Newer
Older
Ricardo Andrade
committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
How to compile the code
========================
Dependencies to install:
Running
=======
The MOMO software has several running modes that can be used by
passing different combinations of flags and parameters by command
line.
Running ./MOMO -h shows the help with all the possible flags:
-h [ --help ] produce help message
-N [ --network-file ] arg input network file (MANDATORY).
-B [ --bounds-file ] arg input file with the bounds for the
input file (MANDATORY).
-o [ --output-file ] arg (=solutions.txt)
output file.
-t [ --optimizer-timeout ] arg (=3600)
Timeout for the optimization procedure
(in seconds).
--maximize arg Reactions to maximize
--minimize arg Reactions to minimize
--reactions-to-fix arg Reactions to fix. Format
reactionID=flux[,reactionID=flux]
(useful for the enumeration)
--number-deletions arg (=0) Consider deletions sets of informed
size.
--enumerate Enumerates deletions. In this case the
objective functions are ignored.
-D [ --deletions-candidates-file ] arg
input file with the reactions that
should be considered for deletion.
-R [ --reference-flux-file ] arg input file with the fluxes that will be
used as reference for the MOMA approach
during enumeration.
-m [ --optimizer-internal-memory ] arg (=2048)
Internal memory used by the optimizer
before using disk space (in Mb).
The network file (-N flag) and the file with the upper and lower
bounds (-B flag) should be always provided when invoking MOMO.
Optimise a flux
---------------
In order to optimise one flux (for example, the biomass reaction) you
should invoke MOMO with at least the following flags:
--maximize (or --minimize, depending how you want to optimize);
The argument for this flag should be the id of the reaction that you
want to optimize according to the SBML file used.
Example:
./MOMO -N yeast_5.01_model.xml -B bounds.txt --maximize=r_2110 -o fba.out
In this example we set the metabolic network as the file
"yeast_5.01_model.xml", the bounds for each reactio of the SBML file
are given by the file "bounds.txt", we set the optimization function
to be the reaction with the id r_2110 and we set the output file to be
"fba.out".
Optimise several fluxes considering deletions
----------------------------------------------
In order to optimise multiple fluxes (for example, the biomass and
ethanol productions) you should invoke MOMO with at least the
following flags:
--maximize (or --minimize, depending how you want to optimize);
The argument for this flag should be the ids of the reactions that you
want to optimize according to the SBML file used, separated by commas.
--number-deletions;
The argument for this flag should be an integer >= 1, representing the
size of the deletion set. So if the parameter is 1, we have single
deletions, if it is 2 then we have pairs of deletions, and so on.
Example:
Enumerate deletions
-------------------
In order to enumerate all deletions for a fixed production state (for
example, given that biomass is equal to 0.4 and that the ethanol is
equal to 6) should invoke MOMO with at least the
following flags:
--enumerate
--number-deletions;
The argument for this flag should be an integer >= 1, representing the
size of the deletion set. So if the parameter is 1, we have single
deletions, if it is 2 then we have pairs of deletions, and so on.
IMPORTANT:
--maximize and--minimize should not be used in the enumeration mode.
Example:
./MOMO -N yeast_5.01_model.xml -B bounds.txt -D candidateReactions.txt -R
fba.out -o enumeration.out --number-deletions=1 --reactions-to-fix
r_2110=0.1,r_1761=17.4 --enumerate
In this example we set the metabolic network as the file
"yeast_5.01_model.xml", the bounds for each reactio of the SBML file
are given by the file "bounds.txt", we selected to enumerate single
deletions (--enumerate and --number-deletions=1) and we fix the
reaction r_2110 (biomass) to 0.1 and the reaction r_1761 (ethanol) to
17.4.
This means we want to enumerate all single deletions that enables a
biomass of 0.1 and an ethanol production of 17.4.