SBML FILE PARSER

SYSTEMS BIOLOGY MARKUP LANGUAGE AND PARS-

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SBML FILE PARSER

Preliminaries

binary name: requirement.c, SBMLparser

language: C
compilation: via Makefile, including re, clean and fclean rules
Authorized functions: all functions included in the libC

Requirement

Write a C file named requirement.c containing a function that splits a string into words.
Separators are all non-alphanumeric characters.
The function must return an array, in which each cell contains a string’s (representing a word)
address.
The last element of the array must be 0, which marks the end of the array.

It should be prototyped the following way:

char ** my_str_to_word_array_synthesis ( char const * str ) ;

For this part, only malloc and free are allowed from the libC.

The rest of the project will not be corrected unless this requirement is fully functional (and
rewritten).

The file must be placed at the root of your git repository.

It will be compiled with our main function, and our Makefile (the -I flag being empty).

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SBML file parser
Many chemical reactions are responsible for living beings’ ability to develop, move, heal, com-
municate; digestion, for instance, is a chain of chemical reactions.
7439 chemical reactions are present in human beings.#br

A chemical reaction consists in transforming one or several reactant(s) into one or several product(s).
Molecules often have crude names, and are either represented by their chemical formulas or by
acronyms; and their reactions are represented by equations such as:

C6 H12 O6 + 6O2 -> 6CO2 + 6H2 O + ATP

ATP + GLCD -> ADP + G6P

Thus, one can demonstrate how a human being functions through the linking of chemical re-
actions that happen in their cells.
This network is called the metabolic network, and is so complex (as you can see below) that it is
a challenge for modern biology.

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In order to organize this huge amount of information, a XML-based format, which uses special-
ized tags for metabolic networks, was created: the SBML format.
The main tags are:

1. <compartment> to define the compartment of the reaction,

2. <species> to define a chemical product,
3. <reaction> to define a chemical reaction,
4. <speciesReference> to refer to a previously defined chemical reaction,
5. <listOfCompartments>, <listOfSpecies>, <listOfReactions>, <listOfReactants>, <listOfProducts>,
which names are self-exlanatory.

If ever you feel curious, you can download the full specifications here.

As an example, here is example.sbml, the SBML file that describes the second aforementioned
reaction:
<? xml version = " 1.0 " encoding = " UTF -8 " standalone = " no " ? >
< sbml xmlns = " http: // www . sbml . org / sbml / level3 / version1 / core " level = " 3 " version = " 1 " >
< model name = " Homo sapiens Glycolysis " id = " Pathway146 " >
< listOfCompartments >
< compartment name = " Homo sapiens , Cell , Cytosol " id = " Cytosol " / >
</ listOfCompartments >
< listOfSpecies >
< species compartment =" Cytosol " name = " Adenosine diphosphate " id = " Compound1034 " / >
< species compartment =" Cytosol " name = " Glucose 6 - phosphate " id = " Compound1083 " / >
< species compartment =" Cytosol " name = " Alpha -D - Glucose " id = " Compound1851 " / >
< species compartment =" Cytosol " name = " Adenosine triphosphate " id = " Compound414 " / >
</ listOfSpecies >
< listOfReactions >
< reaction reversible =" false " name = " Hexokinase -3 " id = " Reaction1232 " >
< listOfReactants >
< speciesReference stoichiometry = " 1 " species = " Compound1851 " / >
< speciesReference stoichiometry = " 1 " species = " Compound414 " / >
</ listOfReactants >
< listOfProducts >
< speciesReference stoichiometry = " 1 " species = " Compound1083 " / >
< speciesReference stoichiometry = " 1 " species = " Compound1034 " / >
</ listOfProducts >
</ reaction >
</ listOfReactions >
</ model >
</ sbml >

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Simple parser

Write a program that prints, in alphabetical order, the list of tags and attributes found in the
SBML file given as argument.
Each tag and each attribute must be unique.

Don’t bother with error management concerning the tags in the SBML file. You’ll get only
well formatted files.

Your program output has to be strictly identical to the one below.

∇ Terminal - + x
B-SYN-200> ./SBMLparser example.sbml
compartment
->id
->name
model
->id
->name
reaction
->id
->name
->reversible
sbml
->level
->version
->xmlns
species
->compartment
->id
->name
speciesReference
->species
->stoichiometry

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Information extraction

Add the -i ID option to your program.

1. If ID is the id of a <compartment> tag, the program must print an alphabetical list of id-
associated chemical products names on the standard output.
2. If ID is the id of a <species> tag, the program must print a quantified and alphabetical list of
the chemical reactions ids that consume
a chemical product on the standard output.
3. If ID is the id of a <reaction> tag, the program must print an alphabetical list of the reactants,
and products of the reaction, on the standard output (identified by their speciesfield).
4. Otherwise, the program must print the list of all chemical products.

The stoichoimetry tag gives the quantity of consumed chemical products.

Your program output has to be strictly identical to the one below.

∇ Terminal - + x
B-SYN-200> ./SBMLparser example.sbml -i Cytosol
List of species in compartment Cytosol
->Adenosine diphosphate
->Adenosine triphosphate
->Alpha-D-Glucose
->Glucose 6-phosphate

∇ Terminal - + x
B-SYN-200> ./SBMLparser example.sbml -i ChuckNorris
List of species
->Adenosine diphosphate
->Adenosine triphosphate
->Alpha-D-Glucose
->Glucose 6-phosphate

∇ Terminal - + x
B-SYN-200> ./SBMLparser example.sbml -i Compound414
List of reactions consuming species Compound414 (quantities)
->Reaction1232 (1)

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 ∇ Terminal - + x
B-SYN-200> ./SBMLparser example.sbml -i Reaction1232
List of reactants of reaction Reaction1232
->Compound1851
->Compound414
List of products of reaction Reaction1232
->Compound1034
->Compound1083

Add the -e option to print the equation of the reaction, if ID is a reaction id.

If the reaction is reversible, the arrow is to be represented by “<->”.

Your program output has to be strictly identical to the one below.

∇ Terminal - + x
B-SYN-200> ./SBMLparser example.smbl -i Reaction1232 -e
1 Compound1851 + 1 Compound414 -> 1 Compound1034 + 1 Compound1083

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SBML to JSON

∇ Terminal - + x
B-SYN-200> ./SBMLparser example.smbl -i Reaction1232 -e
1 Compound1851 + 1 Compound414 -> 1 Compound1034 + 1 Compound1083

Tags and attibutes taken into account will be the one in the SBML file given in the previous
example, and only these ones.

If the -i option must be filled in, and:

1. if the id is a compartment, only this compartment, and the chemical products and reac-
tions referring to it, must be displayed,

2. if the id is a chemical product, only this product, and the compartments and reactions
referring to it, must be displayed,

3. if the id is a reaction, only this reaction, and the chemical products and compartments
referring to it, must be displayed,

4. otherwise, the -json option is ignored.

∇ Terminal - + x
B-SYN-200> ./SBMLparser -h
USAGE
./SBMLparser SBMLfile [-i ID [-e]] [-json]

DESCRIPTION
SBMLfile SBML file
-i ID id of the compartment, reaction or product to be extracted
(ignored if uncorrect)
-e print the equation if a reaction ID is given as argument
(ignored otherwise)
-json transform the file into a JSON file

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 ∇ Terminal - + x
B-SYN-200> ./SBMLparser example.sbml -i Compound414 -json
{
listOfCompartments: [
{
id: Cytosol,
name: Homo sapiens, Cell, Cytosol
}
],
listOfSpecies: [
{
compartment: Cytosol,
id: Compound414,
name: Adenosine triphosphate
}
],
listOfReactions: [
{
id: Reaction1232,
name: Hexokinase-3,
reversible: false
}
]
}

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 ∇ Terminal - + x
B-SYN-200> ./SBMLparser example.sbml -i Reaction1232 -json
{
listOfReactants: [
{
species: Compound1851,
stoichiometry: 1
},
{
species: Compound414,
stoichiometry: 1
}
],
listOfProducts: [
{
species: Compound1083,
stoichiometry: 1
},
{
species: Compound1034,
stoichiometry: 1
}
]
}

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