libSBML 5.2.0 released

This morning Sarah sent the announcement that a new version of libSBML is available for download from:
http://sf.net/projects/sbml/files/libsbml/5.2.0/ 
New this time around is that we also provide binaries for all the SBML Level 3 Extension packages. So if you are interested in providing software support for:

• FBC
• COMP
• LAYOUT
• GROUPS
• REQ
• SPATIAL

you can simply download your favorite binaries (including language bindings) from the experimental directory.

New Features

There are two new features I want to bring to your attention, that is the facility for custom validators and converters. By inheriting form SBMLConverter or SBMLValidator it is now possible for your application to quickly check for specific aspects of documents that is important to you.

Here just one example on how you could check that your SBML model does not contain Algebraic Rules or Fast reactions if your application does not support them.

   1: /** 

2: * Declares a custom validator to be called. This allows you to validate

3: * any aspect of an SBML Model that you want to be notified about. You could

4: * use this to notify your application that a model contains an unsupported

5: * feature of SBML (either as warning).

6: *

7: * In this example the validator will go through the model and test for the

8: * presence of 'fast' reactions and algebraic rules. If either is used a

9: * warning will be added to the error log.

10: */

11: class MyCustomValidator : public SBMLValidator

12: {

13: public:

14: MyCustomValidator() : SBMLValidator() {}

15: MyCustomValidator(const MyCustomValidator& orig) : SBMLValidator(orig) {

16: 

17: }

18: virtual ~MyCustomValidator() {}

19: 

20: virtual SBMLValidator* clone() const { return new MyCustomValidator(*this); }

21: 

22: virtual unsigned int validate() {

23: // if we don't have a model we don't apply this validator.

24: if (getDocument() == NULL || getModel() == NULL)

25: return 0;

26: 

27: // if we have no rules and reactions we don't apply this validator either

28: if (getModel()->getNumReactions() == 0 && getModel()->getNumRules() == 0)

29: return 0;

30: 

31: unsigned int numErrors = 0;

32: // test for algebraic rules

33: for (unsigned int i = 0; i < getModel()->getNumRules(); i++)

34: {

35: if (getModel()->getRule(i)->getTypeCode() == SBML_ALGEBRAIC_RULE) {

36:

37: getErrorLog()->add(SBMLError(99999, 3, 1,

38: "This model uses algebraic rules, however this application does not support them.",

39: 0, 0,

40: LIBSBML_SEV_WARNING, // or LIBSBML_SEV_ERROR if you want to stop

41: LIBSBML_CAT_SBML // or whatever category you prefer

42: ));

43:

44: numErrors++;

45: }

46: }

47: 

48: // test for fast reactions

49: for (unsigned int i = 0; i < getModel()->getNumReactions(); i++)

50: {

51: // test whether value is set, and true

52: if (getModel()->getReaction(i)->isSetFast() &&

53: getModel()->getReaction(i)->getFast()) {

54: 

55: getErrorLog()->add(SBMLError(99999, 3, 1,

56: "This model uses fast reactions, however this application does not support them.",

57: 0, 0,

58: LIBSBML_SEV_WARNING, // or LIBSBML_SEV_ERROR if you want to stop

59: LIBSBML_CAT_SBML // or whatever category you prefer

60: ));

61: 

62: numErrors++;

63: 

64: }

65: }

66: 

67: return numErrors;

68: }

69: 

70:

71: };

72: 

73: 

74: int

75: main (int argc, char *argv[])

76: {

77: if (argc != 2)

78: {

79: cout << endl << "Usage: addCustomValidator filename" << endl << endl;

80: return 1;

81: }

82:

83: const char* filename = argv[1];

84: 

85: // read the file name

86: SBMLDocument* document = readSBML(filename);

87: 

88: // add a custom validator

89: document->addValidator(new MyCustomValidator());

90: 

91: // check consistency like before

92: int numErrors = document->checkConsistency();

93: 

94: // print errors and warnings

95: document->printErrors();

96: 

97: // return number of errors

98: return numErrors;

99: 

100: }

Linux Packages

For this release we provide again DEB and RPM files with binaries compiled on CentOS 4.6 and Ubuntu 8. This means they use a libc version that is reasonably old and will not cause problems on newer distributions.

Listening to feedback from our users the default install prefix has been changed to /usr. And we also include language bindings in them.

The plan was to use the OpenBuildService (OBS),  but unfortunately I was not yet able to create binaries with language bindings for all different distributions. I hope we can sort this out for the next release.