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Dastidar2020_3C_NMDA
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Title
*
FindSim Form
FileType
Version
Experiment Metadata
Transcriber
*
Owner of this Experiment
Organization
*
Organisation of the transcriber
Email
Email id of the transcriber
source
SourceType
*
Paper
InHouse
database
other
From where the experiment data is obtained?
PMID
Pubmed Id of the experiment source
doi
Authors
Author of the original experiment source
Journal
Journal Detail
Year
*
Figure
Table
Notes
Experiment Context
Design
*
TimeSeries
DoseResponse
BarChart
DirectParameter
Type of experiment (dose response/time series/bar chart/direct parameter)?
Species
Species on which experiment was carried out
Cell-Types
Cell-type which was used for the original experiment
Details
Please provide the details of the original experiment
Temperature ("C)
Please provide the temperature (in degree-Celsius) at which the experiment was performed.
Notes
Assuming 20uM of NMDA is equivalent to 5uM Glutamate and therefore translating to ~500nM Ca.
Stimuli
Stimuli
Order
Stimuli
TimeUnits
- None -
s
sec
min
hr
day
ms
msec
us
usec
QuantityUnits
- None -
nM
uM
mM
M
#
uV
mV
V
pA
nA
uA
Hz
ratio
Field
- None -
conc
inject
Vm
Vclamp
rate
weight
What field of the model does the quantity unit represent, (eg. concentration, number).
Entities
Please provide a name for the entity which was provided as stimulus.
Label
label is used only by BarCharts. It uniquely identifies stimulus blocks. By default the BarChart uses the _entity_ name, but in case there are multiple stimuli involving the same entity the _label_ lets one give each a unique identifier.
value
Data
Order
Value 1
Value 2
Value 3
Weight for row 1
-2
-1
0
1
2
Value 1
Value 2
Value 3
Weight for row 2
-2
-1
0
1
2
Weight for row 1
-1
0
1
Readouts
Readouts
Timeunits
*
s
sec
min
hr
day
ms
msec
us
usec
Please provide time unit for the time points at which readout was noted.
QuantityUnits
*
nM
uM
mM
M
#
uV
mV
V
pA
nA
uA
ratio
Please provide the unit in which readout quantity was measured.
Entities
Field
SettleTime
normalization
sampling
- None -
none
start
end
min
max
each
presetTime
dose
Time
Dose
Please provide the dose of the referenced entity used to calculate ratio in readout (used in Dose Response experiment type)
Entities
If the entities here are different from the primary readout entities, it is a ratio calculation. If they are the same, it is a normalization.
display
useXlog
useYlog
plotDt
Data
Order
Parameter
Parameter for
TimeSeries -> Time;
DoseResponse->Dose;
BarChart->"," seperated stimuli entity/label;
Value
stderr
Weight for row 1
-4
-3
-2
-1
0
1
2
3
4
Parameter
Parameter for
TimeSeries -> Time;
DoseResponse->Dose;
BarChart->"," seperated stimuli entity/label;
Value
stderr
Weight for row 2
-4
-3
-2
-1
0
1
2
3
4
Parameter
Parameter for
TimeSeries -> Time;
DoseResponse->Dose;
BarChart->"," seperated stimuli entity/label;
Value
stderr
Weight for row 3
-4
-3
-2
-1
0
1
2
3
4
Parameter
Parameter for
TimeSeries -> Time;
DoseResponse->Dose;
BarChart->"," seperated stimuli entity/label;
Value
stderr
Weight for row 4
-4
-3
-2
-1
0
1
2
3
4
Direct Parameter Data
Order
Direct Parameter Data
field
*
entity
*
units
*
- Select a value -
nM
uM
mM
M
#
s
sec
1/s
1/sec
uV
mV
V
pA
nA
uA
value
*
stderr
Weight for row 1
0
Model Mapping
FileName
- None -
B2AR_Gs_Alpha_AC
cAMP_DOQCS
exc
kholodenko
L
Nitric_Oxide
synSynth17_Ca_CaMKII_v7_08Mar2019
synSynth7
synSynth7_may2_2023
synSynth_FMRP_v1
Test_model_upi_lab_grp
Please add model file
ModelSubset
all
Please list model subsets you want to include in the simulation.
Itemstodelete
Provide shortest unique paths for model entities not present in the original experiment
ParameterChange
Order
entity
field
- None -
concInit
nInit
Kf
Kb
Km
kcat
isBuffered
Value
units
- None -
nM
uM
mM
M
#
s
sec
1/s
1/sec
uV
mV
V
pA
nA
uA
Weight for row 1
-1
0
1
Notes
Current state:
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