Comments (4)
@sonyahanson You can find my modified quickmodel script for this new layout:
quickmodel_layout2.py
I changed lines 73-75 of quickmodel.py.
I used the default inputs.py format but repeated the name of the ligand 4 times.
from assaytools.
Can we define the assay layout using a dictionary like fashion with assay_format
, protein_order
(this will replace the protein
section) and ligand_order
sections in inputs.py.
assay_format
can be row-wise
or column-wise
It will be useful to have assay_format
that defines in which direction each titration series lie, so we can analyse data in different orders and even when the experiments are designed in columns (Column 1 - protein, column 2 buffer etc.)
For example our usual layout would be defined like this:
'assay_format' : 'row-wise'
'ligand_order' : {'A': 'Bosutinib', 'B':'Bosutinib Isomer', 'C':'Erlotinib', 'D':'Gefitinib', 'E':'Bosutinib', 'F': 'Bosutinib Isomer', 'G': 'Erlotinib', 'H': 'Gefitinib'}
'protein_order' : {'A': 'p38, 'B':'buffer, 'C':'p38', 'D':'buffer', 'E':'p38', 'F': 'buffer', 'G': 'p38', 'H': 'buffer'}
And an unusual layout like I did with HSA samples will be defined like this:
'assay_format' : 'row-wise'
'ligand_order' : {'A': 'dansylamide', 'B':'dansylamide', 'C':'dansylamide', 'D':'dansylamide', 'E':'dansylamide, 'F': 'dansylamide', 'G': 'dansylamide', 'H': 'dansylamide'}
'protein_order' : {'A': 'HSA1, 'B':'HSA2', 'C':'HSA3', 'D':'HSA4', 'E':'HSA5', 'F': 'HSA6', 'G': 'buffer', 'H': 'buffer'}
An example for column-wise experiment where only first 4 columns are used:
'assay_format' : 'column-wise'
'ligand_order' : {'1': 'Bosutinib', '2':'Bosutinib', '3':'Gefitinib', '4':'Gefitinib''}
'protein_order' : {'1': 'buffer', '2':'Src', '3':'buffer', '4':'Src'}
from assaytools.
I agree it would be good to have a more flexible plate layout! I think that if we want it this general, it might be good to start the transition to autoprotocol for the initial file parsing: https://github.com/choderalab/assaytools/blob/master/examples/autoprotocol/README.md
We can have our data in a format that's appropriate for the more advanced analysis, while still doing the analysis the same way we are, and then we don't have to manage too many things at once.
from assaytools.
Perhaps as an intermediate, we can create a section in the 'inputs.py' where we can define assay_format
as alternating_row
or block_row
, which seem to be the two formats we have been using recently.
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?
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