Atomizer
Atomizer is a translator tool that can convert SBML models to BNGL models. Moreover, atomizer is capable of extracting implicit information found in SBML models using lexical analysis, reaction stoichiometry and annotation information. Using this information, atomizer converts SBML species to structured BNGL complexes.
This in turn allows for easier identification of modification sites, binding interactions while making the model easier to understand and analyze. Combined with BNGL visualization capabilities, atomizer also allows for easier model comparison of the same biological process.
Getting Started
Make sure you have PyBioNetGen properly installed by running
bionetgen -h
If this command doesn’t print out help information, install PyBioNetGen with
pip install bionetgen
Basics of atomizing a model
Use the atomize method to convert a SBML model to BNGL directly (flat translation)
bionetgen atomize -i mymodel.xml -o mymodel_flat.bngl
Using the -a option allows for atomization of the model (atomized translation)
bionetgen atomize -i mymodel.xml -o mymodel_flat.bngl -a
if the atomization is taking a long time, try the -mr option (please note that this might use up a lot of memory)
bionetgen atomize -i mymodel.xml -o mymodel_flat.bngl -a -mr
If you encounter atomization errors, you can fix it by using a user input JSON file which is given by the -u option (see below)
bionetgen atomize -i mymodel.xml -o mymodel_flat.bngl -a -u user_input.json
Atomizer looks up annotation information on various online resources (namely Pathway Commons, BioGRID and UniProt). This generally allows for easier atomization, reducing user input required. If you don’t have internet connection you can turn this off with the -p option
bionetgen atomize -i mymodel.xml -o mymodel_flat.bngl -a -p
Generally a complex model will require several options with a bit of user input in JSON format (see below), for example
bionetgen atomize -i mymodel.xml -o mymodel_flat.bngl -a -u user_input.json
If the atomizer output is too cluttered you can adjust the output levels with the -ll option
bionetgen atomize -i mymodel.xml -o mymodel_flat.bngl -a -u user_input.json -ll "ERROR"
we suggest using “ERROR” or “WARNING” for -ll argument.
User input format
The user input JSON file has 4 potential fields. Empty fields can be omitted.
{
"reactionDefinition" : [
],
"partialComplexDefinition" : [
],
"binding_interactions" : [
["Partner1", "Partner2"]
],
"modificationDefinition": {
"complex":["molecule1", "molecule2"],
}
}
“binding_interactions” field is an array where each element is also an array of two items. Both items should be the names of species in the model, exactly as written in the SBML. This represents that there is a binding interaction between the two items which in turn tells atomizer that there should be a binding component on both molecules for each other.
“modificationDefinition” field is a dictionary where the key is a complex in the model and the value is an array that reflects what the complex is comprised of.
“reactionDefinition” field is…
“partialComplexDefinition” field is…
Examples of atomization
These tutorials shows how to use Atomization tool to make a BNGL Model from SBML format. We will Use various curated models from the biomodels database. You can download the specific SBML files by clicking on the titles.
Biomodels database model 48
Atomizing the Model: Once you download the SBML file of BMD48, you will have an .xml
file in your directory. Use it as the input to the atomize subcommand as shown below. To show the
effect of using the web services we’ll also add the -p option to not use the web serices at first
bionetgen atomize -i BIOMD0000000048.xml -o BMD48.bngl -a -p
you can name the bngl output file whatever you want. This will print out information on the atomization process. If the output is too cluttered you can look at only the major errors using the following command
bionetgen atomize -i BIOMD0000000048.xml -o BMD48.bngl -a -p -ll "ERROR"
which prints out
ERROR:SCT212:['EGF_EGFR2']:EGF_EGFR2_P:Atomizer needs user information to determine which element is being modified among component species:['EGF', 'EGF', 'EGFR', 'EGFR']:_p
ERROR:ATO202:['EGF_EGFR2', 'EGF_EGFR2_PLCg_P']:(('EGF', 'EGF'), ('EGF', 'EGFR'), ('EGFR', 'EGFR')):We need information to resolve the bond structure of these complexes . Please choose among the possible binding candidates that had the most observed frequency in the reaction network or provide a new one
ERROR:ATO202:['EGF_EGFR2_Shc_Grb2_SOS']:(('EGF', 'Grb2'), ('EGF', 'SOS'), ('EGF', 'Shc'), ('EGFR', 'Grb2'), ('EGFR', 'SOS'), ('EGFR', 'Shc')):We need information to resolve the bond structure of these complexes . Please choose among the possible binding candidates that had the most observed frequency in the reaction network or provide a new one
Structured molecule type ratio: 0.7
the first three “ERROR”s tells us that atomizer needs user input to resolve certain ambiguities in the model. Structured molecule type ratio is the ratio of structured species in the molecule types block of the resulting BNGL to the total number of molecule types, to give an idea of how successful atomizer was at inferring structure of the species in the model.
Before we give atomizer more user input, let’s try removing the -p option to see if atomizer can resolve these automatically
bionetgen atomize -i BIOMD0000000048.xml -o BMD48.bngl -a -ll "ERROR"
which prints out
ERROR:SCT212:['EGF_EGFR2']:EGF_EGFR2_P:Atomizer needs user information to determine which element is being modified among component species:['EGF', 'EGF', 'EGFR', 'EGFR']:_p
ERROR:ATO202:['EGF_EGFR2_PLCg_P']:(('EGF', 'PLCg'), ('EGFR', 'PLCg')):We need information to resolve the bond structure of these complexes . Please choose among the possible binding candidates that had the most observed frequency in the reaction network or provide a new one
Structured molecule type ratio: 0.875
there were multiple instances of “ERROR:MSC02” that warn the user about issues with connections to the BioGRID service which were removed for clarity. Now we only have two errors left.
Resolving errors
Now let’s take a look at the remaining issues one by one
ERROR:SCT212:['EGF_EGFR2']:EGF_EGFR2_P:Atomizer needs user information to determine which element is being modified among component species:['EGF', 'EGF', 'EGFR', 'EGFR']:_p
atomizer is having trouble figuring out where the modification _p is supposed to go, which is a phosphorylation site. We know that EGFR is the molecule that’s being phosphorylated so we make a JSON file (here we call it user-input_1.json)
{
"modificationDefinition": {
"EGF_EGFR2_P": ["EGFR_P", "EGFR", "Epidermal_Growth_Factor", "Epidermal_Growth_Factor"]
}
}
and we rerun atomization with the -u option using this JSON file we created
bionetgen atomize -i BIOMD0000000048.xml -o BMD48.bngl -a -ll "ERROR" -u user-input-1.json
which returns (disregarding connection errors)
ERROR:ATO202:['EGF_EGFR2_PLCg', 'EGF_EGFR2_PLCg_P']:(('EGFR', 'PLCg'), ('Epidermal_Growth_Factor', 'PLCg')):We need information to resolve the bond structure of these complexes . Please choose among the possible binding candidates that had the most observed frequency in the reaction network or provide a new one
which tells us that atomizer can’t resolve where PLCg is binding, let’s add that to the JSON file
{
"binding_interactions": [
["EGFR", "PLCg"]
],
"modificationDefinition": {
"EGF_EGFR2_P": ["EGFR_P", "EGFR", "Epidermal_Growth_Factor", "Epidermal_Growth_Factor"]
}
}
rerunning atomizer should return no errors and you should now have a fully atomized BNGL model. Visualizing the model and using yEd to look at the contact map gives us the following
Biomodels database model 19
This model is an expanded version of BioModel 48. Let’s follow the same strategy and atomize it without any input first and see what atomizer says.
bionetgen atomize -i BIOMD0000000019.xml -o BMD19.bngl -a -ll "ERROR"
this returns
ERROR:ATO202:['EGF_EGFRm2_GAP_Grb2_Prot', 'EGF_EGFRm2_GAP_Grb2_Sos_Prot',
'EGF_EGFRm2_GAP_Shcm_Grb2_Prot', 'EGF_EGFRm2_GAP_Grb2_Sos_Ras_GTP_Prot',
'EGF_EGFRm2_GAP_Shcm_Grb2_Sos_Prot', 'EGF_EGFRm2_GAP_Grb2_Sos_Ras_GDP_Prot',
'EGF_EGFRm2_GAP_Shcm_Grb2_Sos_Ras_GTP_Prot',
'EGF_EGFRm2_GAP_Shcm_Grb2_Sos_Ras_GDP_Prot']:
(('EGF', 'Prot'), ('EGFR', 'Prot'), ('GAP', 'Prot'),
('Grb2', 'Prot')):We need information to resolve the bond structure of these
complexes . Please choose among the possible binding candidates that had the
most observed frequency in the reaction network or provide a new one
Structured molecule type ratio: 0.6363636363636364
which tells us that atomizer is having trouble figuring out which binding interaction to include for Prot. We know that protein binds to EGFR so let’s include that in a user input JSON file
{
"binding_interactions": [
["EGFR", "Prot"]
]
}
and now rerunning the atomization using this user input file
bionetgen atomize -i BIOMD0000000019.xml -o BMD19.bngl -a -ll "ERROR" -u user-input-1.json
now returns no errors. However, looking at the resuling BNGL shows Ras_GTP(Ras_GDP~0~1,egfr,i~0~I,m~0~M,raf) and we know that Ras should be the base species. We can include that using the modificationDefinition section in the user input file
{
"binding_interactions": [
["EGFR", "Prot"]
],
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"]
}
}
rerunning atomization using this user input gives a fully atomized BNGL file. Visualizing the model and using yEd to look at the contact map gives us the following
Biomodels database model 151
Running atomizer on this model with the following
bionetgen atomize -i bmd0000000151.xml -o bmd151.bngl -a -ll "ERROR"
we get the following errors
ERROR:ANN202:Ras_GTP:Rafast:can be mapped through naming conventions but the annotation information does not match
ERROR:ANN202:Ras_GDP:Rafast:can be mapped through naming conventions but the annotation information does not match
ERROR:SCT211:IL6_gp80_gp130_JAKast2_STAT3C_SOCS3_SHP2:[['IL6_gp80', 'IL6_gp80', 'gp130_JAK_ast', 'gp130_JAK', 'SHP2', 'SOC
S3', 'STAT3C'], ['IL6_gp80_gp130_JAKast2_STAT3C_SHP2', 'SOCS3']]:[['IL6_gp80', 'IL6_gp80', 'JAK', 'JAK', 'SHP2', 'SOCS3',
'STAT3'], ['IL6_gp80', 'SOCS3']]:Cannot converge to solution, conflicting definitions
ERROR:SCT211:IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GDP:[['Grb2', 'IL6_gp80', 'IL6_gp80', 'gp130_JAK_ast', 'gp130_JAK
', 'Ras_GDP', 'SHP2ast', 'SOS'], ['Grb2', 'IL6_gp80', 'IL6_gp80', 'gp130_JAK_ast', 'gp130_JAK', 'Ras_GTP', 'SHP2ast', 'SOS
']]:[['Grb2', 'IL6_gp80', 'IL6_gp80', 'JAK', 'JAK', 'Ras_GDP', 'SHP2', 'SOS'], ['Grb2', 'IL6_gp80', 'IL6_gp80', 'JAK', 'JA
K', 'Ras_GTP', 'SHP2', 'SOS']]:Cannot converge to solution, conflicting definitions
ERROR:SCT211:IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GTP:[['Grb2', 'IL6_gp80', 'IL6_gp80', 'gp130_JAK_ast', 'gp130_JAK
', 'Ras_GDP', 'SHP2ast', 'SOS'], ['Grb2', 'IL6_gp80', 'IL6_gp80', 'gp130_JAK_ast', 'gp130_JAK', 'Ras_GTPast', 'SHP2ast', '
SOS']]:[['Grb2', 'IL6_gp80', 'IL6_gp80', 'JAK', 'JAK', 'Ras_GDP', 'SHP2', 'SOS'], ['Grb2', 'IL6_gp80', 'IL6_gp80', 'JAK',
'JAK', 'Ras_GTP', 'SHP2', 'SOS']]:Cannot converge to solution, conflicting definitions
ERROR:ATO202:['IL6_gp80_gp130_JAK2', 'IL6_gp80_gp130_JAK_ast2', 'IL6_gp80_gp130_JAKast2_JAK', 'IL6_gp80_gp130_JAKast2_SOCS
3', 'IL6_gp80_gp130_JAKast2_STAT3C', 'IL6_gp80_gp130_JAKast2_SHP2ast', 'IL6_gp80_gp130_JAKast2_STAT3Cast', 'IL6_gp80_gp130
_JAKast2_SHP2ast_Grb2', 'IL6_gp80_gp130_JAKast2_STAT3C_SOCS3', 'IL6_gp80_gp130_JAKast2_SHP2_Grb2']:(('IL6_gp80', 'IL6_gp80
'), ('IL6_gp80', 'JAK'), ('JAK', 'JAK')):We need information to resolve the bond structure of these complexes . Please cho
ose among the possible binding candidates that had the most observed frequency in the reaction network or provide a new one
first two errors show that atomizer is having problems identifying Ras_GTP, Ras_GDP as Ras. We can tell atomizer the basic building blocks for the atomization in the modificationDefinition block
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"]
}
looking at the other errors we can tall atomizer also is having trouble identifing the binding between IL6 and gp80 since it’s asking about binding interactions between IL6_gp80 and other items, let’s fix that too
{
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"],
"IL6_gp80": ["IL6", "gp80"]
}
}
Rerunning atomizer with this user input using the following
bionetgen atomize -i bmd0000000151.xml -o bmd151.bngl -a -ll "ERROR" -u user_input_151.json
gives the following new set of errors
ERROR:ATO202:['IL6_gp80_gp130_JAK', 'IL6_gp80_gp130_JAK2', 'IL6_gp80_gp130_JAK_ast2']:
(('IL6', 'JAK'), ('JAK', 'gp80')):We need information to resolve the bond structure
of these complexes . Please choose among the possible binding candidates that had the
most observed frequency in the reaction network or provide a new one
ERROR:ATO202:['IL6_gp80_gp130_JAKast2_JAK', 'IL6_gp80_gp130_JAKast2_SHP2ast',
'IL6_gp80_gp130_JAKast2_STAT3C_SHP2', 'IL6_gp80_gp130_JAKast2_SHP2ast_Grb2',
'IL6_gp80_gp130_JAKast2_SHP2_Grb2', 'IL6_gp80_gp130_JAKast2_STAT3C_SOCS3_SHP2',
'IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GDP',
'IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GTP']:
(('IL6', 'SHP2'), ('SHP2', 'gp80')):We need information to resolve the bond structure
of these complexes . Please choose among the possible binding candidates that had the
most observed frequency in the reaction network or provide a new one
ERROR:ATO202:['IL6_gp80_gp130_JAKast2_SOCS3', 'IL6_gp80_gp130_JAKast2_STAT3C_SOCS3']:
(('IL6', 'SOCS3'), ('SOCS3', 'gp80')):We need information to resolve the bond structure of
these complexes . Please choose among the possible binding candidates that had the most
observed frequency in the reaction network or provide a new one
ERROR:ATO202:['IL6_gp80_gp130_JAKast2_STAT3C']:(('IL6', 'STAT3C'), ('STAT3C', 'gp80')):
We need information to resolve the bond structure of these complexes . Please choose among
the possible binding candidates that had the most observed frequency in the reaction network
or provide a new one
ERROR:ATO202:['IL6_gp80_gp130_JAKast2_STAT3Cast']:(('IL6', 'STAT3Cast'), ('STAT3Cast', 'gp80')):
We need information to resolve the bond structure of these complexes . Please choose among
the possible binding candidates that had the most observed frequency in the reaction network
or provide a new one
unfortunately, we know from the model that these are not the correct binding interactions. JAK binds to gp130 and so does SHP2. Let’s add those in
{
"binding_interactions": [
["gp130", "SHP2"],
["gp130", "JAK"]
],
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"],
"IL6_gp80": ["IL6", "gp80"]
}
}
which gives
ERROR:SCT241:IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GDP:
IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GTP:produce the same translation:
['Grb2', 'IL6', 'IL6', 'JAK', 'JAK_ast', 'Ras_GDP', 'SHP2ast', 'SOS', 'gp130', 'gp130',
'gp80', 'gp80']:IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GTP:was emptied
We can tell atomizer the composition of IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GTP with
{
"binding_interactions": [
["gp130", "SHP2"],
["gp130", "JAK"]
],
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"],
"IL6_gp80": ["IL6", "gp80"],
"IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GTP": ["IL6","gp80","gp130","JAK","IL6","gp80","gp130","JAK","SHP2","Grb2","SOS","Ras"]
}
}
which atomizer without errors. Looking at BNGL, we can see that atomizer misses the interaction between SOS and Ras and instead binds SOS to Grb2, we can fix that with this final JSON addition
{
"binding_interactions": [
["gp80", "gp80"],
["gp130", "SHP2"],
["SOS", "Ras"]
],
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"],
"IL6_gp80": ["IL6", "gp80"],
"IL6_gp80_gp130_JAKast2_SHP2ast_Grb2_SOS_Ras_GTP": ["IL6","gp80","gp130","JAK","IL6","gp80","gp130","JAK","SHP2","Grb2","SOS","Ras"]
}
}
which gives us a fully atomized model.
Biomodels database model 543
Model 543 is an expanded version of model 151, please look at BMD151 tutorial before starting here. We will start from a subset of the the final user input JSON file we constructed for BMD151.
We can then use the following command to start atomizing with this user input file (which we named user_input_543)
bionetgen atomize -i bmd0000000543.xml -o bmd543.bngl -a -ll "ERROR" -u user_input_543.json
which gives us the following set of errors and a reasonably well atomized model
ERROR:ATO202:['IFN_R_JAK2m_SHP2']:(('IFN', 'SHP2'), ('JAK', 'SHP2'), ('R', 'SHP2')):
We need information to resolve the bond structure of these complexes .
Please choose among the possible binding candidates that had the most observed
frequency in the reaction network or provide a new one
ERROR:ATO202:['IFN_R_JAK2m_STAT3C']:(('IFN', 'STAT3C'), ('JAK', 'STAT3C'), ('R', 'STAT3C')):
We need information to resolve the bond structure of these complexes . Please choose among
the possible binding candidates that had the most observed frequency in the reaction network
or provide a new one
ERROR:ATO202:['IFN_R_JAK2m_STAT3Cm']:(('IFN', 'STAT3Cm'), ('JAK', 'STAT3Cm'), ('R', 'STAT3Cm')):
We need information to resolve the bond structure of these complexes .
Please choose among the possible binding candidates that had the most observed frequency
in the reaction network or provide a new one
ERROR:SCT241:IL6_gp80_gp130_JAK2m_STAT1:IL6_gp80_gp130_JAK2m_STAT1C:produce the same translation:
['IL6', 'IL6', 'JAKIL_6', 'JAKIL_6', 'STAT1C', 'gp130', 'gp130m', 'gp80', 'gp80']:
IL6_gp80_gp130_JAK2m_STAT1C:was emptied
ERROR:SCT241:IFN_R_JAK:IFN_R_JAK2:produce the same translation:['IFN', 'JAK', 'R']:
IFN_R_JAK2:was emptied
for the first two errors, we add binding interactions [“R”, “SHP2”] and [“R”, “STAT3”]. The third error we notice that atomizer thinks STAT3C and STAT3 are different, we’ll address that by adding `modificationDefinition`shell for STAT species and get the following input file
{
"binding_interactions": [
["gp80", "gp80"],
["gp130", "SHP2"],
["SOS", "Ras"],
["R","SHP2"],
["R","STAT3"]
],
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"],
"STAT3": [],
"STAT3m": ["STAT3"],
"STAT3C": ["STAT3"],
"STAT3Cm": ["STAT3"],
"STAT1": [],
"STAT1m": ["STAT1"],
"STAT1C": ["STAT1"],
"STAT1Cm": ["STAT1"]
}
}
atomizing again we get the following errors
ERROR:ANN202:SOCS1:SOCS3:can be mapped through naming conventions but the annotation information
does not match
ERROR:ANN202:Phosp1:Phosp3:can be mapped through naming conventions but the annotation information
does not match
ERROR:SCT241:IFN_R_JAK:IFN_R_JAK2:produce the same translation:['IFN', 'JAK', 'R']:IFN_R_JAK2:
was emptied
ERROR:SCT241:IL6_gp80_gp130_JAK2m_STAT1:IL6_gp80_gp130_JAK2m_STAT1C:produce the same translation:
['IL6', 'IL6', 'JAKIL_6', 'JAKIL_6', 'STAT1C', 'gp130', 'gp130m', 'gp80', 'gp80']:
IL6_gp80_gp130_JAK2m_STAT1C:was emptied
looking at the 3rd and 4th errors, combined with the previous errors, we can see that atomizer is having trouble resolving types of JAK molecules. We can add `modificationDefinition`s to help with those and some downstream products of JAK
"JAK": [],
"JAKIFN": ["JAK"],
"JAKIL_6":["JAK"]
"R_JAK": ["R","JAKIFN"],
"IFN_R_JAK": ["IFN","R_JAK"],
"IFN_R_JAK2": ["IFN_R_JAK", "IFN_R_JAK"],
"IFN_R_JAK2m": ["IFN_R_JAK2"],
"gp130_JAK": ["gp130", "JAKIL_6"]
adding these to the user input file and rerunning atomization gives
ERROR:ANN202:SOCS1:SOCS3:can be mapped through naming conventions but the annotation information
does not match
ERROR:ANN202:Phosp1:Phosp3:can be mapped through naming conventions but the annotation information
does not match
ERROR:SCT241:IL6_gp80_gp130_JAK2m_STAT1:IL6_gp80_gp130_JAK2m_STAT1C:produce the same translation:
['IL6', 'IL6', 'JAKIL_6', 'JAKIL_6m', 'STAT1C', 'gp130', 'gp130', 'gp80', 'gp80']:
IL6_gp80_gp130_JAK2m_STAT1C:was emptied
looking at the last error, we should give a modificationDefinition for IL6_gp80_gp130_JAK2m_STAT1C
"IL6_gp80_gp130_JAK2m_STAT1C": ["IL6", "gp80", "gp130", "JAK","IL6", "gp80", "gp130", "JAK","STAT1"]
Adding this will result in atomization without any errors. However, looking at BMD543, we find some binding_interactions that should be added to BMD543 user input that are missing in BMD151. We add the following set of binding_interactions
["gp130", "SOCS3"],
["gp130","STAT3"]
["R","STAT1"],
["R","R"],
["R","SOCS1"],
["STAT1","gp130"]
to get the final input file
{
"binding_interactions": [
["gp80", "gp80"],
["SOS", "Ras"],
["R","SHP2"],
["R","STAT3"],
["R","STAT1"],
["R","R"],
["R","SOCS1"],
["gp130", "SHP2"],
["STAT1","gp130"],
["STAT3","gp130"],
["gp130", "SOCS3"]
],
"modificationDefinition": {
"Ras": [],
"Ras_GTP": ["Ras"],
"Ras_GDP": ["Ras"],
"STAT3": [],
"STAT3m": ["STAT3"],
"STAT3C": ["STAT3"],
"STAT3Cm": ["STAT3"],
"STAT1": [],
"STAT1m": ["STAT1"],
"STAT1C": ["STAT1"],
"STAT1Cm": ["STAT1"],
"JAK": [],
"JAKIFN": ["JAK"],
"JAKIL_6":["JAK"],
"R_JAK": ["R","JAKIFN"],
"gp130_JAK": ["gp130", "JAKIL_6"],
"IFN_R_JAK2": ["IFN","R_JAK", "IFN","R_JAK"],
"IFN_R_JAK2m": ["IFN_R_JAK2"],
"IL6_gp80_gp130_JAK2m_STAT1C": ["IL6", "gp80", "gp130", "JAK","IL6", "gp80", "gp130", "JAK","STAT1"]
}
}
and running with this user input file gives us the fully atomized model.