Activity for Anna Zhukova
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Anna Zhukova posted a comment on ticket #128
Added in MAMO version 2022-02-03 as MAMO_0000211
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PKPD model
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Tagging version 2023-02-03
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Fixed ticket 128
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Tickets 45-83 (incorporated by Jonathan)
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Suggested update to "compartmental model"
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Fixed in version 2020-09-23
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Ticket 127
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Add a KiSAO term for "combined solvers"
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Parameter for reactions
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Thank you for the detailed term request! It is added to KiSAO version 2.7 as KISAO_0000534.
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Parameter for number of parallel processes
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Thank you for the detailed term request! It is added to KiSAO version 2.7 as KISAO_0000529.
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Parameter for loopless
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Thank you for the detailed term request! It is added to KiSAO version 2.7 as KISAO_0000532.
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New parameter for fraction of optimum
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Thank you for the detailed term request! It is added to KiSAO version 2.7 as KISAO_0000531.
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Parameter for pFBA factor
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Thank you for a detailed term request! It is added to KiSAO version 2.7 as KISAO_0000533.
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New algorithm for parsimonious FBA
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Thank you for a detailed term request! It is added to KiSAO version 2.7 as KISAO_0000528.
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Algorithm for geometric FBA
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Thank you for a detailed term request! It is added to KiSAO version 2.7 as KISAO_0000527.
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New algorithm for flux variability analysis
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Thank you for a detailed term request! It is added to KiSAO version 2.7 as KISAO_0000526.
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Tagging KiSAO 2.7
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Fixed Tickets 39-44
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SEIR term under population model
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I have added SIR (MAMO_0000207), SIS (MAMO_0000208), SEIR (MAMO_0000209), and SEIS (MAMO_0000209) under compartmental model (MAMO_0000206). These terms are available in MAMO version 2020-08-10 and later,
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Fixed Ticket 126
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New parameter for stop condition
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Thank you for a parameter suggestion. It is now added to KiSAO (starting from v2.6) as KISAO_0000525.
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New term for partitioned leaping
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Dear Jonathan, Thank you for a very well defined term suggestion. It is now added to KiSAO (starting from v2.6) as KISAO_0000524.
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Tickets 35-36
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KISAO terms for parameter estimation / optimization
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Hello Frank, The requested terms should be available since KISAO version 2.5: Simulated Annealing KISAO_0000503 Random Search KISAO_0000504 Particle Swarm KISAO_0000505 Genetic Algorithm KISAO_0000506 - Genetic Algorithm SR KISAO_0000507 Evolutionary Programming KISAO_0000508 - Evolutionary Strategy (SRES) KISAO_0000509 Truncated Newton KISAO_0000510 Steepest Descent KISAO_0000511 Praxis KISAO_0000512 NL2SOL KISAO_0000513 Nelder - Mead KISAO_0000514 Levenberg - Marquardt KISAO_0000515 Hooke & Jeeves...
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Tagging KISAO-2.5
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Fixed ticket 33
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KISAO terms for DFBA
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Hello Matthias, Thank you for the term suggestion and for their detailed description. The terms are now available (starting with KiSAO version 2.4) as KISAO_0000499 (dynamic FBA), KISAO_0000500 (SOA), KISAO_0000501 (DOA) and KISAO_0000502 (DA).
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tagging kisao 2.4
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Ticket 32
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Number of Runs
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Added since KiSAO 2.3.113
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Ticket 31
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KLU solver
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Thank you for the term suggestion! I have added KLU as an algorithm (KISAO_0000497)....
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Tagging version 2.3.12
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Ticket #30
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Term request: synchronous updating policy
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Term request: asynchronous updating policy
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Remove “asynchronous logical model simulation method” (kisao:KISAO_0000450) and “synchronous logical model simulation method” (kisao:KISAO_0000449)
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Let's keep the terms for now then. I have added the sudgected characteristic ter...
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Fixed in version 2.3.11
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Typo (mine): 'dampening' -> 'damping'
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Fixed in version 2.3.11
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Term request: random asynchronous updating policy
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Term request: fully asynchronous updating policy
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Fixed in version 2.3.11
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Term request: synchronous updating policy
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Fixed in version 2.3.11
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Term request: asynchronous updating policy
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Fixed in version 2.3.11
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I have added a term for "Discrete Event Simulation Algorithm" in version 2.3.11
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Replace “Logical Model Simulation Method” (kisao:KISAO_0000448) by “Discrete Event Simulation algorithm”
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Fix definition of integration methods (kisao:KISAO_0000475)
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Fixed in version 2.3.11
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Fixed in version 2.3.11
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Typo in rule-based simulation method
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Tickets 21-29
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Fixed in KiSAO version 2.3.10
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New term requests: maximum Adams order and maximum BDF order
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Ticket 20
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Hi Lucian, I have found out (sorry, that I have not looked better before when adding...
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Added in KiSAO version 2.3.9
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New term request: seed
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New term request: minimum dampening
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Added in KiSAO version 2.3.9
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Added in KiSAO version 2.3.9
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New term request: maximum iterations
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New term request: maximum order
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Added in KiSAO version 2.3.9
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New term request: minimum time step
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New term request: maximum order
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Added in KiSAO version 2.3.9
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Tickets 15-19
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Tree viewer for KiSAO?
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Thank you very much Antoine!
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Thanks Antoine! I'm looking forward to the new version. Cheers
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Tulip python 4.8.0 crashes when applying layout algorithms
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Octave model
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see Ticket 115
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Do not need this term in MAMO at the moment, submitted a request for MAT-file format...
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MATLAB model
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For model formats there are already terms in EDAM ontology (see for example SBML),...
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Added in KiSAO version 2.3.8 with the following ids: - Integration method: KISAO_0000475...
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New KiSAO ids for CVODE / IDA parameters
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KiSAO id for "step size"
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KiSAO id for "step size"
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