kelly workflow for release

omics/kelly/data-raw/VFAdata for BIO00088H R_studio.csv

@@ -0,0 +1,76 @@
+Notes:,,,,,,,,,,,,,,,,,
+Each sample has three replicates,,,,,,,,,,,,,,,,,
+"Concentrations are listed here in mM (millimolar, or ""moles / L *  1000 millimoles / 1 moles"")",,,,,,,,,,,,,,,,,
+CN samples have straw biomass added to AD vials,,,,,,,,,,,,,,,,,
+NC samples have had water added to AD vials,,,,,,,,,,,,,,,,,
+,,,,,,,,,Data for mM to g/l calculations,,,,,,,,
+To calculate from this data,,Change in VFA with time,,,,,,,MW (g/mol),60.05,74.08,88.11,88.11,102.13,102.13,116.1583,116.1583
+,,"Recalculate the data into grams per liter, and change in VFA g/l with time",,,,,,,,Acetate,Propanoate,Isobutyrate,Butyrate,Isopentanoate,Pentanoate,Isohexanoate,Hexanoate
+,,"Calculate the percent representation of each VFA, by mM and by weight",,,,,,,,,,,,,,,
+,,"Useful graphs would include 1) mM or mg/l versus time for VFAs, 2) Delta mg/l versus time for each VFA",,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,
+Sample - Replicate,Time (day),Acetate,Propanoate,Isobutyrate,Butyrate,Isopentanoate,Pentanoate,Isohexanoate,Hexanoate,,,,,,,,
+CN10-1,0,0,0,0,0,0,0,0,0,,,,,,,,
+CN10-2,0,0,0,0,0,0,0,0,0,,,,,,,,
+CN10-3,0,0,0,0,0,0,0,0,0,,,,,,,,
+CN10-1,1,17.239,1.126,0.733,0.538,0.52,0.076,0.025,0.007,,,,,,,,
+CN10-2,1,19.805,1.153,0.736,0.731,0.766,0.098,0.022,0.018,,,,,,,,
+CN10-3,1,21.043,1.235,0.742,0.717,0.793,0.07,0.019,0.023,,,,,,,,
+CN10-1,3,47.847,4.195,0.812,1.465,1.034,0.082,0.058,0.044,,,,,,,,
+CN10-2,3,56.541,4.596,1.193,1.452,1.257,0.096,0.012,0.081,,,,,,,,
+CN10-3,3,54.29,4.258,1.116,1.384,1.237,0.084,0.032,0.081,,,,,,,,
+CN10-1,5,66.582,7.176,1.449,2.096,1.137,0.284,0.053,0.027,,,,,,,,
+CN10-2,5,81.172,8.209,1.927,2.544,1.505,0.317,0.043,0.035,,,,,,,,
+CN10-3,5,70.528,6.831,1.629,2.202,1.285,0.257,0.016,0.029,,,,,,,,
+CN10-1,9,76.325,9.799,2.017,3.352,1.45,0.439,0.055,0.042,,,,,,,,
+CN10-2,9,98.902,11.816,2.675,4.346,1.888,0.579,0.043,0.054,,,,,,,,
+CN10-3,9,100.199,11.236,2.836,4.164,1.888,0.519,0.047,0.047,,,,,,,,
+CN10-1,11,82.171,10.703,2.485,3.976,1.625,0.591,0.057,0.08,,,,,,,,
+CN10-2,11,94.162,11.751,2.719,4.598,1.963,0.649,0.044,0.088,,,,,,,,
+CN10-3,11,89.181,10.756,2.493,4.137,1.835,0.561,0.034,0.064,,,,,,,,
+CN10-1,13,101.508,12.57,3.115,4.895,1.949,0.758,0.041,0.114,,,,,,,,
+CN10-2,13,108.601,13.698,3.31,5.505,2.072,0.814,0.047,0.146,,,,,,,,
+CN10-3,13,107.873,13.669,3.688,5.447,2.043,0.861,0.068,0.157,,,,,,,,
+CN10-1,16,100.422,14.564,3.045,5.623,2.105,0.862,0.063,0.126,,,,,,,,
+CN10-2,16,111.334,15.229,3.06,6.128,2.202,0.859,0.043,0.12,,,,,,,,
+CN10-3,16,112.261,15.044,3.423,6.106,2.271,0.858,0.046,0.121,,,,,,,,
+CN10-1,18,96.766,13.804,3.585,5.66,1.988,0.788,0.056,0.099,,,,,,,,
+CN10-2,18,104.135,14.584,3.38,6.173,2.157,0.827,0.047,0.108,,,,,,,,
+CN10-3,18,99.257,14.082,2.894,5.712,1.998,0.816,0.04,0.093,,,,,,,,
+CN10-1,20,90.968,13.733,3.266,5.697,1.974,0.804,0.055,0.119,,,,,,,,
+CN10-2,20,96.995,13.965,2.346,6.951,2.089,0.853,0.045,0.109,,,,,,,,
+CN10-3,20,107.952,14.742,3.668,6.546,2.227,0.973,0.042,0.108,,,,,,,,
+CN10-1,22,89.43,13.57,2.953,5.681,1.898,0.818,0.048,0.08,,,,,,,,
+CN10-2,22,104.397,14.584,2.946,7.454,2.237,0.918,0.041,0.096,,,,,,,,
+CN10-3,22,110.657,15.274,4.216,7.192,2.467,1.118,0.047,0.125,,,,,,,,
+NC1,1,3.594,0.982,0.395,0.206,0.246,0.031,0.006,0.005,,,,,,,,
+NC2,1,1.604,0.927,0.478,0.242,0.314,0.057,0.004,0.011,,,,,,,,
+NC3,1,1.503,0.867,0.416,0.236,0.295,0.033,0.003,0.01,,,,,,,,
+NC1,3,7.095,1.355,0.413,0.37,0.441,0.086,0.049,0.038,,,,,,,,
+NC2,3,7.441,1.353,0.574,0.41,0.503,0.091,0.05,0.05,,,,,,,,
+NC3,3,7.011,1.446,0.555,0.417,0.563,0.1,0.057,0.034,,,,,,,,
+NC1,5,7.676,1.341,0.68,0.373,0.539,0.075,0.024,0.014,,,,,,,,
+NC2,5,10.885,1.931,0.872,0.522,0.763,0.11,0.043,0.019,,,,,,,,
+NC3,5,8.89,1.558,0.783,0.426,0.641,0.087,0.037,0.015,,,,,,,,
+NC1,9,20.134,3.602,1.405,0.839,1.218,0.231,0.044,0.061,,,,,,,,
+NC2,9,19.093,3.479,1.497,0.885,1.112,0.176,0.033,0.032,,,,,,,,
+NC3,9,20.491,3.837,1.625,0.875,1.492,0.242,0.051,0.041,,,,,,,,
+NC1,11,19.002,3.324,1.56,0.785,1.366,0.201,0.043,0.042,,,,,,,,
+NC2,11,16.193,2.783,1.321,0.633,1.205,0.152,0.033,0.033,,,,,,,,
+NC3,11,11.179,2.143,1.079,0.493,0.951,0.11,0.025,0.022,,,,,,,,
+NC1,13,20.805,3.555,1.863,0.816,1.394,0.217,0.044,0.07,,,,,,,,
+NC2,13,20.702,3.572,1.915,0.788,1.446,0.208,0.044,0.07,,,,,,,,
+NC3,13,20.187,3.34,1.684,0.638,1.364,0.176,0.034,0.063,,,,,,,,
+NC1,16,23.457,4.129,1.754,0.891,1.542,0.208,0.039,0.052,,,,,,,,
+NC2,16,23.79,4.419,2.033,0.886,1.695,0.238,0.048,0.076,,,,,,,,
+NC3,16,19.692,4.146,1.901,0.682,1.449,0.174,0.045,0.057,,,,,,,,
+NC1,18,22.499,3.988,1.543,0.798,1.364,0.162,0.031,0.051,,,,,,,,
+NC2,18,26.354,4.468,1.776,0.856,1.568,0.19,0.041,0.069,,,,,,,,
+NC3,18,18.685,3.869,1.478,0.6,1.202,0.127,0.033,0.032,,,,,,,,
+NC1,20,20.639,3.968,1.626,0.815,1.363,0.167,0.034,0.05,,,,,,,,
+NC2,20,17.364,3.724,1.484,0.656,1.222,0.136,0.03,0.027,,,,,,,,
+NC3,20,20.528,4.211,1.55,0.635,1.312,0.124,0.041,0.033,,,,,,,,
+NC1,22,21.128,3.982,1.86,0.805,1.465,0.22,0.038,0.037,,,,,,,,
+NC2,22,24.633,4.165,1.706,0.738,1.524,0.155,0.045,0.39,,,,,,,,
+NC3,22,29.288,4.129,1.575,0.639,1.458,0.133,0.052,0.025,,,,,,,,

omics/kelly/notes.txt

@@ -15,6 +15,17 @@ Acetate	Propanoate	Isobutyrate	Butyrate	Isopentanoate	Pentanoate	Isohexanoate	He
 60.05	  74.08	      88.11	      88.11	    102.13	      102.13	    116.1583	    116.1583
 
 
-Useful graphs would include 1) mM or mg/l versus time for VFAs, 2) Delta mg/l versus time for each VFA															
-
-
+Useful graphs would include 1) mM or mg/l versus time for VFAs, 2) Delta mg/l versus time for each VFA		
+
+
+They should also be able to do a simple flux measurement:
+change in VFA concentration over a period of time, divided by weight or volume of material. 
+In this case it might be equal to == 
+Delta(Acetate at 3 days - Acetate at 1 day)/ Delta (3days - 1day)/ 50 mls sludge. This would provide a final flux with the units of mg acetate per ml sludge per day.  Let me know if this isn't clear.
+-----So I need to add the lag in days. Check the 50mls bit. Is that going to be a constant in the replicate vial? or is it going to be different? .
+
+
+Perhaps more importantly they should be able to graph and extract the reaction rate, assuming a first order chemical/biological reaction and an exponential falloff rate. I found this as a starting point (https://martinlab.chem.umass.edu/r-fitting-data/) , but I assume Emma has something much more effective already in the pipeline.
+
+
+

omics/kelly/temp/example.R

@@ -0,0 +1,3 @@
+library(tidyverse)
+example <- read_csv("omics/kelly/temp/example.csv") |> janitor::clean_names()
+

omics/kelly/temp/example.csv

@@ -0,0 +1,42 @@
+"","t","fluorI"
+"1",0,10.1385967718684
+"2",1,8.35533475533268
+"3",2,6.76788471742473
+"4",3,5.36280912133003
+"5",4,4.48247204833858
+"6",5,4.18185893519706
+"7",6,3.34896480340668
+"8",7,2.71315594667858
+"9",8,2.62614956633054
+"10",9,2.06087018509515
+"11",10,1.86074194679208
+"12",11,1.97873314323764
+"13",12,1.83378700440039
+"14",13,1.51439267158402
+"15",14,1.30714846254938
+"16",15,0.741412075403802
+"17",16,0.631299882299171
+"18",17,1.02965656564605
+"19",18,0.902298811540632
+"20",19,0.558746438644141
+"21",20,0.400682660920331
+"22",21,0.802962302399545
+"23",22,0.515497522312792
+"24",23,0.905477723273229
+"25",24,0.344178788232269
+"26",25,0.103340446000128
+"27",26,0.879290356441754
+"28",27,0.577592309885709
+"29",28,0.493046226597491
+"30",29,0.366163886781245
+"31",30,0.125189162368687
+"32",31,0.466644952642418
+"33",32,-0.095514224245819
+"34",33,0.177120019463404
+"35",34,0.20511866185474
+"36",35,0.312909299607934
+"37",36,0.184261436760406
+"38",37,0.151930611035154
+"39",38,0.216249309890573
+"40",39,-0.0782341680185992
+"41",40,0.32520930978664