esqlabs / tissuetmdd Goto Github PK

• Target concentration 0.1-100 nM
• kdeg 0.001 - 10 / h,
• Kd 0.001 - 100 nM
• koff 0.001 - 100/h
  is it possible to put all the sliders on log scale too?

Previous parameters:

Target degradation|kdeg
Large Molecule Drug-Target-default|Kd
Large Molecule Drug-Target-default|koff
Target|Reference concentration
Applications|single IV|Application_1|ProtocolSchemaItem|DosePerBodyWeight

New Parameters:

Target Degradation|kdeg
mAb-Target-Test1|Kd
mAb-Target-Test1|koff
Target|Reference concentration
Complex Internalization|kint_kdeg_ratio
mAb|Molecular weight
mAb|Radius (solute)
Applications|3 months, 1 mg/kg|Application_1|ProtocolSchemaItem|DosePerBodyWeight
Applications|3 months, 1 mg/kg|Application_2|ProtocolSchemaItem|DosePerBodyWeight
Applications|3 months, 1 mg/kg|Application_3|ProtocolSchemaItem|DosePerBodyWeight
Applications|3 months, 1 mg/kg|Application_4|ProtocolSchemaItem|DosePerBodyWeight
Applications|3 months, 1 mg/kg|Application_5|ProtocolSchemaItem|DosePerBodyWeight
Applications|3 months, 1 mg/kg|Application_6|ProtocolSchemaItem|DosePerBodyWeight
Applications|3 months, 1 mg/kg|Application_7|ProtocolSchemaItem|DosePerBodyWeight

User needs to run simulation

Tooltips to explain parameters and important app features

To reproduce:

1. Run a simulation on a tissue
2. Change tissue and run/save another simulation
3. change settings to create a "custom" simulation
4. Compare custom with other simulations
5. Change output path in side bar

-> Only one line is drawn for some output path while lines should not overlap.

Colors should not change depending on what simulation is selected

(default units in the simulation) to kDa for the user interface. 1 kDa = 10^-6 kg/µmol

To reproduce:

• Run simulation
• Change administration interval
• Rerun simulation
• Change time range slider

Reorganize the field for the dosing type. It would be nice to change this to a field “Dosing frequency”. If we want to run a simulation with a single dose, we don't mark anything here. If we want to simulate repeated dosing, then we can choose the frequency of drug administration, for example, every day (then the simulation time is 7 days) or every week or every two weeks (in these cases, the simulation time is 2-3 months). The simulation time can be adjusted by selecting a time range (here it would also be convenient to change the units from seconds to days).

These parameters represent the time of administration of the next dose (e.g., 0 day – for the first dose, then 1 day, 2 day, … , 6 day).

Applications|3 months, 1 mg/kg|Application_1|ProtocolSchemaItem| Start time

Applications|3 months, 1 mg/kg|Application_2|ProtocolSchemaItem| Start time

Applications|3 months, 1 mg/kg|Application_3|ProtocolSchemaItem| Start time

Applications|3 months, 1 mg/kg|Application_4|ProtocolSchemaItem| Start time

Applications|3 months, 1 mg/kg|Application_5|ProtocolSchemaItem| Start time

Applications|3 months, 1 mg/kg|Application_6|ProtocolSchemaItem| Start time

Applications|3 months, 1 mg/kg|Application_7|ProtocolSchemaItem| Start time

Wait for Tanya and Wilbert inputs

legend is enough when comparison is on

discrepancy in units between the user input and default units in the model:

Table made by Tania