Activity for Nicolas Le Novère
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Nicolas Le Novère posted a comment on ticket #126
We could have a branch "compartment model in epidemiology", with the various model types as children as described in the section "Variations on the basic SIR model" of https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology
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At the moment, there is the term: ID KISAO:0000352 Preferred Name hybrid method Definitions A simulation methods which combines the advantages of complementary simulation approaches: the whole system is subdivided into appropriate parts and different simulation methods operate on these parts at the same time. However, there could be the need to distinguish between: 1) models which are partitioned and which parts (e.g. processes) are simulated with different solvers, like E-Cell3 2) systems that can...
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Object role for SBO:Containment
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It might be so, but "charge" is universally used in chemistry and biochemistry, including in FBA models, for the electric charge. It would be incredibly confusing to use the term for another meaning.
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Systems Pharmacology
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[adding Vasundra to the discussion. I think the initial mail only went to SF] On 20/01/18 23:49, Varun Kothamachu wrote: 3. Co-transport (Parent term: SBO:0000185 - transport reaction) A biochemical process involving the simultaneous transport of two substances across a membrane via a protein or protein complex. I will change SBO:0000185 - transport reaction to SBO:0000185: translocation reaction (Parent term: SBO:0000167 - biochemical or transport reaction) and create child terms to translocation...
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Make "hydrolysis" a child of "conversion"
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Thank you Vasundra. Many of those terms are already in SBO, but some would indeed be welcome additions. SBO terms are nouns, not verbs. I think the difference comes from the fact that despite its name, Reactome is not a reaction database but a physical entityffunction database (initialy gene product - its original name was the "Genome Knowledge Base"). So the terms characterise a gene product or a chemical compound. But we can draw equivalences. TRANSFORMS TO ? seems to be SBO:0000167 - biochemical...
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OK
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OK
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OK.
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I concur with Lucian
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lattice Boltzmann model
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lattice gas automaton
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Wrong definition. More precise would be: definition logic model in which the boolean...
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Probabilistic Boolean network
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But in the case where we have an existing parameter value and an initialAssignment...
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Again, I might be wrong, but what you describe seems exactly what happens with every...
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I am fine with the new paragraph
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I would tend towards 2. The element with no child does not modify the set of equations...
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I think (but I may be wrong) that we are discussing a non-problem. RateOf is a model...
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Hmmm. So in some discussion, we relax the spec, and in other we define arbitrary...
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[sorry for the silence. I did comment on this one, but must have closed the window...
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I vote for #1. #3 looks logical in surface, but is arbitrary. The max of nothing...
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This is not specific to FBA. Drug amounts are very often expressed in mg per kg of...
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I concur
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If the developers of JSBML and libSBML support this, I have no objection.
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I encountered the same problem. I installed a new freemind. I said yes once and now...
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We do not double the concepts. If synchronicity is a characteristics, synchronous...
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Adding them to the chararcteristics branch would not solve anything. You would still...
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But the update policy is a critical part of the logic modelling approach. Synchronous...
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Those are different. Logic modelling refers to the way the values of variables is...
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I do not mind either way. The people spending their time and effort doing should...
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Yes Chris, but most models do not have a submodel. That was actually part of my modularity...
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Yes Chris, but most models do not have a submodel. That was actually part of my modularity...
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I agree with the wording. And let's be warry of Babylon towers.
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If it ain't broke don't fix it
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I really really have no preference :-/
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NL: When it comes to hybrid modelling, you should use appropriate SBO terms on the...
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I am fine with moving the scope of LocalParameters to the reaction (but not to move...
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As for exchanging only one file, you can always bundle all your SBML documents in...
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For 1) and 2) I am with Frank. SBML has to be valid XML, and therefore follows all...
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I agree with this suggestion.
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I think it is not up to SBML to decide if a model's behaviour is right or wrong....
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The terms from the modeling framework branch are actually used within the SBO terms...
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I agree with this change. It should be made
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I agree with the new wording
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Hi Lucian, iSAO is on the NCBO Bioportal http://bioportal.bioontology.org/ontologies/KISAO?p=classes...
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binary characteristic
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biochemical process model
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synomyms of dependent and independent variables
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Dynamic Bayesian model's position in the hierarchy
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COPASI model
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SBML model
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cell cycle model
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protein complex assembly model
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seeAlso: http://sbml.org
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I initially thought we would have a new main branch "model format", with terms like...
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Maximal Timestep Method
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maximum step size
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maximum step size
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Maximal Timestep Method
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I am not fond of the "metabolic model" either (BTW, the definition of this term is...
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I don't think this is what the division math and domain branch are. All are part...
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See comment about protein assembly model. How would that term be used? Would that...
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Why does Wolfram need this term? The wikipedia page talks about the complex, that...
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OK
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I am fine with that term, rephrasing the definition as "model using ..."
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State of MAMO support in BioModels DB
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Actually it is easier to delete the static feature of 41 and create a new child "static...
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Agreed
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Scrap that. This needs a more complete discussion. Random effects is effectively...
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is_a measure of variability
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is_a measure of variability
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is_a measure of variability
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measure of variability
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fixed effects model
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random effects model
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I am not too sure about the definition. "organism's life cycle" can cover a multicellular...
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Added terms for logic models, piecewise linear ...
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S system model
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fuzzy logic model
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generalized logical model
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multi-valued logical model
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Markov chain
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Qualitative piecewise linear differential equation model
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discrete time piecewise linear differential equation model
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piecewise linear differential equation model
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Markov random field
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Markov decision process
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Hidden Markov model
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nonlinear mixed effect model
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nonlinear model
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linear mixed effect model
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