-
Notifications
You must be signed in to change notification settings - Fork 1
/
NEWS.txt
245 lines (163 loc) · 7.57 KB
/
NEWS.txt
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
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
SBMLToolbox NEWS -- History of user-visible changes
---------------------------------------------------
Version 4.1.0 Released 2012-01-13
---------------------------------------------------
* New features:
- The toolbox now supports the creation of SBML with
the Level 3 Flux Balance Constraints (fbc) package.
---------------------------------------------------
Version 4.0.1 Released 2011-08-30
---------------------------------------------------
* Bug fixes:
- The functions that create structures now also create
empty substructures as appropriate.
- The structure created by the Model_create function can
be exported without crashing. Thanks to Kieran Smallbone
for reporting this.
* New features:
- There are new functions that will create substructures
within the MATLAB_SBML structure functions. For
example, m = Model_createCompartment(m) will return
a model structure with a compartment structure
created and added to the model.
---------------------------------------------------
Version 4.0.0 Released 2011-07-18
---------------------------------------------------
This release reflects the fact that the libSBML-matlab
binding now includes both the import and export of SBML.
Thus OutputSBML is not included in this release of
SBMLToolbox.
SBMLToolbox 4.0.0 has full support for all levels and
versions of SBML up to Level 3 Version 1 Core.
Simulation capability has been extended to include support
for varying parameters.
Some of the functionality has been removed. This includes
those functions that required the Symbolic Toolbox for
MATLAB and any functions involving a Graphical User Interface.
Thus ALL functionality of SBMLToolbox-4.0.0 is available
using Octave as well as MATLAB. This was functionality that
appeared to be unused.
The documentation has been overhauled and is now available
in html format.
---------------------------------------------------
Version 3.1.2 Released 2010-04-27
---------------------------------------------------
This release adds a missing file to the windows installer
for libSBML-4.0.1 that is embedded in the windows
installer for SBMLToolbox.
There are no functional changes.
---------------------------------------------------
Version 3.1.1 Released 2010-04-12
---------------------------------------------------
* Bug fixes:
- Tracker issue #2954118.
When an output filename is specified for the ode function
it needs to be communicated to the event handling functions.
This is now fixed.
- Tracker issue #2945261.
OutputSBML crashed if there was no KineticLaw math. This
has been fixed. Thanks to Kieran Smallbone for reporting
this.
- The Model_create function was failing to add more recent
fields that the OutputSBML function expects; namely
time_symbol; delay_symbol and namespaces. Thanks to
Wolfram Liebermeister for reporting this.
---------------------------------------------------
Version 3.1.0 Released 2010-01-28
---------------------------------------------------
* New Dependencies
- libSBML-4.0.1
* New features:
- SBML Level 2 Version 4 support is now implemented.
- The functions that validate the MATLAB_SBML structures return
a message indicating which elements within the structure have
caused the failure. This message is an optional second return
argument.
- Simulation of models that use functionDefinitions within rules
has been implemented.
- A function to produce an analytical solution of a model has
been implemented.
- All functions are completely Octave compatible with the
exception of functions using the Symbolic Toolbox.
* Bug fixes:
- Tracker issue #2780454.
The Model_create function was not correctly specifying level
and version. This has been fixed. Thanks to Kieran Smallbone
for reporting it.
- Tracker issue #1928173.
The OutputSBML function was failing to correctly output an empty
stoichiometryMath structure in an L2V3 model. This was due to the
fact that for L2V3 models the stoichiometryMath element was correctly
derived from an SBase object and thus became a structure rather
than just a field in a MATLAB_SBML structure. This has been
corrected.
- Tracker issue #1912974.
The validation of a model with a large number of errors caused
MATLAB to crash. This was due to an error in the calculation
of the memory needed to store and report the errors.
- Tracker issue #1912971.
There was a typo in the RunTest function that caused it
not to run. This is fixed.
- Tracker issue #1912965.
The functions that generate the code to simulate events
failed to take into account the fact that the structure of
the 'trigger' had changed. This has been fixed.
- More rigorous testing revealed several small bugs in the
event handling functions; which have now been corrected.
Version 3.0.0
- uses libSBML-3.1.0
- added the GetStoichiometrySparse function contributed by
Arsen Batagov. This returns the stoichiometry matrix as a
sparse matrix and is much quicker for larger models.
- The TranslateSBML function has a second optional argument
that indicates whether the model is to be validated prior
to import. The default value is 0; indicating no
validation. In the case of no argument to the function;
which opens a browse window to locate the file to import;
the user is prompted to indicate whether validation should
be done. In the case of validation errors these are
displayed to the user, who will be prompted as to
whether to import the model regardless.
- removed the ReadAndValidate function as this was
essentially a version of TranslateSBML that
performed validation.
- added support for SBML Level 2 Version 2 and
Level 2 Version 3. This support does not extend
to the GUI's that could be used to view individual
components of a model.
- fixed bug in DetermineSpeciesRoleInReaction
which failed for a level 1 model
version 2.0.2
uses libsbml-2.3.4
added a time_symbol field to the Model structure
which contains the declaration of the csymbol time
if it has been used in the imported model
- this symbol is then used in the WriteODEFunction
as the time variable
changed the isSBML_Model function so that it does not
fail if the structure contains additional fields
compartment added to function written by WriteODEFunction
so variable compartments and non-unit volume models
are dealt with
functions in AccessToSymbols changed so that the names reflect
the equivalent functions in AccessModel
ReadAndValidateSBML - an additional function that validates
the sbml file being read before importing it
OutputODEFunction - an additional function with flags to
indicate whether to display the output or write the data
to a comma separated variable file (csv)
DisplayODEFunction - changed to always display the output
OutputSBML - corrected the bug whereby if the user entered
no argument MATLAB crashed
Empty kinetic law is created as an empty structure with
an empty parameter structure; this allows the parameters
to be counted
version 2.0.1 beta
Upgraded to use libsbml 2.3.2
Readme updated with information about all functions
OutputSBML adapted to allow an output filename to be
spoecified as an argument
version 2.0.0 beta release with simulation functions that passed the beta release of the semantic-test-suite
Version 1.0.2 is the first official release of the SBMLToolbox separate from libsbml.
Version 1.0.1 was released unofficially to interested parties.
Version 1.0.0 was the initial libsbml binding version (libsbml 2.0.3)