Merge pull request #4 from sclamons/master

Bug fixes and major improvements to tutorial notebooks.

Author: sclamons

README.rst

@@ -10,31 +10,41 @@ Tools for Common Murray Lab Protocols
 
 Code for common tasks in the Murray lab. Supports Python >=3.6 only.
 
-Install with the following (probably requires sudo): ``pip install git+git://github.com/sclamons/murraylab_tools.git@master``
+Install with the following (probably requires sudo): ``pip install git+git://github.com/biocircuits/murraylab_tools.git@master``
 
-To update, run (also with superuser privilege): ``pip install --upgrade --no-deps git+git://github.com/sclamons/murraylab_tools.git@master``
+To update, run (also with superuser privilege): ``pip install --upgrade --no-deps git+git://github.com/biocircuits/murraylab_tools.git@master``
 
 Currently includes the following subpackages:
 
+utilities: Simple Quality-Of-Life Improvement Tools
+===================================================
+
+* A code block that will automatically text or email you when your code is done running.
+
 echo: Echo Setup for TX-TL Experiments (and others)
 =============================================
 
 Code to produce Echo source plate setup instructions and picklists for one of the following cases:
 
 * A TX-TL experiment with a TX-TL setup spreadsheet.
-* A 2-dimensional dilution series, in TX-TL.
-* Association of one or more substances on one or more source plates (not in TX-TL)
+* Programmatically-constructed TX-TL experiments, including easy 2D dilution series setup plus arbitrary additions.
+* Fully general well contents, as defined by a spreadsheet of source materials and a spreadsheet listing what goes in each.
 
 For details, see the "Echo Setup Usage Examples" ipython notebook under "examples".
 
 biotek: Tidying and Analysis of Biotek Plate Reader Data
 ========================================================
 
-Code for converting raw excel/CSV data from a Biotek plate reader into tidy format.
+Code for converting raw excel/CSV data from a Biotek plate reader into tidy format, plus a class to make plotting Biotek data traces quick and easy (BiotekCellPlotter).
 
 Also contains convenience functions for analysis of Biotek timecourse data:
 
+* Fluorescence calibration against lab data (TX-TL data only)
 * Background subtraction
 * Endpoint averaging
+* Data smoothing (spline fit or moving average)
+* Smoothed derivative calculation
+* OD normalization
+* Growth curve summarazation with logistic curve fits
 
 For details, see the "Biotek Analysis Usage Examples" ipython notebook under "examples".

examples/2D_dilution_series/inputs/dilution_setup_example_plate.dat

@@ -224,3 +224,107 @@ H04
 H19
 H23
 H24
+K01
+K02
+K03
+K04
+K05
+K06
+K07
+K08
+K09
+K10
+K11
+K13
+K15
+K17
+K18
+K19
+L01
+L02
+L03
+L04
+L05
+L06
+L07
+L08
+L09
+L10
+L11
+L13
+L15
+L17
+L18
+L19
+H21
+I15
+I17
+I19
+I23
+I24
+M01
+M02
+M03
+M04
+M05
+M06
+M07
+M08
+M09
+M10
+M11
+M13
+M15
+M17
+M18
+M19
+J12
+J14
+J16
+J20
+J22
+J23
+N01
+N02
+N03
+N04
+N05
+N06
+N07
+N08
+N09
+N10
+N11
+N13
+N15
+N17
+N18
+N19
+J21
+J24
+K12
+K14
+K20
+K21
+O01
+O02
+O03
+O04
+O05
+O06
+O07
+O08
+O09
+O10
+O11
+O13
+O15
+O17
+O18
+O19
+K16
+K22
+K23
+L12
+L20
+L21

examples/2D_dilution_series/outputs/dilution_setup_example.test_EchoInput.csv

@@ -1,6 +1,6 @@
 Source Plate,Source Plate Type,Source Well,Sample ID,Destination Plate Name,Destination Well,Transfer Volume,Sample Comment
-Source[1],384PP_AQ_BP,F24,Cavendish,Nunc_384_black_glassbottom,D2,100,Actual concentration: 1.00 nM
-Source[1],384PP_AQ_BP,F24,Cavendish,Nunc_384_black_glassbottom,D3,100,Actual concentration: 1.00 nM
-Source[1],384PP_AQ_BP,F24,Cavendish,Nunc_384_black_glassbottom,E2,100,Actual concentration: 1.00 nM
-Source[1],384PP_AQ_BP,F24,Cavendish,Nunc_384_black_glassbottom,E3,100,Actual concentration: 1.00 nM
-Source[1],384PP_AQ_BP,H02,Gros Michel,Nunc_384_black_glassbottom,F5,300,Actual concentration: 3.00 nM
+Source[1],384PP_AQ_BP,K16,Cavendish,Nunc_384_black_glassbottom,D2,100,Actual concentration: 1.00 nM
+Source[1],384PP_AQ_BP,K16,Cavendish,Nunc_384_black_glassbottom,D3,100,Actual concentration: 1.00 nM
+Source[1],384PP_AQ_BP,K16,Cavendish,Nunc_384_black_glassbottom,E2,100,Actual concentration: 1.00 nM
+Source[1],384PP_AQ_BP,K16,Cavendish,Nunc_384_black_glassbottom,E3,100,Actual concentration: 1.00 nM
+Source[1],384PP_AQ_BP,K22,Gros Michel,Nunc_384_black_glassbottom,F5,300,Actual concentration: 3.00 nM

examples/2D_dilution_series/outputs/dilution_setup_example.test_experiment_overview.txt

@@ -10,8 +10,8 @@ Viscous:
 	total volume: 0.50 uL
 
 On the source plate:
-	Add 21.4uL of Cavendish in well: F24
-	Add 21.3uL of Gros Michel in well: H02
+	Add 21.4uL of Cavendish in well: K16
+	Add 21.3uL of Gros Michel in well: K22
 
 On destination plate:
 	Pipette 0.50 ul of Viscous into wells:, E4

examples/2D_dilution_series/outputs/dilution_setup_example_EchoInput.csv

@@ -17,9 +17,9 @@ water:
 	total volume: 177.50 uL
 
 On the source plate:
-	Add 65.0uL of txtl_mm in wells: J01, J02, J03, J04, J05, J06, J07, J08, J09, J10
-	Add 38.5uL of txtl_mm in well: J11
-	Add 32.0uL of GFP Plasmid in well: J13
-	Add 48.0uL of ATc in well: J15
-	Add 65.0uL of water in wells: J17, J18
-	Add 47.5uL of water in well: J19
+	Add 65.0uL of txtl_mm in wells: O01, O02, O03, O04, O05, O06, O07, O08, O09, O10
+	Add 38.5uL of txtl_mm in well: O11
+	Add 32.0uL of GFP Plasmid in well: O13
+	Add 48.0uL of ATc in well: O15
+	Add 65.0uL of water in wells: O17, O18
+	Add 47.5uL of water in well: O19