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authorChristoph Helma <helma@in-silico.ch>2016-01-20 12:41:33 +0100
committerChristoph Helma <helma@in-silico.ch>2016-01-20 12:41:33 +0100
commitb90e598248489797456fee4c6661cfbe62b8e8ec (patch)
tree6d9e96786e4f6b94b938a8ba5109cc7b36f4229b
parentff73a102a87d9e8e409ddf925f2e9477d60cafa7 (diff)
Sinatra app skeleton
-rw-r--r--.gitignore4
-rw-r--r--Gemfile2
-rw-r--r--application.rb21
-rw-r--r--config.ru3
-rw-r--r--data.json1
-rw-r--r--protein_corona.rb118
6 files changed, 147 insertions, 2 deletions
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..59e48cf
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+data
+papers
+*tmp
+*swp
diff --git a/Gemfile b/Gemfile
deleted file mode 100644
index 1aa98e4..0000000
--- a/Gemfile
+++ /dev/null
@@ -1,2 +0,0 @@
-source "http://rubygems.org"
-gemspec
diff --git a/application.rb b/application.rb
new file mode 100644
index 0000000..add7646
--- /dev/null
+++ b/application.rb
@@ -0,0 +1,21 @@
+require 'sinatra'
+require "sinatra/reloader" if development?
+require_relative 'protein_corona.rb'
+also_reload './protein_corona.rb'
+
+get '/?' do
+ @data = JSON.parse(File.read("./data.json")).select{|id,features| features["composition"]["Core composition"] == '[Au]'} # Silver has too may missing values
+ @example = @data[@data.keys.sample]["physchem"]
+ content_type :json
+ JSON.pretty_generate(@example)
+end
+
+get '/predict/?' do
+end
+
+post '/predict/?' do
+ @features = params
+ @neighbors = neighbors params
+ @features[@endpoint_name] = prediction @neighbors
+ @prediction = predict params
+end
diff --git a/config.ru b/config.ru
new file mode 100644
index 0000000..a09f5f7
--- /dev/null
+++ b/config.ru
@@ -0,0 +1,3 @@
+SERVICE = "nano-lazar"
+require File.expand_path './application.rb'
+run Sinatra::Application
diff --git a/data.json b/data.json
new file mode 100644
index 0000000..1b0658f
--- /dev/null
+++ b/data.json
@@ -0,0 +1 @@
+{"G15.AC":{"composition":{"Core composition":"[Au]","Surface modifier1":"N-Acetyl-L-cysteine","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.02751,"Cell.association (Log2 transformed)":-5.184},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":22.36,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":57.53,"Z-Average Hydrodynamic Diameter Change":35.1667,"Volume Mean Hydrodynamic Diameter [nm]":21.94,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":21.75,"Volume Mean Hydrodynamic Diameter Change":-0.1854,"Number Mean Hydrodynamic Diameter [nm]":23.49,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":18.38,"Number Mean Hydrodynamic Diameter Change":-5.117,"Intensity Mean Hydrodynamic Diameter [nm]":23.49,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":70.97,"Intensity Mean Hydrodynamic Diameter Change":47.4778,"Polydispersity index [nm]":0.084,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.27,"Polydispersity index Change":0.1867,"ZETA POTENTIAL [mV]":-21.78,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-9.11,"ZETA POTENTIAL Change":12.6717,"Localized Surface Plasmon Resonance (LSPR) index":0.182530253,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.454404195,"Localized Surface Plasmon Resonance (LSPR) index Change":0.2719,"LSPR peak position (nm) [nm]":518.77,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":2.927,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":255.4430266,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.026465833}},"G15.AHT":{"composition":{"Core composition":"[Au]","Surface modifier1":"6-Amino-1-hexanethiol","Surface modifier2":null,"Classification":"Cationic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.49705,"Cell.association (Log2 transformed)":-1.009},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":30.95,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":90.06,"Z-Average Hydrodynamic Diameter Change":59.1089,"Volume Mean Hydrodynamic Diameter [nm]":11.76,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":67.79,"Volume Mean Hydrodynamic Diameter Change":56.032,"Number Mean Hydrodynamic Diameter [nm]":47.5,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":53.87,"Number Mean Hydrodynamic Diameter Change":6.3667,"Intensity Mean Hydrodynamic Diameter [nm]":47.5,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":106.7,"Intensity Mean Hydrodynamic Diameter Change":59.2033,"Polydispersity index [nm]":0.399,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.215,"Polydispersity index Change":-0.1837,"ZETA POTENTIAL [mV]":15.22,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-8.79,"ZETA POTENTIAL Change":-24.005,"Localized Surface Plasmon Resonance (LSPR) index":0.458209658,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.525747071,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0675,"LSPR peak position (nm) [nm]":526.28,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":4.602,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":240.7287996,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.038405008}},"G15.Ala-SH":{"composition":{"Core composition":"[Au]","Surface modifier1":"Thiolated L-alanine","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.02203,"Cell.association (Log2 transformed)":-5.505},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":22.64,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":44.43,"Z-Average Hydrodynamic Diameter Change":21.7911,"Volume Mean Hydrodynamic Diameter [nm]":22.32,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":44.8,"Volume Mean Hydrodynamic Diameter Change":22.48,"Number Mean Hydrodynamic Diameter [nm]":35.03,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":34.07,"Number Mean Hydrodynamic Diameter Change":-0.9633,"Intensity Mean Hydrodynamic Diameter [nm]":35.03,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":63.72,"Intensity Mean Hydrodynamic Diameter Change":28.6878,"Polydispersity index [nm]":0.147,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.184,"Polydispersity index Change":0.0367,"ZETA POTENTIAL [mV]":-24.08,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-6.73,"ZETA POTENTIAL Change":17.355,"Localized Surface Plasmon Resonance (LSPR) index":0.223533915,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.274761252,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0512,"LSPR peak position (nm) [nm]":518.33,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":4.79,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":247.0191324,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.021712246}},"G15.Asn-SH":{"composition":{"Core composition":"[Au]","Surface modifier1":"Thiolated L-asparagine","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.01955,"Cell.association (Log2 transformed)":-5.676},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":23.09,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":37.75,"Z-Average Hydrodynamic Diameter Change":14.6628,"Volume Mean Hydrodynamic Diameter [nm]":21.22,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":74.66,"Volume Mean Hydrodynamic Diameter Change":53.4389,"Number Mean Hydrodynamic Diameter [nm]":23.04,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":31.4,"Number Mean Hydrodynamic Diameter Change":8.3653,"Intensity Mean Hydrodynamic Diameter [nm]":23.04,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":68.92,"Intensity Mean Hydrodynamic Diameter Change":45.8817,"Polydispersity index [nm]":0.15,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.207,"Polydispersity index Change":0.0568,"ZETA POTENTIAL [mV]":-20.27,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-8.29,"ZETA POTENTIAL Change":11.975,"Localized Surface Plasmon Resonance (LSPR) index":0.273619886,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.327264445,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0536,"LSPR peak position (nm) [nm]":518.57,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":3.552,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":240.1767044,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.055952944}},"G15.AUT":{"composition":{"Core composition":"[Au]","Surface modifier1":"11-Amino-1-undecanethiol","Surface modifier2":null,"Classification":"Cationic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.40174,"Cell.association (Log2 transformed)":-1.316},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":23.8,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":55.98,"Z-Average Hydrodynamic Diameter Change":32.1767,"Volume Mean Hydrodynamic Diameter [nm]":4.11,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":221.93,"Volume Mean Hydrodynamic Diameter Change":217.8197,"Number Mean Hydrodynamic Diameter [nm]":29.49,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":25.25,"Number Mean Hydrodynamic Diameter Change":-4.2398,"Intensity Mean Hydrodynamic Diameter [nm]":29.49,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":83.34,"Intensity Mean Hydrodynamic Diameter Change":53.8511,"Polydispersity index [nm]":0.326,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.273,"Polydispersity index Change":-0.0532,"ZETA POTENTIAL [mV]":16.35,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-7.95,"ZETA POTENTIAL Change":-24.295,"Localized Surface Plasmon Resonance (LSPR) index":0.365435833,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.389573359,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0241,"LSPR peak position (nm) [nm]":523.23,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":5.741,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":244.2281341,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":1.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.038100112}},"G15.CALNN":{"composition":{"Core composition":"[Au]","Surface modifier1":"Peptide sequence 'CALNN'","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.0071,"Cell.association (Log2 transformed)":-7.138},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":25.22,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":38.8,"Z-Average Hydrodynamic Diameter Change":13.5742,"Volume Mean Hydrodynamic Diameter [nm]":21.32,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":36.99,"Volume Mean Hydrodynamic Diameter Change":15.6669,"Number Mean Hydrodynamic Diameter [nm]":23.12,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":34.38,"Number Mean Hydrodynamic Diameter Change":11.2597,"Intensity Mean Hydrodynamic Diameter [nm]":23.12,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":41.33,"Intensity Mean Hydrodynamic Diameter Change":18.2156,"Polydispersity index [nm]":0.144,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.154,"Polydispersity index Change":0.0101,"ZETA POTENTIAL [mV]":-21.42,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-6.54,"ZETA POTENTIAL Change":14.88,"Localized Surface Plasmon Resonance (LSPR) index":0.206909736,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.26532699,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0584,"LSPR peak position (nm) [nm]":519.87,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":2.976,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":259.0438079,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.049275338}},"G15.CIT":{"composition":{"Core composition":"[Au]","Surface modifier1":"Citrate","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.02336,"Cell.association (Log2 transformed)":-5.42},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":18.65,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":54.03,"Z-Average Hydrodynamic Diameter Change":35.3825,"Volume Mean Hydrodynamic Diameter [nm]":19.47,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":38.58,"Volume Mean Hydrodynamic Diameter Change":19.1137,"Number Mean Hydrodynamic Diameter [nm]":28.3,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":32.35,"Number Mean Hydrodynamic Diameter Change":4.0509,"Intensity Mean Hydrodynamic Diameter [nm]":28.3,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":64.47,"Intensity Mean Hydrodynamic Diameter Change":36.1691,"Polydispersity index [nm]":0.138,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.217,"Polydispersity index Change":0.0789,"ZETA POTENTIAL [mV]":-25.26,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-8.5,"ZETA POTENTIAL Change":16.7539,"Localized Surface Plasmon Resonance (LSPR) index":0.210430919,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.292836119,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0824,"LSPR peak position (nm) [nm]":517.68,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":5.488,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":272.7685577,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.013232215}},"G15.cPEG5K-SH":{"composition":{"Core composition":"[Au]","Surface modifier1":"Carboxymethyl-poly(ethylene glycol)-thiol (5kDa)","Surface modifier2":null,"Classification":"Neutral"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.00467,"Cell.association (Log2 transformed)":-7.742},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":45.72,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":44.6,"Z-Average Hydrodynamic Diameter Change":-1.12,"Volume Mean Hydrodynamic Diameter [nm]":46.42,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":43.94,"Volume Mean Hydrodynamic Diameter Change":-2.4767,"Number Mean Hydrodynamic Diameter [nm]":50.95,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":41.77,"Number Mean Hydrodynamic Diameter Change":-9.1811,"Intensity Mean Hydrodynamic Diameter [nm]":50.95,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":46.96,"Intensity Mean Hydrodynamic Diameter Change":-3.9944,"Polydispersity index [nm]":0.115,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.093,"Polydispersity index Change":-0.0222,"ZETA POTENTIAL [mV]":-12.29,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-7.48,"ZETA POTENTIAL Change":4.81,"Localized Surface Plasmon Resonance (LSPR) index":0.250940122,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.280491349,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0296,"LSPR peak position (nm) [nm]":520.6,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":0.142,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":241.5200528,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.007185452}},"G15.cPEG5K-SH (LD)":{"composition":{"Core composition":"[Au]","Surface modifier1":"Carboxymethyl-poly(ethylene glycol)-thiol (5kDa) (low density)","Surface modifier2":null,"Classification":"Neutral"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.00422,"Cell.association (Log2 transformed)":-7.887},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":19.85,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":38.69,"Z-Average Hydrodynamic Diameter Change":18.8444,"Volume Mean Hydrodynamic Diameter [nm]":20.14,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":33.52,"Volume Mean Hydrodynamic Diameter Change":13.3878,"Number Mean Hydrodynamic Diameter [nm]":21.49,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":30.34,"Number Mean Hydrodynamic Diameter Change":8.8556,"Intensity Mean Hydrodynamic Diameter [nm]":21.49,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":40.44,"Intensity Mean Hydrodynamic Diameter Change":18.95,"Polydispersity index [nm]":0.086,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.154,"Polydispersity index Change":0.0672,"ZETA POTENTIAL [mV]":-6.33,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-5.91,"ZETA POTENTIAL Change":0.4133,"Localized Surface Plasmon Resonance (LSPR) index":0.211466307,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.263698153,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0522,"LSPR peak position (nm) [nm]":519.07,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":1.67,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":258.6099131,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.008213753}},"G15.CTAB":{"composition":{"Core composition":"[Au]","Surface modifier1":"Hexadecyltrimethylammonium bromide","Surface modifier2":null,"Classification":"Cationic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.01719,"Cell.association (Log2 transformed)":-5.862},"physchem":{"Core size [nm]":14.9,"Density [g/cm^3]":19.1,"MW [g/mol]":197.0,"Z-Average Hydrodynamic Diameter [nm]":15.6,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":59.7,"Z-Average Hydrodynamic Diameter Change":44.1005,"Volume Mean Hydrodynamic Diameter [nm]":2.75,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":69.66,"Volume Mean Hydrodynamic Diameter Change":66.9171,"Number Mean Hydrodynamic Diameter [nm]":35.99,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":17.68,"Number Mean Hydrodynamic Diameter Change":-18.3089,"Intensity Mean Hydrodynamic Diameter [nm]":35.99,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":105.1,"Intensity Mean Hydrodynamic Diameter Change":69.1175,"Polydispersity index [nm]":0.465,"Polydispersity index Human serum (Sigma #H4522) [nm]":0.371,"Polydispersity index Change":-0.0939,"ZETA POTENTIAL [mV]":-5.01,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":-9.26,"ZETA POTENTIAL Change":-4.2475,"Localized Surface Plasmon Resonance (LSPR) index":0.326141556,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":0.365810851,"Localized Surface Plasmon Resonance (LSPR) index Change":0.0397,"LSPR peak position (nm) [nm]":518.9,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":4.008,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":213.3235479,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":9.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.068568202}},"G15.DDT@BDHDA":{"composition":{"Core composition":"[Au]","Surface 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Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":4.12,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":610.3022261,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.026045373}},"S40.MBA":{"composition":{"Core composition":"[Ag]","Surface modifier1":"4-Mercaptobenzoic acid","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.04448,"Cell.association (Log2 transformed)":-4.491},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":6.05,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":630.6403901,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":1.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.049404822}},"S40.MES":{"composition":{"Core composition":"[Ag]","Surface modifier1":"2-Mercaptoethanesulfonate","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.1276,"Cell.association (Log2 transformed)":-2.97},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":4.39,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":659.0982742,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.05896227}},"S40.MHDA":{"composition":{"Core composition":"[Ag]","Surface modifier1":"16-Mercaptohexadecanoic acid","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.30968,"Cell.association (Log2 transformed)":-1.691},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":3.55,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":655.5775498,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.03713835}},"S40.mPEG5K-SH":{"composition":{"Core composition":"[Ag]","Surface modifier1":"Methoxy-poly(ethylene glycol)-thiol (5kDa)","Surface modifier2":null,"Classification":"Neutral"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.19326,"Cell.association (Log2 transformed)":-2.371},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":0.83,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":688.4761522,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.005647305}},"S40.MUTA":{"composition":{"Core composition":"[Ag]","Surface modifier1":"(11-Mercaptoundecyl)-N,N,N-trimethylammonium","Surface modifier2":null,"Classification":"Cationic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.73653,"Cell.association (Log2 transformed)":-0.441},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":2.1,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":747.9733811,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":12.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.019042823}},"S40.nPEG5K-SH":{"composition":{"Core composition":"[Ag]","Surface modifier1":"Amino-poly(ethylene glycol)-thiol (5kDa)","Surface modifier2":null,"Classification":"Neutral"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.24261,"Cell.association (Log2 transformed)":-2.043},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":0.4,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":689.2859255,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.007516076}},"S40.PLL-SH":{"composition":{"Core composition":"[Ag]","Surface modifier1":"Thiolated poly(L-lysine)","Surface modifier2":null,"Classification":"Cationic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.94668,"Cell.association (Log2 transformed)":-0.079},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) 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(Sigma #H4522) [cm^2]":10.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.014004945}},"S40.SA":{"composition":{"Core composition":"[Ag]","Surface modifier1":"Stearic acid","Surface modifier2":null,"Classification":"Anionic"},"tox":{"Cell.association (Net cell association [mL/ug(Mg)])":0.13245,"Cell.association (Log2 transformed)":-2.916},"physchem":{"Core size [nm]":38.4,"Density [g/cm^3]":10.5,"MW [g/mol]":108.0,"Z-Average Hydrodynamic Diameter [nm]":null,"Z-Average Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Z-Average Hydrodynamic Diameter Change":null,"Volume Mean Hydrodynamic Diameter [nm]":null,"Volume Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Volume Mean Hydrodynamic Diameter Change":null,"Number Mean Hydrodynamic Diameter [nm]":null,"Number Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Number Mean Hydrodynamic Diameter Change":null,"Intensity Mean Hydrodynamic Diameter [nm]":null,"Intensity Mean Hydrodynamic Diameter Human serum (Sigma #H4522) [nm]":null,"Intensity Mean Hydrodynamic Diameter Change":null,"Polydispersity index [nm]":null,"Polydispersity index Human serum (Sigma #H4522) [nm]":null,"Polydispersity index Change":null,"ZETA POTENTIAL [mV]":null,"ZETA POTENTIAL Human serum (Sigma #H4522) [mV]":null,"ZETA POTENTIAL Change":null,"Localized Surface Plasmon Resonance (LSPR) index":null,"Localized Surface Plasmon Resonance (LSPR) index Human serum (Sigma #H4522)":null,"Localized Surface Plasmon Resonance (LSPR) index Change":null,"LSPR peak position (nm) [nm]":null,"Total protein (BCA assay) Human serum (Sigma #H4522) [ug]":1.18,"Autot (ICP-AES) Human serum (Sigma #H4522) [nmol]":653.5183257,"Total surface area (SAtot) Human serum (Sigma #H4522) [cm^2]":11.0,"Protein density Human serum (Sigma #H4522) Mean [ug/cm^2]":0.0,"Protein density Human serum (Sigma #H4522) SEM [ug/cm^2]":0.013965863}}}
diff --git a/protein_corona.rb b/protein_corona.rb
new file mode 100644
index 0000000..35970dc
--- /dev/null
+++ b/protein_corona.rb
@@ -0,0 +1,118 @@
+require 'json'
+require 'yaml'
+require 'csv'
+#require_relative "../lazar/lib/lazar.rb"
+#include OpenTox
+
+class Object
+ def numeric?
+ true if Float(self) rescue false
+ end
+end
+
+def euclidean_distance(a, b)
+ sq = a.zip(b).map{|a,b| (a - b) ** 2}
+ Math.sqrt(sq.inject(0) {|s,c| s + c})
+end
+
+def dot_product(a, b)
+ products = a.zip(b).map{|a, b| a * b}
+ products.inject(0) {|s,p| s + p}
+end
+
+def magnitude(point)
+ squares = point.map{|x| x ** 2}
+ Math.sqrt(squares.inject(0) {|s, c| s + c})
+end
+
+def cosine_similarity(a, b)
+ dot_product(a, b) / (magnitude(a) * magnitude(b))
+end
+
+#@endpoint = @data.collect{|r| r[5]}
+
+def neighbors query
+end
+
+def csv2json
+ csv = CSV.read("data/MergedSheets_edit.csv")
+ csv.collect!{|row| row[0..36].collect{|c| c.numeric? ? c.to_f : c } }.compact
+ feature_names = [
+ "ID",
+ csv[0][1],
+ csv[0][2],
+ csv[0][3],
+ csv[6][4],
+ "#{csv[0][5]} (#{csv[6][5]} [#{csv[11][5]}])", # endpoint
+ "#{csv[0][6]} (#{csv[6][6]})", # endpoint
+ "#{csv[6][7]} [#{csv[11][7]}]",
+ "#{csv[6][8]} [#{csv[11][8]}]",
+ "#{csv[6][9]} [#{csv[11][9]}]",
+ ]
+ (10..10+5*3).step(3) do |i|
+ feature_names += [
+ "#{csv[6][i]} [#{csv[11][i]}]",
+ "#{csv[6][i+1]} #{csv[8][i+1]} [#{csv[11][i+1]}]",
+ "#{csv[6][i+2]} #{csv[8][i+2]}",
+ ]
+ end
+ feature_names += [
+ "#{csv[6][28]}",
+ "#{csv[6][29]} #{csv[8][29]}",
+ "#{csv[6][30]} #{csv[8][30]}",
+ ]
+ (31..34).each do |i|
+ feature_names << "#{csv[6][i]} #{csv[8][i]} [#{csv[11][i]}]"
+ end
+ (35..36).each do |i|
+ feature_names << "#{csv[6][i]} #{csv[8][i]} #{csv[10][i]} [#{csv[11][i]}]"
+ end
+ data = {}
+ csv.drop(12).each do |row|
+ id = row.first
+ data[id] = {}
+ row.each_with_index do |col,i|
+ if i == 0
+ data[id][:composition] = {}
+ elsif i < 5
+ data[id][:composition][feature_names[i]] = col
+ elsif i < 7
+ data[id][:tox] ||= {}
+ data[id][:tox][feature_names[i]] = col
+ else
+ data[id][:physchem] ||= {}
+ data[id][:physchem][feature_names[i]] = col
+ end
+ end
+ end
+ File.open("data.json","w+"){|f| f.puts data.to_json}
+ data
+end
+
+#puts data.to_yaml
+=begin
+R.assign "endpoint", endpoint
+(0..data[0].size).each do |c|
+ if data.collect{|r| r[c]}.uniq.size > 1
+ begin
+ R.assign "feature", data.collect{|r| r[c]}
+ R.eval "r <- cor(-log(endpoint),-log(feature),use='complete')"
+ r = R.eval("r").to_ruby
+ p "#{c}: #{r}" if r > 0.3 or r < -0.3
+ rescue
+ end
+ end
+end
+
+
+csv[0..13].each do |row|
+ row.each_with_index do |col,i|
+ features[i] = features[i].to_s+", "+col.to_s
+ end
+end
+
+puts features.select{|f| f.match(/Mean/)}.to_yaml
+
+ #n+=1
+ #p n,row.first unless row.first.match /^[G|S]/
+=end