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hranihrani
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Merge pull request #11 from BhallaLab/develop
More features and bugfixes for findSim.
2 parents 3d11d6f + 74816ad commit 326297e

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‎Curated/FindSim-Bhalla1999_fig2C.tsv‎

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Model mapping
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modelSource DOQCS
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fileName
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fileName models/synSynth7.g
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citationId
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citation
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authors

‎Curated/FindSim-Jain2009_Fig3B.tsv‎

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modelSource DOQCS
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fileName
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fileName models/synSynth7.g
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citationId
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citation
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authors

‎Non-Curated/HH_Fig13.tsv‎

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Experiment metadata
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transcriber Upinder S. Bhalla
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organization NCBS
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emailId bhalla@ncbs.res.in
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exptSource Paper
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citationId PMID: 10486198
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authors Hodgkin and Huxley
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journal Journal of Physiology 117, 500-544 (1952)
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Experiment context
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species loligo pelagi
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cell-types giant axon
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temperature (Celsius) 5
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Include pathway BDNF,TrKB
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details Figure 13
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notes Classic HH data,
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Stimuli
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compartment soma
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timeUnits msec
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quantityUnits nA
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entities soma
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field inject
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Data
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Time Value
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0 2000
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0.1 0
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Readouts
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readoutType TimeSeries
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timeUnits msec
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quantityUnits mV
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useRatio FALSE
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useXlog FALSE
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useYlog FALSE
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entities soma
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field Vm
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useNormalization FALSE
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Data
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Time Value stderr
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0 -45
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1 25
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2 -20
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3 -75
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4 -74
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5 -73
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10 -66
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15 -65
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Model mapping
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modelSource HH
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fileName loadhh.py
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citationId HH demo implemented in MOOSE.
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citation
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authors Hodgkin and Huxley
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modelSubset all
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modelLookup soma:elec/soma
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scoringFormula abs((expt-sim)/(expt+sim+1e-9))
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solver CrankNicolson
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notes

‎Non-Curated/HH_vclamp4.tsv‎

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Experiment metadata
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transcriber Upinder S. Bhalla
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organization NCBS
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emailId bhalla@ncbs.res.in
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exptSource Paper
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citationId PMID: 10486198
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authors Hodgkin and Huxley
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journal Journal of Physiology 117, 500-544 (1952)
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Experiment context
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exptType TimeSeries
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species loligo pelagi
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cell-types giant axon
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temperature (Celsius) 5
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details Figure 13
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notes Classic HH data,
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Stimuli
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timeUnits msec
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quantityUnits mV
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entities soma
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field Vclamp
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Data
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Time Value
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0 -65
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10 -25
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60 -65
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100 -65
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Readouts
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readoutType TimeSeries
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timeUnits msec
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quantityUnits uA
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useXlog FALSE
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useYlog FALSE
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entities soma
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field current
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useNormalization FALSE
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Data
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Time Value stderr
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0 0
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10 0
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11 -7
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12 -2
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13 1.5
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14 3.2
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16 6
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20 6.9
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60 6.9
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61 1.2
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62 0.8
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63 0.6
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64 0.4
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100 0
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Model mapping
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modelSource HH
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fileName
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citationId HH demo implemented in MOOSE.
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citation
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authors Hodgkin and Huxley
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modelSubset all
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modelLookup soma:soma
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scoringFormula abs((expt-sim)/(datarange+1e-3))
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solver CrankNicolson
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notes

‎TestTSV/bc_ratio_sb8.tsv‎

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Experiment metadata
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transcriber Upi Bhalla
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organization National Centre for Biological Sciences
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emailId nishaav@ncbs.res.in
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exptSource Paper
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citationId PMID: 8410192
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authors Schaechter and Benowitz
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journal JNeurosci 1993
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Experiment context
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exptType barchart
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species rats
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cell-types All cerebral cortex
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temperature (Celsius)
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Include pathway PKC
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details Figure 8
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notes
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Stimuli
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timeUnits sec
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quantityUnits uM
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field conc
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Data
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Entity Value
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Ca 1.0
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DAG 100
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AA 50
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Readouts
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timeUnits sec
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quantityUnits ratio
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useRatio TRUE
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useXlog FALSE
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useYlog FALSE
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ratioReferenceTime 150
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ratioReferenceEntities PKC_active
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entities PKC_active
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field conc
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useSum TRUE
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useNormalization FALSE
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settleTime 150
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Data
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Entity Value stderr
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000 1.00 0
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001 2.50 0
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010 12.0 0
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011 19.5 0
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100 9.0 0
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101 18.0 0
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110 17.0 0
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111 19.5 0
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Model mapping
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modelSource Local path
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fileName models/synSynth7.g
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citationId
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citation
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authors
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modelSubset Ca/Ca,Arachidonic_Acid,PKC,DAG
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modelLookup Ca:Ca/Ca,AA:Arachidonic_Acid,DAG:DAG,PKC_active:PKC_active
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scoringFormula abs((expt-sim)/(expt+sim+1e-9))
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itemstodelete PKC_act_raf,PKC_inact_GAP,PKC_act_GEF,PKC_phosph_neurogranin,PKC_phosph_ng_CaM,phosph_AC2
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solver Runge kutta method (gsl)
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notes The molecule PDB is used in this figure as a DAG analogue, at 1 uM. Unsure how to scale it. Clearly has a larger effect than synthetic DAG from Fig 7.
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parameterChange
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Object parameter Value
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Ca/Ca concInit 0.0001
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Ca/Ca isBuffered 1
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DAG concInit 0
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DAG isBuffered 1
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Arachidonic_Acid concInit 0
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Arachidonic_Acid isBuffered 1
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‎TestTSV/dp.tsv‎

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Experiment metadata
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transcriber Upinder S. Bhalla
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organization NCBS
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emailId bhalla@ncbs.res.in
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exptSource Paper
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citationId PMID: 15548210
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authors Bhalla
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journal Test Journal
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Experiment context
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exptType DirectParameter
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species rat
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cell-types hippocampal CA1 pyramidal neuron
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temperature (Celsius) 30
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Include all
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details Figure 1 panel B
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notes Direct param readouts test script.
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Readouts
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readoutType DirectParameter
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quantityUnits 1/sec
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field kcat
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Data
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entity Value stderr
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MAPK_phosph_PLA2 20 5.0
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MAPK_phosph_4EBP 0.1 0.05
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Readouts
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readoutType DirectParameter
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quantityUnits uM
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field Km
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Data
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entity Value stderr
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MAPK_phosph_PLA2 27 5.0
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MAPK_phosph_4EBP 20 1.0
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modelSource internal
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fileName models/synSynth7.g
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citationId
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citation
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authors Bhalla
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modelSubset all
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modelLookup MAPK_phosph_PLA2:MAPK_p_p/MAPK_p_p,MAPK_phosph_4EBP:MAPK_p_p/MAPK_4E_BP_phospho
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scoringFormula abs((expt-sim)/(expt+sim+1e-9))
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solver none
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notes Test for direct measure of parameters. Note that each Readouts entry can be used for a different parameter, but may apply to many objects.

‎TestTSV/dp_Kd_tau.tsv‎

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Experiment metadata
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transcriber Upinder S. Bhalla
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organization NCBS
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emailId bhalla@ncbs.res.in
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exptSource Paper
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citationId PMID: 15548210
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authors Bhalla
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journal Test Journal
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Experiment context
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exptType DirectParameter
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species rat
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cell-types hippocampal CA1 pyramidal neuron
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temperature (Celsius) 30
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Include all
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details Figure 1 panel B
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notes Direct param readouts test script.
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Readouts
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readoutType DirectParameter
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quantityUnits sec
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field tau
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Data
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entity Value stderr
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RecLigandBinding 0.04 0.01
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makeTernary 160 50
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readoutType DirectParameter
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quantityUnits uM
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field Kd
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Data
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entity Value stderr
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RecLigandBinding 0.6 0.1
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makeTernary 0.015 0.005
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Model mapping
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modelSource internal
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fileName models/synSynth7.g
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citationId
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citation
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authors Bhalla
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modelSubset kinetics/mGluR,G_GDP
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itemstodelete Activate_Gq
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modelLookup RecLigandBinding:RecLigandBinding,makeTernary:Rec_Glu_bind_Gq
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scoringFormula abs((expt-sim)/(expt+sim+1e-9))
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solver none
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notes Test for direct measure of Kd and tau parameters, which are not native fields.

‎TestTSV/dr_j2c.tsv‎

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Experiment metadata
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transcriber Nisha Ann Viswan
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organization NCBS
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emailId nishaav@ncbs.res.in
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exptSource Paper
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citationId PMID: 10486198
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authors Yuen and Mobley
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journal Exp Neurol 1999
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Experiment context
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exptType DoseResponse
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species
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cell-types
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temperature-in-Celsius
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includePathway BDNF,TrKB,Sos
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details
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notes
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Stimuli
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timeUnits sec
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quantityUnits nM
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entities BDNF
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field conc
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Data
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Time Value
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Readouts
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timeUnits sec
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quantityUnits nM
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useXlog FALSE
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useYlog FALSE
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useNormalization FALSE
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settleTime 300
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ratioReferenceTime 0
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ratioReferenceEntities
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ratioReferenceDose 0
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entities SHC_p
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field conc
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Data
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Dose Value sem
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0 0 0
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1 6.5 0
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2 12.5 0
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3.8 14 0
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7.5 18 0
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Model mapping
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modelSource Local path
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fileName models/synSynth7.g
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citationId
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citation
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authors
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modelSubset kinetics/BDNF,kinetics/TrKB,SHC,SHC_p,SHC_p_dephospho
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modelLookup BDNF:BDNF/BDNF,SHC_p:SHC_p
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scoringFormula abs((expt-sim)/(expt+sim+1e-9))
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itemstodelete BDNF_TrKB2_p_clx/PLC_g_phospho
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solver Runge kutta method (gsl)
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notes Jain2009_Fig2C
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parameterChange
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Object parameter Value
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SHC_p_dephospho Kf 0.2

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