choderalab · jchodera · Dec 3, 2017 · Mar 15, 2018 · Mar 15, 2018 · Mar 15, 2018
diff --git a/...ion/20171119_p38_single_well_binding_assay/20171117 Single well binding assay design.xlsx b/...ion/20171119_p38_single_well_binding_assay/20171117 Single well binding assay design.xlsx
diff --git a/...e_well_binding_assay/Lab notebook for p38 single well binding assay (start_20171119).gdoc b/...e_well_binding_assay/Lab notebook for p38 single well binding assay (start_20171119).gdoc
@@ -0,0 +1 @@
+{"url": "https://drive.google.com/open?id=1S3vW12yoHmg4dV2Gco6dwx7lkPh-qGjztDn1L69WnvQ", "doc_id": "1S3vW12yoHmg4dV2Gco6dwx7lkPh-qGjztDn1L69WnvQ", "email": "john.chodera@choderalab.org"}
diff --git a/...es/sequential-titration/20171119_p38_single_well_binding_assay/calculate_Lstated_array.py b/...es/sequential-titration/20171119_p38_single_well_binding_assay/calculate_Lstated_array.py
@@ -0,0 +1,69 @@
+# Generate Numpy array of stated ligand concentration(Lstated) for logarithmic dilution along a row.
+# 
+# Example output:
+# 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-6,0.0001e-6], np.float64)
+#
+# Usage:	
+#	python calculate_Lstated_array.py --n_wells 12 --h_conc 8e-06 --l_conc 2.53e-09 --dilution logarithmic
+#       python calculate_Lstated_array.py --n_wells 6 --h_conc 100 --l_conc 10 --dilution linear
+
+
+from __future__ import print_function, division
+import numpy as np
+import argparse
+import sys
+
+# Argument parser
+parser = argparse.ArgumentParser(prog="calculate_Lstated_array")
+parser.add_argument("--n_wells", dest="n_wells", help="Enter target number of different concentrations.", type=int)
+parser.add_argument("--h_conc", dest= "highest_conc", help="The highest concentration in the series (Unit: M).", type=float)
+parser.add_argument("--l_conc", dest="lowest_conc", help="The lowest concentration in the series (Unit: M).", type=float)
+parser.add_argument("--dilution", dest="dilution_method", help="Defines logarithmic or linear dilution.Enter 'logarithmic' or 'linear.'.", type=str)
+args = parser.parse_args()
+
+n = args.n_wells
+print("Number of wells: ", n)
+highest_conc = args.highest_conc
+print("Highest concentration (M): ", highest_conc)
+lowest_conc = args.lowest_conc
+print("Lowest concentration (M): ", lowest_conc)
+dilution_method = args.dilution_method
+print("Dilution method is {}.".format(dilution_method))
+
+
+if dilution_method == "logarithmic":
+
+     # Calculate dilution factor
+    DF = (highest_conc / lowest_conc)**(1.0/(n-1))
+    print("Dilution factor: {}".format(DF))
+
+    # Calculate concentration of solute in each well
+    Ltot = np.zeros(n)
+    for i, conc  in enumerate(Ltot):
+        Ltot[i] = highest_conc/(DF**i)
+
+elif dilution_method == "linear":
+
+    # Calculate interval, i.e. concentration difference between consecutive dilution points
+    interval = (highest_conc - lowest_conc)/(n-1)
+    print("Linear concentration interval(M): {} ".format(interval) )
+
+    # Calculate linear dilution array
+    Ltot = np.zeros(n)
+    for i, conc  in enumerate(Ltot):
+        Ltot[i] = highest_conc - i*interval
+
+else:
+
+    sys.exit("Error in --dilution argument! It must be specified as '--dilution linear' or '--dilution logarithmic' .")
+
+
+# Create a string that codes for Lstated array:
+array_string = "np.array(["
+for i in range(n-1):
+    array_string = array_string + str(Ltot[i]) + ","
+array_string = array_string + str(Ltot[n-1]) + "], np.float64)"
+
+# Print with matching format for input.py file
+print("Copy this line to Lstated section of assaytools input.py file: ")
+print(array_string)
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 15-48-06_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 15-48-06_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 15-52-45_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 15-52-45_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-17-59_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-17-59_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-26-29_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-26-29_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-41-35_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-41-35_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-46-13_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-46-13_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-59-09_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 16-59-09_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-04-42_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-04-42_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-19-31_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-19-31_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-24-20_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-24-20_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-37-37_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-37-37_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-42-23_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-42-23_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-58-04_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 17-58-04_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-02-55_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-02-55_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-16-02_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-16-02_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-20-31_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-20-31_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-35-42_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-35-42_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-40-27_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-40-27_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-54-33_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-54-33_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-59-10_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 18-59-10_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-12-49_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-12-49_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-17-19_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-17-19_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-31-32_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-31-32_plate_1.xml
diff --git a/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-36-19_plate_1.xml b/...ion/20171119_p38_single_well_binding_assay/infinite reads/2017-11-20 19-36-19_plate_1.xml
diff --git a/examples/sequential-titration/20180309_ p38_and_boiled_p38_with_Bos_test/.DS_Store b/examples/sequential-titration/20180309_ p38_and_boiled_p38_with_Bos_test/.DS_Store
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc0_20180309_183711.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc0_20180309_183711.xml
diff --git a/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc10_20180309_204718.xml b/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc10_20180309_204718.xml
diff --git a/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc11_20180309_210021.xml b/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc11_20180309_210021.xml
diff --git a/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc12_20180309_211322.xml b/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc12_20180309_211322.xml
diff --git a/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc13_20180309_212628.xml b/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc13_20180309_212628.xml
diff --git a/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc14_20180309_213931.xml b/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc14_20180309_213931.xml
diff --git a/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc15_20180309_215232.xml b/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc15_20180309_215232.xml
diff --git a/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc16_20180309_220535.xml b/...l-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc16_20180309_220535.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc1_20180309_185013.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc1_20180309_185013.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc2_20180309_190314.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc2_20180309_190314.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc3_20180309_191615.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc3_20180309_191615.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc4_20180309_192912.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc4_20180309_192912.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc5_20180309_194135.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc5_20180309_194135.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc6_20180309_195438.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc6_20180309_195438.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc7_20180309_200741.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc7_20180309_200741.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc8_20180309_202110.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc8_20180309_202110.xml
diff --git a/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc9_20180309_203415.xml b/...al-titration/20180309_ p38_and_boiled_p38_with_Bos_test/p38_Bos_conc9_20180309_203415.xml
diff --git a/examples/sequential-titration/20180316_p38_and_boiled_p38_with_Bos_test/.DS_Store b/examples/sequential-titration/20180316_p38_and_boiled_p38_with_Bos_test/.DS_Store
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc0_20180316_151003.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc0_20180316_151003.xml
diff --git a/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc10_20180316_173812.xml b/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc10_20180316_173812.xml
diff --git a/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc11_20180316_175119.xml b/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc11_20180316_175119.xml
diff --git a/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc12_20180316_180420.xml b/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc12_20180316_180420.xml
diff --git a/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc13_20180316_181722.xml b/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc13_20180316_181722.xml
diff --git a/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc14_20180316_183025.xml b/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc14_20180316_183025.xml
diff --git a/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc15_20180316_184327.xml b/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc15_20180316_184327.xml
diff --git a/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc16_20180316_185636.xml b/...al-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc16_20180316_185636.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc1_20180316_152305.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc1_20180316_152305.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc2_20180316_153609.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc2_20180316_153609.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc3_20180316_160633.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc3_20180316_160633.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc4_20180316_161933.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc4_20180316_161933.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc5_20180316_163234.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc5_20180316_163234.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc6_20180316_164537.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc6_20180316_164537.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc7_20180316_165840.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc7_20180316_165840.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc8_20180316_171209.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc8_20180316_171209.xml
diff --git a/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc9_20180316_172511.xml b/...ial-titration/20180316_p38_and_boiled_p38_with_Bos_test/p38_Bos_conc9_20180316_172511.xml
diff --git a/...ples/sequential-titration/Plotting p38 sequential titration test data from 20180316.ipynb b/...ples/sequential-titration/Plotting p38 sequential titration test data from 20180316.ipynb
diff --git a/examples/sequential-titration/Plotting p38 sequential titration test data.ipynb b/examples/sequential-titration/Plotting p38 sequential titration test data.ipynb
diff --git a/...es/sequential-titration/Preliminary data exploration for sequential titration assay.ipynb b/...es/sequential-titration/Preliminary data exploration for sequential titration assay.ipynb
diff --git a/examples/sequential-titration/README.md b/examples/sequential-titration/README.md
@@ -0,0 +1,5 @@
+# Sequential titration assay example
+
+This directory contains data from a sequential titration assay conducted by Mehtap Isik, Chodera lab.
+
+More details forthcoming.
diff --git a/...say/20171119_p38_single_well_binding_assay/20171117 Single well binding assay design.xlsx b/...say/20171119_p38_single_well_binding_assay/20171117 Single well binding assay design.xlsx
diff --git a/...e_well_binding_assay/Lab notebook for p38 single well binding assay (start_20171119).gdoc b/...e_well_binding_assay/Lab notebook for p38 single well binding assay (start_20171119).gdoc
@@ -0,0 +1 @@
+{"url": "https://drive.google.com/open?id=1S3vW12yoHmg4dV2Gco6dwx7lkPh-qGjztDn1L69WnvQ", "doc_id": "1S3vW12yoHmg4dV2Gco6dwx7lkPh-qGjztDn1L69WnvQ", "email": "john.chodera@choderalab.org"}
diff --git a/examples/single-well-assay/20171119_p38_single_well_binding_assay/calculate_Lstated_array.py b/examples/single-well-assay/20171119_p38_single_well_binding_assay/calculate_Lstated_array.py
@@ -0,0 +1,69 @@
+# Generate Numpy array of stated ligand concentration(Lstated) for logarithmic dilution along a row.
+# 
+# Example output:
+# 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-6,0.0001e-6], np.float64)
+#
+# Usage:	
+#	python calculate_Lstated_array.py --n_wells 12 --h_conc 8e-06 --l_conc 2.53e-09 --dilution logarithmic
+#       python calculate_Lstated_array.py --n_wells 6 --h_conc 100 --l_conc 10 --dilution linear
+
+
+from __future__ import print_function, division
+import numpy as np
+import argparse
+import sys
+
+# Argument parser
+parser = argparse.ArgumentParser(prog="calculate_Lstated_array")
+parser.add_argument("--n_wells", dest="n_wells", help="Enter target number of different concentrations.", type=int)
+parser.add_argument("--h_conc", dest= "highest_conc", help="The highest concentration in the series (Unit: M).", type=float)
+parser.add_argument("--l_conc", dest="lowest_conc", help="The lowest concentration in the series (Unit: M).", type=float)
+parser.add_argument("--dilution", dest="dilution_method", help="Defines logarithmic or linear dilution.Enter 'logarithmic' or 'linear.'.", type=str)
+args = parser.parse_args()
+
+n = args.n_wells
+print("Number of wells: ", n)
+highest_conc = args.highest_conc
+print("Highest concentration (M): ", highest_conc)
+lowest_conc = args.lowest_conc
+print("Lowest concentration (M): ", lowest_conc)
+dilution_method = args.dilution_method
+print("Dilution method is {}.".format(dilution_method))
+
+
+if dilution_method == "logarithmic":
+
+     # Calculate dilution factor
+    DF = (highest_conc / lowest_conc)**(1.0/(n-1))
+    print("Dilution factor: {}".format(DF))
+
+    # Calculate concentration of solute in each well
+    Ltot = np.zeros(n)
+    for i, conc  in enumerate(Ltot):
+        Ltot[i] = highest_conc/(DF**i)
+
+elif dilution_method == "linear":
+
+    # Calculate interval, i.e. concentration difference between consecutive dilution points
+    interval = (highest_conc - lowest_conc)/(n-1)
+    print("Linear concentration interval(M): {} ".format(interval) )
+
+    # Calculate linear dilution array
+    Ltot = np.zeros(n)
+    for i, conc  in enumerate(Ltot):
+        Ltot[i] = highest_conc - i*interval
+
+else:
+
+    sys.exit("Error in --dilution argument! It must be specified as '--dilution linear' or '--dilution logarithmic' .")
+
+
+# Create a string that codes for Lstated array:
+array_string = "np.array(["
+for i in range(n-1):
+    array_string = array_string + str(Ltot[i]) + ","
+array_string = array_string + str(Ltot[n-1]) + "], np.float64)"
+
+# Print with matching format for input.py file
+print("Copy this line to Lstated section of assaytools input.py file: ")
+print(array_string)