul method)
_move_reports() (simul.simul.Simul method)
_ps1_header_init() (simul.simul.Simul method)
_run_par_comput() (simul.copasi.copasi.Copasi method)
(simul.pl_simul.PLSimul method)
(simul.simul.Simul method)
_write_all_fits() (simul.copasi.copasi.Copasi method)
(simul.simul.Simul method)
_write_best_fits() (simul.copasi.copasi.Copasi method)
(simul.simul.Simul method)
_write_params() (simul.simul.Simul method)
A
analyse_data() (pl.pe.parest.ParEst method)
(pl.ps1.parscan1.ParScan1 method)
(pl.ps2.parscan2.ParScan2 method)
(pl.sim.sim.Sim method)
C
call_proc() (in module utils.parcomp)
check_model_loading() (in module simul.copasi.model_checking)
check_task_report() (in module simul.copasi.model_checking)
check_task_selection() (in module simul.copasi.model_checking)
cleanup() (in module sbpipe_cleanup)
Copasi (class in simul.copasi.copasi)
copasi_model_checking() (in module simul.copasi.model_checking)
copasi_preproc() (in module snakemake.preproc)
E
emit() (__init__.NullHandler method)
escape_special_chars() (in module utils.re_utils)
F
files_with_pattern_recur() (in module utils.io)
G
generate_data() (in module snakemake.data_generation)
(pl.pe.parest.ParEst method)
(pl.ps1.parscan1.ParScan1 method)
(pl.ps2.parscan2.ParScan2 method)
(pl.sim.sim.Sim method)
generate_report() (pl.pe.parest.ParEst method)
(pl.ps1.parscan1.ParScan1 method)
(pl.ps2.parscan2.ParScan2 method)
(pl.sim.sim.Sim method)
generate_tarball() (pl.pipeline.Pipeline method)
generic_postproc() (in module snakemake.pe_postproc)
(in module snakemake.ps1_postproc)
(in module snakemake.ps2_postproc)
(in module snakemake.sim_postproc)
generic_preproc() (in module snakemake.preproc)
get_all_fits() (simul.simul.Simul method)
get_best_fits() (simul.simul.Simul method)
get_index() (in module sbpipe_move_datasets)
get_lang() (simul.pl_simul.PLSimul method)
get_lang_err_msg() (simul.pl_simul.PLSimul method)
get_lang_options() (simul.pl_simul.PLSimul method)
get_latex_header() (in module report.latex_reports)
get_models_folder() (pl.pipeline.Pipeline method)
get_pattern_pos() (in module utils.io)
get_rand_alphanum_str() (in module utils.rand)
get_rand_num_str() (in module utils.rand)
get_sim_columns() (simul.simul.Simul method)
get_sim_data_folder() (pl.pipeline.Pipeline method)
get_sim_plots_folder() (pl.pipeline.Pipeline method)
get_simul_obj() (pl.pipeline.Pipeline method)
get_working_folder() (pl.pipeline.Pipeline method)
git_clone() (in module utils.io)
git_pull() (in module utils.io)
git_retrieve() (in module utils.io)
I
is_output_file_clean() (in module utils.parcomp)
is_py_package_installed() (in module utils.dependencies)
is_r_package_installed() (in module utils.dependencies)
L
latex_report() (in module report.latex_reports)
latex_report_pe() (in module report.latex_reports)
latex_report_ps1() (in module report.latex_reports)
latex_report_ps2() (in module report.latex_reports)
latex_report_sim() (in module report.latex_reports)
load() (pl.pipeline.Pipeline method)
M
main() (in module __init__)
(in module sbpipe_cleanup)
(in module sbpipe_move_datasets)
model_checking() (in module snakemake.model_checking)
(simul.copasi.copasi.Copasi method)
move_dataset() (in module sbpipe_move_datasets)
N
nat_sort_key() (in module utils.re_utils)
NewProj (class in pl.create.newproj)
NullHandler (class in __init__)
P
parcomp() (in module utils.parcomp)
ParEst (class in pl.pe.parest)
ParScan1 (class in pl.ps1.parscan1)
ParScan2 (class in pl.ps2.parscan2)
parse() (pl.pe.parest.ParEst method)
(pl.pipeline.Pipeline method)
(pl.ps1.parscan1.ParScan1 method)
(pl.ps2.parscan2.ParScan2 method)
(pl.sim.sim.Sim method)
pdf_report() (in module report.latex_reports)
pe() (simul.copasi.copasi.Copasi method)
(simul.pl_simul.PLSimul method)
(simul.simul.Simul method)
pe_collect() (in module snakemake.pe_collection)
pe_combine_param_best_fits_stats() (in module snakemake.pe_analysis)
pe_combine_param_ple_stats() (in module snakemake.pe_analysis)
pe_ds_preproc() (in module snakemake.pe_analysis)
pe_objval_vs_iters_analysis() (in module snakemake.pe_analysis)
pe_parameter_density_analysis() (in module snakemake.pe_analysis)
pe_parameter_pca_analysis() (in module snakemake.pe_analysis)
pe_postproc() (in module snakemake.pe_postproc)
pe_sampled_2d_ple_analysis() (in module snakemake.pe_analysis)
pe_sampled_ple_analysis() (in module snakemake.pe_analysis)
Pipeline (class in pl.pipeline)
pl (module)
pl.create (module)
pl.create.newproj (module)
pl.pe (module)
pl.pe.parest (module)
pl.pipeline (module)
pl.ps1 (module)
pl.ps1.parscan1 (module)
pl.ps2 (module)
pl.ps2.parscan2 (module)
pl.sim (module)
pl.sim.sim (module)
PLSimul (class in simul.pl_simul)
preproc() (in module snakemake.preproc)
progress_bar() (in module utils.parcomp)
progress_bar2() (in module utils.parcomp)
ps1() (simul.copasi.copasi.Copasi method)
(simul.pl_simul.PLSimul method)
(simul.simul.Simul method)
ps1_analyse_plot() (in module snakemake.ps1_analysis)
ps1_analyse_plot_homogen() (in module snakemake.ps1_analysis)
ps1_header_init() (in module snakemake.ps1_postproc)
ps1_postproc() (in module snakemake.ps1_postproc)
(simul.simul.Simul method)
ps2() (simul.copasi.copasi.Copasi method)
(simul.pl_simul.PLSimul method)
(simul.simul.Simul method)
ps2_analyse_plot() (in module snakemake.ps2_analysis)
ps2_postproc() (in module snakemake.ps2_postproc)
(simul.simul.Simul method)
Python (class in simul.python.python)
Q
quick_debug() (in module utils.parcomp)
R
refresh() (in module utils.io)
remove_file_silently() (in module utils.io)
replace_str_in_file() (in module utils.io)
replace_str_in_report() (in module utils.io)
(simul.pl_simul.PLSimul method)
(simul.simul.Simul method)
report (module)
report.latex_reports (module)
run() (pl.create.newproj.NewProj method)
(pl.pe.parest.ParEst method)
(pl.pipeline.Pipeline method)
(pl.ps1.parscan1.ParScan1 method)
(pl.ps2.parscan2.ParScan2 method)
(pl.sim.sim.Sim method)
run_cmd() (in module utils.parcomp)
run_cmd_block() (in module utils.parcomp)
run_copasi_model() (in module snakemake.data_generation)
run_generic_model() (in module snakemake.data_generation)
run_jobs_local() (in module utils.parcomp)
run_jobs_lsf() (in module utils.parcomp)
run_jobs_sge() (in module utils.parcomp)
S
sbpipe() (in module __init__)
sbpipe_cleanup (module)
sbpipe_license() (in module __init__)
sbpipe_logo() (in module __init__)
sbpipe_move_datasets (module)
sbpipe_version() (in module __init__)
set_basic_logger() (in module __init__)
set_color_logger() (in module __init__)
set_console_logger() (in module __init__)
set_logger() (in module __init__)
severity2string() (in module simul.copasi.model_checking)
Sim (class in pl.sim.sim)
sim() (simul.copasi.copasi.Copasi method)
(simul.pl_simul.PLSimul method)
(simul.simul.Simul method)
sim_analyse_gen_stats_table() (in module snakemake.sim_analysis)
sim_analyse_plot_comb_sims() (in module snakemake.sim_analysis)
sim_analyse_plot_sep_sims() (in module snakemake.sim_analysis)
sim_analyse_summarise_data() (in module snakemake.sim_analysis)
sim_postproc() (in module snakemake.sim_postproc)
Simul (class in simul.simul)
simul (module)
simul.copasi (module)
simul.copasi.copasi (module)
simul.copasi.model_checking (module)
simul.pl_simul (module)
simul.python (module)
simul.python.python (module)
simul.simul (module)
snakemake (module)
snakemake.data_generation (module)
snakemake.model_checking (module)
snakemake.pe_analysis (module)
snakemake.pe_collection (module)
snakemake.pe_postproc (module)
snakemake.preproc (module)
snakemake.ps1_analysis (module)
snakemake.ps1_postproc (module)
snakemake.ps2_analysis (module)
snakemake.ps2_postproc (module)
snakemake.sim_analysis (module)
snakemake.sim_postproc (module)
U
utils (module)
utils.dependencies (module)
utils.io (module)
utils.parcomp (module)
utils.rand (module)
utils.re_utils (module)
W
which() (in module utils.dependencies)
write_mat_on_file() (in module utils.io)
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