Comments (1)
This is the input file used for the quickmodel competition assay analysis.
inputs = {
'xml_file_path' : "$GITHUB/assaytools/examples/competition-fluorescence-assay/data/",
'file_set' : {'Abl': glob("$GITHUB/assaytools/examples/competition-fluorescence-assay/data/Abl Gef gain 120 bw1020 2016-01-19 15-59-53_plate*.xml"),
'Abl-IMA': glob("$GITHUB/assaytools/examples/competition-fluorescence-assay/data/Abl Gef Ima gain 120 bw1020 2016-01-19 16-22-45_plate*.xml")},
'ligand_order' : ['Gefitinib','Gefitinib','Gefitinib','Gefitinib'],
'section' : '280_BottomRead',
'Lstated' : np.array([20.0e-6,9.15e-6,4.18e-6,1.91e-6,0.875e-6,0.4e-6,0.183e-6,0.0837e-6,0.0383e-6,0.0175e-6,0.008e-6,0.0], np.float64), # ligand concentration
'Pstated' : 0.5e-6 * np.ones([12],np.float64), # protein concentration, M
'assay_volume' : 100e-6, # assay volume, L
'well_area' : 0.3969, # well area, cm^2 for 4ti-0203 [http://4ti.co.uk/files/3113/4217/2464/4ti-0201.pdf]
}
Here is an alternative that captures this information slightly better to eventually be fed into a Bayesian model for fitting the competition assay:
inputs = {
'xml_file_path' : "$GITHUB/assaytools/examples/competition-fluorescence-assay/data/",
'file_set' : {'Abl': glob("$GITHUB/assaytools/examples/competition-fluorescence-assay/data/Abl Gef gain 120 bw1020 2016-01-19 15-59-53_plate*.xml"),
'Abl-IMA': glob("$GITHUB/assaytools/examples/competition-fluorescence-assay/data/Abl Gef Ima gain 120 bw1020 2016-01-19 16-22-45_plate*.xml")},
'ligand_order' : ['Gefitinib','Gefitinib','Gefitinib','Gefitinib'],
'competitive_ligand' : 'Imatinib',
'section' : '280_BottomRead',
'Lstated' : np.array([20.0e-6,9.15e-6,4.18e-6,1.91e-6,0.875e-6,0.4e-6,0.183e-6,0.0837e-6,0.0383e-6,0.0175e-6,0.008e-6,0.0], np.float64), # ligand concentration, M
'Astated' : 10.0e-6 * np.ones([12],np.float64), # competitive ligand concentration, M
'Pstated' : 0.5e-6 * np.ones([12],np.float64), # protein concentration, M
'assay_volume' : 100e-6, # assay volume, L
'well_area' : 0.3969, # well area, cm^2 for 4ti-0203 [http://4ti.co.uk/files/3113/4217/2464/4ti-0201.pdf]
}
from assaytools.
Related Issues (20)
- Could we just set a slightly more restrictive prior on F_PL? HOT 1
- Missing dependencies HOT 4
- Cut a new assaytools release HOT 2
- Fix win install HOT 1
- Make better error message when using wrong path in quickmodel inputs file.
- Travis build failing - libgfortran related? HOT 5
- Deprecate assaytools-dev package HOT 3
- Travis is still broken HOT 1
- Clean up old branches
- Make Docs clearer for General Binding Model
- Integrate scripts/ into installed codebase and use entry-points instead
- Analysis for the single-well titration experiment HOT 2
- getting error in assaytools parser.py when running quickmodel HOT 9
- xml2png python 3.6 travis tests are failing HOT 1
- security alert for pyyaml dependency HOT 2
- Adding Quickmodel script the option to use informed F_PL priors HOT 1
- New release? HOT 1
- Add new `GeneralBindingModel` API that accepts/returns concentrations instead of log concentrations
- Getting print out of 'Skipping analysis of rows: []' for each protein from parser.py when running quickmodel HOT 3
- how to omit a well from analysis?
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from assaytools.