Why do some Shared_Object_pathways do not have any
molecule, enzyme and reactions?
It is because some of the pathway do not use any of the shared objects molecule or enzyme or reaction.
What are the biological pathways represented on DOQCS?
The majority of biological pathways represented on DOQCS are neuronal signaling
pathways. There are signaling pathways from other systems like MAPK pathway
in Xenopus oocytes, E.coli chemotaxis pathway, Firefly luciferase pathway, cardiac
pathways among others.
What is an entry date?
An entry date is the date on which the model was deposited on DOQCS.
What is the difference between "Developer" and "Transcriber"?
A Developer is the original creator of the model in its original format
cited in a publication.
What is a Kinetikit file or .g file?
A Transcriber transliterates whenever possible the original model format into the
GENESIS format for Kinetikit which is available on DOQCS. Transliterated models match
the original published model in all parameters. Sometimes when converting original
model formats to GENESIS better matches to published literature would be possible
by using different parameters from original model publication. Modified parameters
are obtained by curve fitting or by personal correspondence with the developer
of the model. Such translated models always contain a note specifying the changes
made from the original published models.
A Kinetikit file or a .g file is a text file which contains the model description
in the GENESIS scripting language that can be "read" by Kinetikit to simulate the
model. These files end with the .g extension.
What information does a .g file have?
The .g file has the information required by Kinetikit to create the model for
Where can I download a .g file?
The .g file can be downloaded from either the accession entry or pathway entry
for a model.
What is the difference between acc.g and path.g?
The acc.g file is the .g file for the composite network model with the parameters
set for the specific network behavior. The path.g file has parameters set for specific
participating pathways within the composite network.
Why do some pathways have no separate Kinetikit files available?
Sometimes there are no separate files for the accession and the pathways therein.
This is because both system behavior of the network and the behavior of the participating
pathways can be seen through the same .g file.
How can I run the model?
The user can run a .g model file by downloading the .g file, Kinetikit interface
and GENESIS. Detailed instructions for running the model are available
Where can I get Kinetikit and what are the system requirements?
Kinetikit and GENESIS can be downloaded from
What information is give in "Connected to" section?
Size: ~1.2 MB download and 4 MB uncompressed
Requirements: The software requires a PC with Linux operating system (Kernel 2.4
or later, for example, Red Hat Linux 7.2 and higher).
The connected to table lists how the query term is related to other entries
in the database.
What does Enzyme Type mean ? What is the difference between explicit
and Classical Michaelis-Menten representations in the database?
The Enzyme Type refers to the mathematical formulation used for the
Why is there a difference in the results returned by Accession search and
Model search in "Connected to"?
The Michaelis-Menten reaction scheme is E + S <=====> E.S -----> E + P
In the explicit representation, each of these reactions is computed and
there is an intermediate enzyme-substrate complex E.S which is formed.
This formulation is somewhat more chemically complete. Note that it is
still an approximation as no backward reaction is permitted for product
In the classical representation, the computation of rate (i.e, rate of
formation of P) is done using the equation rate = [E][S].kcat/(Km + [S])
where [E] is the total amount of free enzyme.
These two forms usually behave similarly, but give different effects when
there is enzyme saturation and more than one substrate is present.
Other, more complex enzymatic mechanisms are well known, but can be
represented as assemblies of simple reactions.
An accession name is essentially the name of a model on DOQCS. Default
accession searches on DOQCS are done in the name field and the results are not
exact word matches; e.g querying for CaMKII in accession list will yield
fig3_CaMKII, CaMKII and CaMKII_2003 among the search results.
My question is not answered in this FAQ. Whom should I contact?
Osc_Ca_IP3metabolism is a model on DOQCS that has CaMKII as one of its
participating molecules. But this is not returned as a result for CaMKII
accession search because the model name is "Osc_Ca_IP3metabolism" and does not
have CaMKII in its name. The Model serach in Connected to listing yields all
accessions that have CaMKII as a participating molecule.
Accession name results: models that have the queried term in the accession name.
Connected to model search results: models that have the queried term anywhere in
the model, not necessarily in the accession name.
You may contact Dr.Upinder S. Bhalla at this email ID firstname.lastname@example.org or
HarshaRani at this email ID email@example.com