Updated master to SVN trunk revision 572
This commit is contained in:
Yury V Bukhman
Binary file not shown.
|
After Width: | Height: | Size: 48 KiB |
@@ -63,13 +63,28 @@ a:visited { color: #428bca !important;}
|
||||
border: 1px solid black;
|
||||
margin: 20px auto 0;
|
||||
width: 1600px;
|
||||
padding-left: 50px;
|
||||
padding-left: 50px;
|
||||
overflow: hidden; /* MB: added so that float left stuffs won't collapse. */
|
||||
}
|
||||
|
||||
#contents {
|
||||
padding: 5px 25px;
|
||||
}
|
||||
|
||||
/* MB: Options in GCAT. For unordered list */
|
||||
#options {
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
list-style: none;
|
||||
}
|
||||
|
||||
/* MB: 1 option in GCAT. */
|
||||
#options li {
|
||||
float: left;
|
||||
width: 33%;
|
||||
padding: 0 100px 0 0;
|
||||
}
|
||||
|
||||
/*#mainContent{
|
||||
margin:0;
|
||||
min-height:500px;
|
||||
|
||||
@@ -55,7 +55,11 @@ class AssaysController < ApplicationController
|
||||
flash.now[:error] = @result[:error_message] #.join("\n")
|
||||
#do not allow bad guys to fill disc space with invalid files
|
||||
FileUtils.rm @result[:path]
|
||||
render :action => 'inputfile_error_message'
|
||||
# render :action => 'inputfile_error_message'
|
||||
@error_msg = @result[:error_message]
|
||||
@console_msg = @result[:console_msg]
|
||||
render :action => 'inputfile_error_message'
|
||||
|
||||
else
|
||||
# parse the output text file into a hash in order to create a table in Assays#show
|
||||
@table = output_table(@result, !@result[:layout_file].nil?)
|
||||
@@ -70,4 +74,4 @@ class AssaysController < ApplicationController
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
+71
-12
@@ -32,8 +32,10 @@ class Assay
|
||||
include ActiveModel::Validations
|
||||
include ActiveModel::Conversion
|
||||
extend ActiveModel::Naming
|
||||
attr_accessor :input_file, :transformation, :transformation_input, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type,
|
||||
:plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input
|
||||
attr_accessor :input_file, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type,
|
||||
:plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input, :console_out, :specg_min,
|
||||
:specg_max, :totg_min, :totg_max, :lagT_min, :lagT_max,:transformation, :transformation_input
|
||||
|
||||
|
||||
# (1) Validation of input data file
|
||||
validates_presence_of :input_file, :message => '- No input file was specified.'
|
||||
@@ -117,7 +119,7 @@ class Assay
|
||||
if self.transformation == '-1'
|
||||
self.transformation = Float(self.transformation_input)
|
||||
else
|
||||
self.transformation = self.transformation.to_i
|
||||
self.transformation = self.transformation.to_f
|
||||
end
|
||||
|
||||
# Soothing parameter for growth curve model. Applied for Loess model only.
|
||||
@@ -128,6 +130,8 @@ class Assay
|
||||
# (3) blank value (A Real Number)
|
||||
if self.blank_value == 'default'
|
||||
self.blank_value = nil
|
||||
elsif self.blank_value == 'zero'
|
||||
self.blank_value = 0
|
||||
else
|
||||
self.blank_value = Float(self.blank_value_input)
|
||||
end
|
||||
@@ -156,6 +160,20 @@ class Assay
|
||||
self.remove_jumps = false
|
||||
end
|
||||
|
||||
## (7) Heatmap values
|
||||
if (self.specg_min != '' && self.specg_max != '')
|
||||
self.specg_max = Float(self.specg_max)
|
||||
self.specg_min = Float(self.specg_min)
|
||||
end
|
||||
if (self.totg_min != '' && self.totg_max != '')
|
||||
self.totg_min = Float(self.totg_min)
|
||||
self.totg_max = Float(self.totg_max)
|
||||
end
|
||||
if (self.lagT_min != '' && self.lagT_max != '')
|
||||
self.lagT_max = Float(self.lagT_max)
|
||||
self.lagT_min = Float(self.lagT_min)
|
||||
end
|
||||
|
||||
|
||||
############################################################################################
|
||||
|
||||
@@ -201,7 +219,11 @@ class Assay
|
||||
if(File.size(inputfile) > MAX_FILE_SIZE)
|
||||
return {:error_message => "Error: File too big. Maximum file size allowed is #{MAX_FILE_SIZE/(10**6)} MB.", :path => inputfile}
|
||||
end
|
||||
|
||||
|
||||
# Try to override stdout to redirect the console output.
|
||||
$stdout = File.new(out_dir_path + '/console.out', 'w')
|
||||
$stdout.sync = true
|
||||
|
||||
# use web interface parsed parameters to call R function/library via Rinruby
|
||||
R.eval ('library(GCAT)')
|
||||
R.assign "out.dir", out_dir_path
|
||||
@@ -253,9 +275,12 @@ class Assay
|
||||
|
||||
# (2) transformation. N value (A Real Number)
|
||||
R.assign "add.constant", self.transformation
|
||||
# R.assign "add.constant", 0
|
||||
# (3) blank value (A Real Number)
|
||||
if (self.blank_value == nil)
|
||||
R.eval "blank.value <- NULL"
|
||||
elsif (self.blank_value == 0)
|
||||
R.eval "blank.value <- 0"
|
||||
else
|
||||
R.assign "blank.value", self.blank_value
|
||||
end
|
||||
@@ -303,16 +328,40 @@ class Assay
|
||||
R.assign 'use.linear.param', 'F'
|
||||
R.assign 'smooth.param', 0.1 # default value
|
||||
end
|
||||
|
||||
## Heatmap values
|
||||
if (self.specg_max != '' && self.specg_min != '')
|
||||
R.assign 'specMin', self.specg_min
|
||||
R.assign 'specMax', self.specg_max
|
||||
R.eval "specRange <- c(specMin, specMax)"
|
||||
else
|
||||
R.eval 'specRange <- NA'
|
||||
end
|
||||
if (self.totg_min != '' && self.totg_max != '')
|
||||
R.assign 'totMin', self.totg_min
|
||||
R.assign 'totMax', self.totg_max
|
||||
R.eval "totalRange <- c(totMin, totMax)"
|
||||
else
|
||||
R.eval 'totalRange <- NA'
|
||||
end
|
||||
if (self.lagT_min != '' && self.lagT_max != '')
|
||||
R.assign 'lagT_min', self.lagT_min
|
||||
R.assign 'lagT_max', self.lagT_max
|
||||
R.eval "lagRange <- c(lagT_min, lagT_max)"
|
||||
else
|
||||
R.eval 'lagRange <- NA'
|
||||
end
|
||||
|
||||
# This block evaluates the files (csv or xlsx, single.plate or multiple.plate)
|
||||
R.eval ('R_file_return_value <- gcat.analysis.main(file, single.plate, layout.file, out.dir=out.dir, graphic.dir = out.dir, add.constant, blank.value,
|
||||
start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param,
|
||||
points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
|
||||
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"),
|
||||
start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param, lagRange = lagRange,
|
||||
totalRange = totalRange, specRange = specRange, points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8,
|
||||
plate.ncol = 12, input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"),
|
||||
layout.sheet.headers = c("Strain", "Media Definition"), silent = T, verbose = F, return.fit = F, overview.jpgs = T)')
|
||||
|
||||
# good file returns a list of file path(length is more than 1), bad file returns error message string(array length = 1)
|
||||
print R.R_file_return_value
|
||||
|
||||
R.eval ('R_array_return_length <- length(R_file_return_value)')
|
||||
unless R.R_array_return_length == 1
|
||||
puts R.R_file_return_value, "\n"
|
||||
@@ -323,16 +372,23 @@ class Assay
|
||||
if(error_message.include? "Error in <remove.points>")
|
||||
num_data_points = error_message.split("data has ").last.gsub("\n\n", "")
|
||||
error_message = "Invalid 'Points to ignore'. Please select a value in the range (1-#{num_data_points})."
|
||||
else
|
||||
# debugger
|
||||
console_message = error_message
|
||||
split_s = error_message.split(":")
|
||||
print split_s
|
||||
split_s.each {|x| error_message = x}
|
||||
end
|
||||
return {:error_message => error_message, :path => inputfile}
|
||||
return {:error_message => error_message, :path => inputfile, :console_msg => console_message}
|
||||
end
|
||||
|
||||
|
||||
# process generated files
|
||||
raise "no files generated" if files.empty?
|
||||
#search for "_overview.jpg files" from Array of files
|
||||
overviewFiles = ""
|
||||
pdfFile = ""
|
||||
txtFile = ""
|
||||
consoleOut = ""
|
||||
files_Array_Size = files.size - 1
|
||||
|
||||
for i in 0..files_Array_Size
|
||||
@@ -368,6 +424,7 @@ class Assay
|
||||
|
||||
# build array named overviewFiles that contains "_overview.jpg files"
|
||||
overviewFiles = overviewFiles.split("\n")
|
||||
|
||||
raise "no overview files generated" if overviewFiles.empty?
|
||||
|
||||
if self.plate_type == 'm'
|
||||
@@ -375,18 +432,20 @@ class Assay
|
||||
else
|
||||
zipfile = out_dir_path + "/singlePlateAnalysis.zip"
|
||||
end
|
||||
|
||||
consoleOut = out_dir_path + "/console.out"
|
||||
self.console_out = consoleOut
|
||||
# create Zip files at current directory
|
||||
Zip::File.open(zipfile, Zip::File::CREATE) { |zf|
|
||||
files.each{|file| zf.add(File.basename(file), file)}
|
||||
#files.each{|file| zf.add(file.sub(out_dir_path + "/", ""), file))}
|
||||
#zf.add(File.basename(consoleOut), consoleOut)
|
||||
}
|
||||
|
||||
#return results unless error
|
||||
#zip files, jpg of overviews, txt file for datagrid, pdf file
|
||||
|
||||
|
||||
{:status => status, :overviewFiles => overviewFiles, :zipfile => zipfile, :txtFile => txtFile, :pdfFile => pdfFile, :inputfile => inputfile, :layout_file => layout_file, :model => self.model}
|
||||
{:status => status, :overviewFiles => overviewFiles, :zipfile => zipfile, :txtFile => txtFile, :pdfFile => pdfFile, :inputfile => inputfile, :layout_file => layout_file, :model => self.model,
|
||||
:consoleout => consoleOut}
|
||||
end # end of r_calculation method
|
||||
|
||||
|
||||
|
||||
@@ -1,112 +1,106 @@
|
||||
<%= form_for @assay do |f| %>
|
||||
|
||||
<% if @assay.errors.any? %>
|
||||
<div id="error_explanation">
|
||||
<h2><%= pluralize(@assay.errors.count, "error") %> prohibited this assay from being saved:</h2>
|
||||
|
||||
<ul>
|
||||
<% @assay.errors.full_messages.each do |msg| %>
|
||||
<% if @assay.errors.any? %>
|
||||
<div id="error_explanation">
|
||||
<h2><%= pluralize(@assay.errors.count, "error") %> prohibited this assay from being saved:</h2>
|
||||
<ul>
|
||||
<% @assay.errors.full_messages.each do |msg| %>
|
||||
<li><%= msg %></li>
|
||||
<% end %>
|
||||
</ul>
|
||||
</div>
|
||||
<% end %>
|
||||
|
||||
|
||||
<h3>Plate Type</h3>
|
||||
<%= f.radio_button(:plate_type, 's', :checked => true) %>
|
||||
<%= f.label(:plate_type_single, "Single-plate") %><br />
|
||||
<%= f.radio_button(:plate_type, 'm', :checked => false) %>
|
||||
<%= f.label(:plate_type_single, "Multiple-plate") %><br />
|
||||
|
||||
<h3>Input Data File</h3>
|
||||
Please specify a plate results file to upload for analysis:<br>
|
||||
|
||||
<div class="field">
|
||||
<%= f.file_field :input_file %>
|
||||
</div>
|
||||
|
||||
<h3><span data-tooltip="Optionally upload a companion .csv file containing identifying information for all wells in the experiments(s) to be analyzed, including strain identifiers and growth media (or growth environment) definitions, which are used for graphic output.">Plate Layout File</span></h3>
|
||||
Optionally upload a plate layout file:<br>
|
||||
|
||||
<div class="field">
|
||||
<%= f.file_field :layout_file %>
|
||||
</div>
|
||||
|
||||
<div class="actions" style="margin-top:30px;">
|
||||
<%= link_to "Single-Plate Example File","/resources/YPDAFEXglucoseTests_2-25-10.csv" %><br>
|
||||
<%= link_to "Single-Plate Layout Example File","/resources/YPDAFEXglucoseTests_2-25-10_Layout.csv" %><br>
|
||||
<%= link_to "Multi-Plate Example File","/resources/test_YYYY_MM_DD_HH_MM_SS.csv" %><br>
|
||||
<%= link_to "Multi-Plate Layout Example File","/resources/MultiPlateLayout_plateID.csv" %>
|
||||
|
||||
</div>
|
||||
|
||||
<h3><span data-tooltip="OD value for blank well read. As the default option <NULL>, GCAT will automatically take the first OD reading of each well to be the blank.">Media background</span></h3>
|
||||
|
||||
<%= f.radio_button(:blank_value, "default", {:checked => true, :class => "user_enter3 user_enter3_no"}) %>
|
||||
<%= f.label(:blank_value_blank_value_default, "Take the first OD reading of each well to be the blank") %><br />
|
||||
|
||||
<%= f.radio_button(:blank_value, "user", {:class => "user_enter3 user_enter3_yes"}) %>
|
||||
<%= f.label(:blank_value_user, "User Input.") %>
|
||||
|
||||
<div class="field optional_input3" style="display:none">
|
||||
|
||||
<%= f.text_field :blank_value_input, :placeholder => 'Enter your OD blank value here' %>
|
||||
</div>
|
||||
|
||||
<h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
|
||||
|
||||
<%= f.radio_button(:transformation, 1, {:checked => true, :class => "user_enter2 user_enter2_no"}) %>
|
||||
<%= f.label(:transformation_one, "log(x + 0.1)") %><br />
|
||||
|
||||
<%= f.radio_button(:transformation, 0, {:class => "user_enter2 user_enter2_no"}) %>
|
||||
<%= f.label(:transformation_zero, "log(x)") %><br />
|
||||
|
||||
<%= f.radio_button(:transformation, -1, {:class => "user_enter2 user_enter2_yes"}) %>
|
||||
<%= f.label(:transformation_any, "log(x + δ)") %>
|
||||
|
||||
<div class="field optional_input2" style="display:none">
|
||||
|
||||
<%= f.text_field :transformation_input, :placeholder => 'Enter your n value here'%>
|
||||
</div>
|
||||
|
||||
<h3><span data-tooltip="Choose the preferred growth curve model selection available below.">Growth curve model</span></h3>
|
||||
|
||||
|
||||
<%= f.radio_button(:model, 1, {:checked => true, :class => "user_enter1 user_enter1_no"})%>
|
||||
<%= f.label(:model_one, "Sigmoid curve") %>
|
||||
|
||||
<%#= f.radio_button(:model, 0, {:class => "user_enter1 user_enter1_no"}) %>
|
||||
<%#= f.label(:model_zero, "Sigmoid + linear") %>
|
||||
|
||||
<%= f.radio_button(:model, -1, {:class => "user_enter1 user_enter1_yes"}) %>
|
||||
<%= f.label(:model_any, "LOESS. The default smoothing value is 0.1.") %>
|
||||
|
||||
<div class="field optional_input1" style="display:none">
|
||||
<%= f.text_field :loess_input, :placeholder => 'Enter the smoothing value here.'%>
|
||||
</div>
|
||||
|
||||
<h3><span data-tooltip="Enter the index of the timepoint at which the wells were inoculated with the culture.
|
||||
" >Inoculation timepoint</span></h3>
|
||||
|
||||
<div class="field">
|
||||
<%= f.label :start_index, "Enter the timepoint index (positive integer only). The default value is 2. " %><br />
|
||||
<%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '2') %>
|
||||
</div>
|
||||
|
||||
<h3><span data-tooltip="Enter a threshold to determine the presence of a growing culture. GCAT rejects curves where the density measurements never reach this value above the specified inoculation timepoint." >Growth Threshold</span></h3>
|
||||
|
||||
<div class="field">
|
||||
<%= f.label :growth_threshold, "Enter the growth threshold. The default value is 0.05. " %><br />
|
||||
<%= f.text_field(:growth_threshold, :type => 'number', :min =>'0', :size => '3', :value => '0.05', :step => "0.01") %>
|
||||
</div>
|
||||
|
||||
<h3><span data-tooltip="Enter indices (as a comma-separated list) of any erroneous reads that should be removed across the entire experiment. " >Points to ignore</span></h3>
|
||||
<div class="field">
|
||||
<%= f.label :remove_points,"Enter a comma-separated list of points. Example: 2,3,4,5 (positive integers only). The default is an empty list." %><br />
|
||||
<%= f.text_field :remove_points %>
|
||||
</div>
|
||||
|
||||
<% end %>
|
||||
</ul>
|
||||
</div>
|
||||
<% end %>
|
||||
<div class="actions" style="margin-top:30px;">
|
||||
<%= link_to "GCAT Users Manual","/resources/GCAT_users_manual.pdf" %> </br>
|
||||
<%= link_to "GCAT Release Notes","/resources/Release_Notes.pdf" %>
|
||||
</div>
|
||||
<section>
|
||||
<ul id="options">
|
||||
<li>
|
||||
<h3>Plate Type</h3>
|
||||
<%= f.radio_button(:plate_type, 's', :checked => true) %>
|
||||
<%= f.label(:plate_type_single, "Single-plate") %><br />
|
||||
<%= f.radio_button(:plate_type, 'm', :checked => false) %>
|
||||
<%= f.label(:plate_type_single, "Multiple-plate") %><br />
|
||||
</li>
|
||||
<li>
|
||||
<h3>Input Data File</h3>
|
||||
Please specify a plate results file to upload for analysis:<br>
|
||||
<div class="field">
|
||||
<%= f.file_field :input_file %>
|
||||
</div>
|
||||
<div class="actions" style="margin-top:30px;">
|
||||
<%= link_to "Single-Plate Example File","/resources/YPDAFEXglucoseTests_2-25-10.csv" %><br>
|
||||
<%= link_to "Multi-Plate Example File","/resources/test_YYYY_MM_DD_HH_MM_SS.csv" %><br>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="Optionally upload a companion .csv file containing identifying information for all wells in the experiments(s) to be analyzed, including strain identifiers and growth media (or growth environment) definitions, which are used for graphic output.">Plate Layout File</span></h3>
|
||||
Optionally upload a plate layout file:<br>
|
||||
<div class="field">
|
||||
<%= f.file_field :layout_file %>
|
||||
</div>
|
||||
<div class="actions" style="margin-top:30px;">
|
||||
<%= link_to "Single-Plate Layout Example File","/resources/YPDAFEXglucoseTests_2-25-10_Layout.csv" %><br>
|
||||
<%= link_to "Multi-Plate Layout Example File","/resources/MultiPlateLayout_plateID.csv" %>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="OD value for blank well read. As the default option <NULL>, GCAT will automatically take the first OD reading of each well to be the blank.">Media background</span></h3>
|
||||
<%= f.radio_button(:blank_value, "zero", {:class => "user_enter3 user_enter3_no"}) %>
|
||||
<%= f.label(:blank_value_zero, "0" ) %> <br/>
|
||||
<%= f.radio_button(:blank_value, "default", {:class => "user_enter3 user_enter3_no"}) %>
|
||||
<%= f.label(:blank_value_default, "Take the first OD reading of each well to be the blank") %><br>
|
||||
<%= f.radio_button(:blank_value, "user", {:checked => true, :class => "user_enter3 user_enter3_yes"}) %>
|
||||
<%= f.label(:blank_value_user, "User Input.") %>
|
||||
<div class="field optional_input3" style="display:none">
|
||||
<%= f.text_field :blank_value_input, :placeholder => 'Enter your OD blank value here' %>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
|
||||
<%= f.radio_button(:transformation, 0, {:checked => true, :class => "user_enter2 user_enter2_no"}) %>
|
||||
<%= f.label(:transformation_zero, "log(x)") %><br />
|
||||
<%= f.radio_button(:transformation, 0.1, {:class => "user_enter2 user_enter2_no"}) %>
|
||||
<%= f.label(:transformation_one, "log(x + 0.1)") %><br />
|
||||
<%= f.radio_button(:transformation, -1, {:class => "user_enter2 user_enter2_yes"}) %>
|
||||
<%= f.label(:transformation_any, "log(x + δ)") %>
|
||||
<div class="field optional_input2" style="display:none">
|
||||
<%= f.text_field :transformation_input, :placeholder => 'Enter your δ value here'%>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="Choose the preferred growth curve model selection available below.">Growth curve model</span></h3>
|
||||
<%= f.radio_button(:model, 1, {:checked => true, :class => "user_enter1 user_enter1_no"})%>
|
||||
<%= f.label(:model_one, "Sigmoid curve") %><br />
|
||||
<%#= f.radio_button(:model, 0, {:class => "user_enter1 user_enter1_no"}) %>
|
||||
<%#= f.label(:model_zero, "Sigmoid + linear") %>
|
||||
<%= f.radio_button(:model, -1, {:class => "user_enter1 user_enter1_yes"}) %>
|
||||
<%= f.label(:model_any, "LOESS. The default smoothing value is 0.1.") %>
|
||||
<div class="field optional_input1" style="display:none">
|
||||
<%= f.text_field :loess_input, :placeholder => 'Enter the smoothing value here.'%>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="Enter the index of the timepoint at which the wells were inoculated with the culture.
|
||||
" >Inoculation timepoint</span></h3>
|
||||
<div class="field">
|
||||
<%= f.label :start_index, "Enter the timepoint index (positive integer only). The default value is 2. " %><br />
|
||||
<%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '2') %>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="Enter a threshold to determine the presence of a growing culture. GCAT rejects curves where the density measurements never reach this value above the specified inoculation timepoint." >Growth Threshold</span></h3>
|
||||
<div class="field">
|
||||
<%= f.label :growth_threshold, "Enter the growth threshold. The default value is 0.05. " %><br />
|
||||
<%= f.text_field(:growth_threshold, :type => 'number', :min =>'0', :size => '3', :value => '0.05', :step => "0.01") %>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="Enter indices (as a comma-separated list) of any erroneous reads that should be removed across the entire experiment. " >Points to ignore</span></h3>
|
||||
<div class="field">
|
||||
<%= f.label :remove_points,"Enter a comma-separated list of points. Example: 2,3,4,5 (positive integers only). The default is an empty list." %><br />
|
||||
<%= f.text_field :remove_points %>
|
||||
</div>
|
||||
<!--<h3><span data-tooltip="GCAT automatically detects sudden changes in OD ('jumps'). Check this box if these instances should be removed when possible. If only one or two jumps are present GCAT will attempt to remove only the affected region." >Remove Jumps</span></h3>-->
|
||||
<%#= f.check_box(:remove_jumps) %>
|
||||
<%#= f.label(:remove_jumps, "Employ the jump detection algorithm to attempt to remove problematic points.") %>
|
||||
@@ -122,26 +116,44 @@ Optionally upload a plate layout file:<br>
|
||||
<%= f.text_field(:plate_dimensions_column, :type => 'number', :min =>'1', :size => '3', :value => '12') %>
|
||||
</div>
|
||||
<%
|
||||
=end %>
|
||||
<div id="time" class="field">
|
||||
<h3><span data-tooltip="Select a correctly formatted timestamp (see user manual for details). The timestamp will be used to convert the time entries into the number of hours." >Timestamp format</span></h3>
|
||||
<%= f.label :timestamp_format %><br />
|
||||
<%#= f.text_field(:timestamp_format, :value => '1/3600', :id => 'adam') %>
|
||||
<%= f.select :timestamp_format, options_for_select(date_time_options()) %>
|
||||
</div>
|
||||
|
||||
|
||||
<div class="actions" style="margin-top:30px;">
|
||||
=end %>
|
||||
</li>
|
||||
<li>
|
||||
<div id="time" class="field">
|
||||
<h3><span data-tooltip="Select a correctly formatted timestamp (see user manual for details). The timestamp will be used to convert the time entries into the number of hours." >Timestamp format</span></h3>
|
||||
<%= f.label :timestamp_format %><br />
|
||||
<%#= f.text_field(:timestamp_format, :value => '1/3600', :id => 'adam') %>
|
||||
<%= f.select :timestamp_format, options_for_select(date_time_options()) %>
|
||||
</div>
|
||||
</li>
|
||||
<li>
|
||||
<h3><span data-tooltip="Select the range for the heatmaps for easier comparison.">Heatmap options</span></h3>
|
||||
<div class="field">
|
||||
<%= f.label "Enter the range for the total growth." %><br />
|
||||
<%= f.text_field(:totg_min, :type => 'number', :min => '0', :size => '2') %>
|
||||
<%= f.label "-" %>
|
||||
<%= f.text_field(:totg_max, :type => 'number', :min => '1', :size => '2') %>
|
||||
</div>
|
||||
<div class="field">
|
||||
<%= f.label "Enter the range for the specific growth." %><br />
|
||||
<%= f.text_field(:specg_min, :type => 'number', :min => '0', :size => '2') %>
|
||||
<%= f.label "-" %>
|
||||
<%= f.text_field(:specg_max, :type => 'number', :min => '1', :size => '2') %>
|
||||
</div>
|
||||
<div class="field">
|
||||
<%= f.label "Enter the range for the lag time." %><br />
|
||||
<%= f.text_field(:lagT_min, :type => 'number', :min => '0', :size => '2') %>
|
||||
<%= f.label "-" %>
|
||||
<%= f.text_field(:lagT_max, :type => 'number', :min => '1', :size => '2') %>
|
||||
</div>
|
||||
</li>
|
||||
<div class="actions" style="margin-top:30px; clear:both;">
|
||||
<%= f.submit %>
|
||||
</div>
|
||||
|
||||
<div class="actions" style="margin-top:30px;">
|
||||
<%= mail_to "gcat.help@glbrc.wisc.edu","Please Send Any Questions To The GLBRC Help Desk And Be Sure To Include 'GCAT' In Your Subject Title", :subject => "GCAT" %>
|
||||
<div class="actions" style="margin-top:30px; clear:both;">
|
||||
<%= mail_to "gcat.help@glbrc.wisc.edu","Please Send Any Questions To The GLBRC Help Desk And Be Sure To Include 'GCAT' In Your Subject Title", :subject => "GCAT" %>
|
||||
</div>
|
||||
|
||||
|
||||
<div class="actions" style="margin-top:30px;">
|
||||
<%= link_to "GCAT Users Manual","/resources/GCAT_users_manual.pdf" %>
|
||||
</div>
|
||||
|
||||
<% end %>
|
||||
</ul>
|
||||
</section>
|
||||
<% end %>
|
||||
@@ -1,6 +1,21 @@
|
||||
<div id="form-container">
|
||||
<h1>Error</h1>
|
||||
<p>Please resubmit your file.</p>
|
||||
<%= link_to 'New Assay', new_assay_path%>
|
||||
<h1>Error</h1>
|
||||
<%= @error_msg %>
|
||||
</br></br>
|
||||
<button type="button" id ="show">Full console message</button>
|
||||
<div id="console" style="display:none;">
|
||||
<code><%= @console_msg %></code>
|
||||
</div>
|
||||
<script>
|
||||
$(function() {
|
||||
$('button#show').click(function(event){
|
||||
event.preventDefault();
|
||||
$('div#console').toggle();
|
||||
});
|
||||
});
|
||||
</script>
|
||||
</br>
|
||||
<h5>Please resubmit your file.</h5>
|
||||
<%= link_to 'New Assay', new_assay_path%>
|
||||
<br><br><br>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
<div id="form-container">
|
||||
<h1>Growth Curve Analysis Tool</h1>
|
||||
|
||||
<div style="width:25%;">
|
||||
<div style="width:45%;">
|
||||
This tool processes microbial growth curve data collected in a microtiter plate format and
|
||||
generates a table of biologically meaningful growth curve characteristics, as well as relevant
|
||||
plots. These characteristics can be used to select strains with optimal growth properties.
|
||||
|
||||
@@ -39,4 +39,4 @@
|
||||
</tr>
|
||||
<% end %>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -19,6 +19,7 @@
|
||||
Copyright © 2012 The Board of Regents of the University of Wisconsin System
|
||||
<%= image_tag 'lgplv.jpg' %>
|
||||
<%= image_tag 'GLBRC_horz_cmyk_small.jpg' %>
|
||||
<%= image_tag 'DOE_Logo_Color.png', :size => "292x72" %>
|
||||
</div>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
BIN
Binary file not shown.
BIN
Binary file not shown.
BIN
Binary file not shown.
BIN
Binary file not shown.
|
Before Width: | Height: | Size: 38 KiB |
BIN
Binary file not shown.
-141
@@ -1,141 +0,0 @@
|
||||
"row" "plate" "well" "media" "strain" "model" "lag.time, hrs" "lag.time.SE, hrs" "inflection.time, hrs" "max.spec.growth.rate, log.OD/hr" "max.spec.growth.rate.SE, log.OD/hr" "baseline, log.OD" "baseline.SE, log.OD" "amplitude, log.OD" "amplitude.SE, log.OD" "plateau, log.OD" "inoc.log.OD" "max.log.OD" "projected.growth, log.OD" "achieved.growth, log.OD" "baseline.OD" "amplitude.OD" "plateau.OD" "inoc.OD" "max.OD" "projected.growth.OD" "achieved.growth.OD" "shape.par" "shape.par.SE" "R.squared" "RSS" "empty" "asymp.not.reached" "tank" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" "Media.Definition"
|
||||
1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "gompertz sigmoid" 0 1.75346931682115 9.008895 0.00387129154161333 0.000169526575673485 0.106012627582768 0.00533332981254499 0.0949774510885174 0.0112054786798504 0.200990078671286 0.112280003029694 0.184252861643961 0.0887100756415918 0.0719728586142672 0.111835916217944 0.0996340592954781 0.222612641821245 0.118826091485523 0.202319805224487 0.103786550335722 0.0834937137389644 NA NA 0.955970181896242 0.00271004795972447 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 11 "Control strain plate" "Sample" "USDA" "" "YP"
|
||||
11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards sigmoid" 2.40987768343735 0.0533048366613944 4.21845083333333 0.0460029603516824 0.000724536080633502 0.0730406465985917 0.00147448206809288 0.20195449827016 0.00148223339842928 0.274995144868751 0.073266311037202 0.274994924460913 0.201728833831549 0.201728613423711 0.0757742625906743 0.22379232217684 0.316524282953919 0.0760170539793741 0.31652399278168 0.240507228974545 0.240506938802306 0.265875936579388 0.100708043886741 0.997917404710374 0.00135388203716233 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 12 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose"
|
||||
12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "logistic sigmoid." 3.07823403673893 0.0432348209213164 5.3624375 0.0732442091237218 0.00083385044900585 0.0859165104025432 0.00136428289761777 0.336085729465356 0.00149532007847134 0.4220022398679 0.0889960026247708 0.422002205393214 0.333006237243129 0.333006202768443 0.0897153446116215 0.399458994539777 0.525011940504746 0.0930762868815243 0.52501188793044 0.431935653623222 0.431935601048915 NA NA 0.99892015420286 0.00211931922664724 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 13 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose"
|
||||
13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards sigmoid" 3.31104934964427 0.0428738829656516 6.24426055555555 0.087498859778052 0.000646229427574331 0.0670789160536515 0.00264084512090784 0.496808437832399 0.00261152544308038 0.56388735388605 0.0759549213884333 0.563886450845895 0.487932432497617 0.487931529457461 0.0693798660836618 0.643467662335959 0.757491228661656 0.0789139371187617 0.75748964157722 0.678577291542894 0.678575704458458 1.22323321021831 0.0913419736269564 0.999523017751576 0.00210815425649153 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 14 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose"
|
||||
14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "richards sigmoid" 3.16160945641398 0.0130132752242264 5.69610027777778 0.0871403267354909 0.000229646786119097 0.08737718548213 0.000697693868328928 0.569725537718312 0.000706582348719082 0.657102723200442 0.0877050574005534 0.656913955188774 0.569397665799888 0.56920889778822 0.0913082277184576 0.767781795419447 0.92919481815215 0.0916660957048965 0.928830682251893 0.837528722447253 0.837164586546997 0.128377244056841 0.0158490082737876 0.999930578411107 0.000418173571721894 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 15 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose"
|
||||
15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "gompertz sigmoid" 1.97362812374979 0.160218470960237 6.10126222222222 0.0637129438472813 0.000882845743042059 0.0636642130548074 0.00677504517335327 0.715651375940815 0.00877835119047133 0.779315588995622 0.0726054464623438 0.769574985282588 0.706710142533278 0.696969538820244 0.0657344789473957 1.0455186500407 1.17997975267831 0.0753061873456158 1.15884851638065 1.10467356533269 1.08354232903504 NA NA 0.996368548540555 0.0284187363816137 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 16 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose"
|
||||
16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" "gompertz sigmoid" 0 6.85707287937896 22.1409086111111 0.00240032503165892 0.000622808682835668 0.183471250816661 0.0241038377523601 0.144528358183154 0.243574028025108 0.327999608999814 0.193008393297115 0.240674524494353 0.134991215702699 0.0476661311972385 0.201380426209075 0.155494462222733 0.388188429507373 0.212892973647493 0.27210692827532 0.175295455859879 0.0592139546278265 NA NA 0.790451631963756 0.00713078905920281 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 19 "Control strain plate" "Sample" "USDA" "" "YP"
|
||||
19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "gompertz sigmoid" 1.9906115468579 0.0691975318131243 3.47962611111111 0.0490374116952237 0.00113344212179788 0.113611335614137 0.00175358527026848 0.199753898562767 0.00189317967250483 0.313365234176905 0.113618321003616 0.313364980275983 0.199746913173288 0.199746659272367 0.120316613087275 0.221102206170602 0.368021087850449 0.120324438962491 0.368020740508678 0.247696648887958 0.247696301546187 NA NA 0.99399012987845 0.00350258662967115 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 20 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose"
|
||||
20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic sigmoid." 2.74248926201157 0.0354379553926203 4.43294833333333 0.0945867701955495 0.00125702159577835 0.120482088801679 0.00134117834599991 0.32177887516419 0.00144348747790325 0.442260963965869 0.122204770404787 0.442260963925467 0.320056193561082 0.32005619352068 0.12804053622706 0.379579682895796 0.556221805261732 0.129985465672481 0.556221805198858 0.426236339589251 0.426236339526377 NA NA 0.998757902847438 0.00205103195615211 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 21 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose"
|
||||
21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards sigmoid" 3.06558696223571 0.0312092193543957 5.3624375 0.121127558311403 0.000999219504341884 0.0914412547332416 0.00245736106561066 0.492484364444972 0.00245078801862176 0.583925619178214 0.10090202921227 0.583925619102095 0.483023589965944 0.483023589889825 0.0957524045344744 0.636376529891633 0.793063517352536 0.106168264278383 0.79306351721605 0.686895253074153 0.686895252937667 1.80996092627302 0.117497603933281 0.999544726321195 0.00181967924857191 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 22 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose"
|
||||
22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards sigmoid" 2.77641833187198 0.0527034516734386 5.62460111111111 0.129882570160111 0.00113584996869085 0.0943645434950579 0.00505890911787811 0.678399507081888 0.00501032007418759 0.772764050576946 0.11484805727615 0.77276399934955 0.657915993300795 0.657915942073399 0.0989602917302299 0.97072108167106 1.16574421483214 0.12170299001548 1.16574410388671 1.04404122481666 1.04404111387123 1.58781592816572 0.131684393376964 0.999371589849352 0.00464022682166854 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 23 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose"
|
||||
23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards sigmoid" 2.62155170729439 0.0528519100950448 5.64843416666667 0.120898389355078 0.000856667358787892 0.106939412411106 0.00473823154418831 0.792250602933212 0.00464150376049532 0.899190015344318 0.119165060839678 0.899150109300876 0.78002495450464 0.779985048461198 0.112866826518918 1.20836098124136 1.45761167700228 0.126555853197717 1.45751360540077 1.33105582380456 1.33095775220305 0.651987010079984 0.0715475157170284 0.999508942394936 0.00516491712891745 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 24 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose"
|
||||
24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" "gompertz sigmoid" 0 5.0780526120225 14.0138366666667 0.00262196611873332 0.00018437938744914 0.128373333313586 0.0113746241547247 0.0999846427550281 0.0508218894501574 0.228357976068614 0.134971123503685 0.189191289569101 0.0933868525649285 0.0542201660654161 0.136977395010588 0.105153945825447 0.256535054410289 0.144503734616262 0.208272060219704 0.112031319794027 0.0637683256034425 NA NA 0.855383080839261 0.00575026814686199 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 27 "Control strain plate" "Sample" "Internal source" "" "YP"
|
||||
27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "gompertz sigmoid" 0.891438154862617 0.0875315924591966 2.31180638888889 0.0535113235044828 0.00124573544664028 0.0881434958395649 0.00304307272545713 0.207061853609148 0.00316468246722843 0.295205349448713 0.0894254262692569 0.295205293059733 0.205779923179456 0.205779866790477 0.0921448290236948 0.230058652994932 0.343402197264266 0.0935457804829503 0.343402121511189 0.249856416781316 0.249856341028238 NA NA 0.991724253334924 0.00363563892033091 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 28 "Control strain plate" "Sample" "Internal source" "" "YP+0.25% glucose"
|
||||
28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic sigmoid." 1.64713494830746 0.0412877829637357 3.38429388888889 0.0931935829835479 0.00118142556806869 0.0808528949077067 0.00187894210009506 0.326765480130978 0.00196420648303134 0.407618375038685 0.0874704775763749 0.407618375014084 0.32014789746231 0.320147897437709 0.0842113918182088 0.386476282813275 0.503233380311918 0.0914100428976898 0.503233380274936 0.411823337414228 0.411823337377247 NA NA 0.998561073647885 0.00184537988196709 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 29 "Control strain plate" "Sample" "Internal source" "" "YP+0.5% glucose"
|
||||
29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards sigmoid" 2.00035124383545 0.0281455446975304 4.31378305555555 0.124952394681256 0.000705710849322313 0.066176309959304 0.00266242484922488 0.497003217300128 0.00264805311701161 0.563179527259432 0.0884800685969233 0.563179527257016 0.474699458662509 0.474699458660092 0.0684150727790216 0.643787807270277 0.756247669737942 0.0925124770869246 0.756247669733698 0.663735192651017 0.663735192646773 2.09745464546466 0.104168274133155 0.999771040591133 0.00072098110255013 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 30 "Control strain plate" "Sample" "Internal source" "" "YP+1% glucose"
|
||||
30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards sigmoid" 2.0490071997567 0.0662248504953823 4.76661111111111 0.13306744704186 0.00129515567791922 0.0751622402050358 0.00684502394093866 0.656973009903259 0.00678618652478681 0.732135250108295 0.103854790297524 0.732135243114114 0.628280459810771 0.62828045281659 0.0780590412170139 0.92894459216055 1.07951615758535 0.10943934186153 1.07951614304083 0.970076815723817 0.970076801179305 1.62672197615846 0.161151121349594 0.999229593966034 0.00459582695233057 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 31 "Control strain plate" "Sample" "Internal source" "" "YP+2% glucose"
|
||||
31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "logistic sigmoid." 1.98629177172554 0.0661342221284037 5.19560611111111 0.122957280170312 0.00117607964263019 0.0764858915144976 0.00452433442917892 0.793858352641992 0.00487921879564307 0.870344244156489 0.106676773149917 0.870336478987225 0.763667471006573 0.763659705837308 0.0794869603035999 1.21191432864705 1.38773267508318 0.112574582376872 1.38771413400679 1.27515809270631 1.27513955162992 NA NA 0.998885750680602 0.0103824045406066 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 32 "Control strain plate" "Sample" "Internal source" "" "YP+5% glucose"
|
||||
32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" "gompertz sigmoid" 0 3.37960900118466 11.4875327777778 0.00260114799703032 0.000171113335294184 0.0996380871643661 0.00702344449132755 0.0812678741827026 0.0218737314876996 0.180905961347069 0.105000794559007 0.157379078978817 0.075905166788062 0.0523782844198106 0.104771014904237 0.084661410443271 0.198302487242874 0.110711492881175 0.17043921871877 0.0875909943616988 0.0597277258375952 NA NA 0.906033844889994 0.00328284811832938 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 35 "Control strain plate" "Sample" "ATCC" "" "YP"
|
||||
35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "gompertz sigmoid" 0.983948183597175 0.112859786286644 2.47863777777778 0.0501739409645355 0.00144200881080694 0.0661469359457048 0.00364271202623762 0.205919623922245 0.00380546132645363 0.27206655986795 0.0672650583629558 0.272066410063879 0.204801501504994 0.204801351700923 0.0683836896010714 0.228654445601205 0.312674369836174 0.0695789414490573 0.312674173192226 0.243095428387117 0.243095231743168 NA NA 0.987488271024703 0.00577672548033825 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 36 "Control strain plate" "Sample" "ATCC" "" "YP+0.25% glucose"
|
||||
36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards sigmoid" 1.86398050594022 0.0558531581780885 3.55112527777778 0.0944346403793218 0.00150539518734246 0.0602064687184575 0.00349724664000438 0.368213525552587 0.00348116438514935 0.428419994271045 0.0619674090584591 0.428419978577839 0.366452585212586 0.36645256951938 0.0620558052105851 0.445150582608455 0.534830565662769 0.0639276697585029 0.534830541576357 0.470902895904266 0.470902871817855 0.41241007480043 0.120556305314198 0.997911612798025 0.00385752298874987 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 37 "Control strain plate" "Sample" "ATCC" "" "YP+0.5% glucose"
|
||||
37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "logistic sigmoid." 1.99006793380884 0.0351079474960275 4.12311861111111 0.121142575431043 0.00106707303416645 0.0644342397186312 0.00208740714872881 0.517632133522502 0.00221049055518603 0.582066373241133 0.0750837822538967 0.582066368203544 0.506982590987236 0.506982585949648 0.0665554389527234 0.678049544482632 0.789732868500092 0.0779744622314236 0.789732859484154 0.711758406268668 0.71175839725273 NA NA 0.999269039916925 0.00268951955610802 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 38 "Control strain plate" "Sample" "ATCC" "" "YP+1% glucose"
|
||||
38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "logistic sigmoid." 1.98431414913883 0.0344438902457988 4.48061444444444 0.130673511563394 0.000910297701821604 0.0736708018228489 0.00232986507621017 0.655420765541249 0.00247952515524191 0.729091567364097 0.0914028197402174 0.729091436186734 0.63768874762388 0.637688616446517 0.0764523809998565 0.925952721450692 1.07319639269875 0.0957102901077889 1.07319612074233 0.977486102590961 0.977485830634544 NA NA 0.999493885845309 0.00307265449990923 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 39 "Control strain plate" "Sample" "ATCC" "" "YP+2% glucose"
|
||||
39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "logistic sigmoid." 2.10388607358557 0.0485609580954195 5.24327222222222 0.128060724388346 0.000947720103104396 0.0637480626845324 0.00338335491744478 0.806179689301617 0.00365527295985513 0.869927751986149 0.0914242899462062 0.869921741898693 0.778503462039943 0.778497451952487 0.0658238441354071 1.23933666273098 1.38673841018529 0.0957338154859682 1.38672406572182 1.29100459469932 1.29099025023585 NA NA 0.999357534856407 0.00631075803154068 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 40 "Control strain plate" "Sample" "ATCC" "" "YP+5% glucose"
|
||||
40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" "Empty"
|
||||
44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" "Empty"
|
||||
45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" "Empty"
|
||||
46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "logistic sigmoid." 9.73707675795057 0.0985970533305578 14.6811622222222 0.0827678159518767 0.00119202041574655 -0.000880352187845948 0.00297599235664884 0.821196181140969 0.00723578634320824 0.820315828953123 0.00130662738981984 0.80016942429868 0.819009201563303 0.79886279690886 -0.000879964791548726 1.27321739163809 1.27121704036991 0.00130748139930459 1.22591802114689 1.2699095589706 1.22461053974758 NA NA 0.997343483064722 0.0337108649740508 "E*" "L" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" "Empty"
|
||||
47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" "Empty"
|
||||
48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards sigmoid" 3.77043529293613 0.0360628422979525 7.69807694444444 0.0922143076373947 0.000396448194603239 0.0415079420521979 0.00249398077489825 0.670137254883342 0.00244318042181785 0.71164519693554 0.0610249599211764 0.711620409573069 0.650620237014363 0.650595449651893 0.0423814404664091 0.954505567660092 1.03734032901714 0.0629254443914062 1.03728982934981 0.974414884625737 0.974364384958405 1.49636190326278 0.0645036016880811 0.999821079386736 0.00149128792010239 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 51 "Control strain plate" "Sample" "USDA" "" "AFEX"
|
||||
51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards sigmoid" 3.81401380371595 0.0414172658123116 7.84107527777778 0.0912912497086539 0.000430847222656137 0.0416798125769253 0.00284816947390064 0.69143284133484 0.00278081561682767 0.733112653911766 0.0607785098125833 0.73305639362929 0.672334144099182 0.672277883816707 0.0425606105081318 0.996574258830031 1.08154967821066 0.0626635185773581 1.08143257293199 1.0188861596333 1.01876905435464 1.38211643616927 0.068441420394402 0.999776277423773 0.00199878407126496 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 52 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose"
|
||||
52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards sigmoid" 4.10969518183839 0.0412228717219101 8.43690166666667 0.0887040084623295 0.000394405492929288 0.0340862871852733 0.00276975733383969 0.70953425876434 0.00269646137747281 0.743620545949613 0.0553702983243347 0.743521928280257 0.688250247625278 0.688151629955922 0.034673881973359 1.03304416561189 1.10353769905694 0.0569319223405151 1.10333026330024 1.04660577671642 1.04639834095972 1.51337755174144 0.0684110305817092 0.999797902728699 0.00192728932795894 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 53 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose"
|
||||
53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards sigmoid" 4.24887937601734 0.0432115785663927 8.81823055555555 0.0859527181410838 0.000375029672246797 0.0356447291331235 0.00283858611378653 0.730548134285546 0.00274599564832944 0.766192863418669 0.0570847529310588 0.765947841016383 0.70910811048761 0.708863088085324 0.0362876182839384 1.07621834228765 1.15155936096669 0.0587455383807147 1.15103224530362 1.09281382258598 1.0922867069229 1.43679372443259 0.0664148620205159 0.999795584571703 0.00207184898977108 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 54 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose"
|
||||
54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards sigmoid" 4.18007396642371 0.0466407733724283 8.81823055555555 0.0839684559025767 0.000369760007946289 0.0335662062693272 0.00302321134929714 0.761208314991861 0.00289043066835203 0.794774521261188 0.0523578984758354 0.794000059559319 0.742416622785352 0.741642161083483 0.0341359077403089 1.14086149330819 1.21394174372853 0.0537528115582857 1.21222779441756 1.16018893217025 1.15847498285928 1.13197498623035 0.0608907037432053 0.999775581271097 0.00245341232352351 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 55 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose"
|
||||
55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards sigmoid" 4.31631141456833 0.0375067738225389 9.10422722222222 0.0746869165814573 0.000251011212616688 0.0449034082917984 0.00217539454600581 0.811374096629365 0.0020199781451565 0.856277504921164 0.0531730581528585 0.847610694845515 0.803104446768305 0.794437636692656 0.0459268271704429 1.25099895262068 1.35438019247854 0.0546121385565925 1.33406339459093 1.29976805392195 1.27945125603434 0.475355275365838 0.0354989182491613 0.99984356158066 0.00187490302158927 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 56 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose"
|
||||
56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards sigmoid" 2.71231721101246 0.051377222191618 6.24426055555555 0.114869798087755 0.000679522317637316 0.0686814145642472 0.00460568272264885 0.729956501290573 0.00454362062059059 0.798637915854821 0.10099640348141 0.798636815214796 0.697641512373411 0.697640411733386 0.0710949195446084 1.07499034630887 1.22251161803554 0.10627266302607 1.22250917185165 1.11623895500947 1.11623650882558 1.70292251675116 0.10179548101048 0.999686879664103 0.00266681050440312 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 59 "Control strain plate" "Sample" "USDA" "" "AFEX"
|
||||
59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards sigmoid" 3.01070188606209 0.0455540510180634 6.55409027777778 0.115107998074341 0.000641488536342826 0.0614813761638786 0.00401667627257402 0.743382938801471 0.00395687893333818 0.804864314965349 0.0885306662587629 0.804861736607772 0.716333648706586 0.716331070349009 0.0634106915579287 1.10303794283843 1.23639303316638 0.0925677570623027 1.23638726695289 1.14382527610408 1.14381950989059 1.57881072796814 0.0887320125722592 0.999717695034928 0.00263054987530885 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 60 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose"
|
||||
60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards sigmoid" 2.97864249972838 0.0440943285573364 6.55409027777778 0.114576828102917 0.000592514268492699 0.0574375614416587 0.0038875686917152 0.760494448227834 0.00382450823238821 0.817932009669493 0.0846335570605372 0.817926981908608 0.733298452608956 0.733293424848071 0.059119138718029 1.13933374880962 1.26580931746965 0.0883181871040035 1.26579792555084 1.17749113036565 1.17747973844683 1.48473851369249 0.0802727796034772 0.999751240782926 0.00242858216652038 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 61 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose"
|
||||
61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards sigmoid" 2.92985461453388 0.0457749726886301 6.57792333333333 0.113561152688866 0.000574978160263558 0.060472124586291 0.00402516587449496 0.782067831893148 0.00395231319695858 0.842539956479439 0.0880742344239483 0.842528715447582 0.754465722055491 0.754454481023634 0.0623379840467781 1.18598785054918 1.32225792630317 0.0920691881463056 1.32223182187456 1.23018873815686 1.23016263372825 1.37581261909432 0.0764095517760612 0.999754748600533 0.00252958095458289 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 62 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose"
|
||||
62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards sigmoid" 3.04342230131477 0.0449382687527419 6.81625388888889 0.111344220886614 0.00053211483862603 0.0556626629934722 0.00387136841849492 0.807214512297039 0.00378851478092936 0.862877175290511 0.0817091172313295 0.862843943373837 0.781168058059181 0.781134826142507 0.0572409770684312 1.24165517922426 1.36996971193357 0.0851401153555837 1.36989095460621 1.28482959657798 1.28475083925063 1.25155544499941 0.0687282596513218 0.999773222693453 0.00254586287935126 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 63 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose"
|
||||
63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards sigmoid" 3.40984196234943 0.0273360225985238 7.17374972222222 0.104909950247054 0.000320509638786788 0.0670946887710371 0.00214797629965173 0.835221165477497 0.00207744941670489 0.902315854248534 0.0807525020643599 0.901946971348112 0.821563352184174 0.821194469283752 0.0693967332430874 1.30532384995973 1.46530579421431 0.0841025502173454 1.46439655277464 1.38120324399697 1.38029400255729 0.753286731439822 0.0336141517371988 0.999897955876558 0.00130605700907156 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 64 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose"
|
||||
64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards sigmoid" 2.43102440775711 0.0454605985590097 5.50543583333333 0.126842367574397 0.000788090696060512 0.0539690230506907 0.00446798137137374 0.690558562368951 0.00442509749533481 0.744527585419641 0.0857310638249255 0.74452755483612 0.658796521594716 0.658796491011195 0.0554519069684636 0.994829458783827 1.10544655635026 0.0895132793671187 1.10544649195829 1.01593327698314 1.01593321259117 1.86325174039779 0.111013983680208 0.999682108231503 0.00226178478453787 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 67 "Control strain plate" "Sample" "Internal source" "" "AFEX"
|
||||
67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards sigmoid" 2.48092971341753 0.0462358408909463 5.62460111111111 0.126022327995321 0.000766265198216623 0.0498912361992905 0.00451231731412719 0.714630509305857 0.00446315308100269 0.764521745505147 0.0803254380277494 0.764521612664574 0.684196307477398 0.684196174636825 0.0511567623538203 1.04343151382482 1.14796685416386 0.0836396678533904 1.14796656882673 1.06432718631047 1.06432690097334 1.6892416239556 0.102428344960951 0.999685472160361 0.00245503448373934 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 68 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.25% glucose"
|
||||
68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards sigmoid" 2.42408640744135 0.0532786618803828 5.62460111111111 0.124384376977411 0.000823105161949976 0.0492950122622815 0.00516311815303983 0.727641420856731 0.00510226521814267 0.776936433119012 0.0803276492472531 0.776936116027565 0.696608783871759 0.696608466780311 0.0505302243276007 1.07019213302561 1.17479940590863 0.0836420640212081 1.17479871629844 1.09115734188742 1.09115665227723 1.58714593821028 0.108898701673299 0.999619231516236 0.00307919508939737 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 69 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.5% glucose"
|
||||
69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards sigmoid" 2.3516083906569 0.0596596631244507 5.69610027777778 0.122918277329311 0.000825310524938601 0.0456238028839663 0.00577234400145717 0.757677923259936 0.00569718881396185 0.803301726143903 0.0794802281473059 0.803300765454603 0.723821497996597 0.723820537307297 0.0466805786671931 1.1333167393977 1.23290119927319 0.0827241518553661 1.23289905414994 1.15017704741783 1.15017490229457 1.50943196721409 0.109906089971898 0.999597425228284 0.00351671862436235 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 70 "Control strain plate" "Sample" "Internal source" "" "AFEX+1% glucose"
|
||||
70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards sigmoid" 2.5236010165651 0.0587446480551128 5.93443083333333 0.120073445181908 0.000783304897530514 0.0450247442396835 0.00549978744950499 0.786911440589629 0.00540921373997301 0.831936184829312 0.0732958505454819 0.831929765474958 0.75864033428383 0.758633914929476 0.0460537433930304 1.19660160399639 1.29776333060356 0.0760488394635108 1.29774858049386 1.22171449114005 1.22169974103035 1.2397630247936 0.0944772278955165 0.999601760903923 0.00394547420222901 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 71 "Control strain plate" "Sample" "Internal source" "" "AFEX+2% glucose"
|
||||
71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards sigmoid" 2.58690524730753 0.0503605394422555 6.17276138888889 0.109989495010269 0.000552298616707589 0.0475039668950725 0.00430649396880978 0.83068144919568 0.00419058755640174 0.878185416090752 0.0684271066193943 0.878046704871374 0.809758309471358 0.80961959825198 0.0486503609989841 1.2948820530738 1.40652889340594 0.0708225662291506 1.40619510399936 1.33570632717678 1.33537253777021 0.776030021315298 0.0590320987662605 0.999743045862095 0.00295407387389294 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 72 "Control strain plate" "Sample" "Internal source" "" "AFEX+5% glucose"
|
||||
72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards sigmoid" 2.17498330451382 0.0502798395951241 5.12410694444444 0.122218804779539 0.000784428545413071 0.0435682252869189 0.00476512105024793 0.699692212079932 0.00470444935542924 0.743260437366851 0.0678435113592805 0.743259718765618 0.67541692600757 0.675416207406337 0.0445312553256874 1.01313299408815 1.10278033345246 0.0701978215718182 1.10277882239246 1.03258251188064 1.03258100082064 1.18141837167591 0.0894530619922231 0.999633683586648 0.00265620405353138 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 75 "Control strain plate" "Sample" "ATCC" "" "AFEX"
|
||||
75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards sigmoid" 2.51277041358427 0.0385075634064252 5.50543583333333 0.124302687102611 0.000662579603795554 0.0363365047244458 0.00363658784524449 0.715682301787501 0.00358889800467861 0.752018806511947 0.0575296223014987 0.75201790943738 0.694489184210448 0.694488287135881 0.0370047447805615 1.04558191041505 1.12127814693769 0.0592166466248745 1.12127624399387 1.06206150031282 1.062059597369 1.22124196187785 0.0728117473772727 0.999746251949321 0.00205128571327075 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 76 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.25% glucose"
|
||||
76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards sigmoid" 2.53563260737677 0.0376782240880802 5.60076805555555 0.122775490964049 0.000617718940237756 0.0383224027816064 0.00352849516406259 0.723989555808605 0.00348019897003327 0.762311958590212 0.0604113492179259 0.762310653602122 0.701900609372286 0.701899304384196 0.0390661767078291 1.06264585810741 1.14322554568591 0.0622734220263796 1.14322274880392 1.08095212365953 1.08094932677754 1.22916202573701 0.0694532756349596 0.999772141364762 0.00189783824442075 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 77 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.5% glucose"
|
||||
77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "logistic sigmoid." 2.60565520411145 0.0279148207786424 5.67226722222222 0.122180167529517 0.000572646164016784 0.0367511554868138 0.00173132045208087 0.75510174924411 0.00189799830326426 0.791852904730924 0.0552120643649708 0.791846881057418 0.736640840365953 0.736634816692447 0.0374348287497246 1.12782801723342 1.20748289466742 0.0567646930486905 1.20746959755124 1.15071820161873 1.15070490450255 NA NA 0.999760229166242 0.00222986115644153 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 78 "Control strain plate" "Sample" "ATCC" "" "AFEX+1% glucose"
|
||||
78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "logistic sigmoid." 2.59552092034145 0.0233507552285751 5.7914325 0.12311239814861 0.000459924953718036 0.0376321525320693 0.00147723901592513 0.788206013379693 0.00162316638429969 0.825838165911762 0.0581595525832075 0.82582810286149 0.767678613328555 0.767668550278282 0.0383492084922821 1.19944710612095 1.28379416176132 0.0598840894646306 1.2837711799415 1.22391007229669 1.22388709047687 NA NA 0.999844012469462 0.00158372380662876 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 79 "Control strain plate" "Sample" "ATCC" "" "AFEX+2% glucose"
|
||||
79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards sigmoid" 2.65619332146438 0.0304232772610151 6.00593 0.113927548226674 0.000394015356154558 0.0448535113624544 0.00262903429411648 0.830698452896991 0.00255902360970839 0.875551964259445 0.0596126030160059 0.875406838654098 0.815939361243439 0.815794235638092 0.0458746399354508 1.29492107489454 1.4001997528856 0.0614252739377605 1.39985144771812 1.33877447894784 1.33842617378036 0.630436857242866 0.0359660377290858 0.999878122228538 0.0014247167012055 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 80 "Control strain plate" "Sample" "ATCC" "" "AFEX+5% glucose"
|
||||
80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "richards sigmoid" 14.4916170457847 0.0217082069318843 18.6612825 0.0889624209370597 0.000433181631551599 0.00193467418446847 0.000448535101404725 0.976169168246482 0.0129778271847923 0.97810384243095 0.00193467418448112 0.752023542360525 0.976169168246469 0.750088868176044 0.00193654687405509 1.65426868422052 1.65940879994385 0.00193654687406775 1.12128819301358 1.65747225306978 1.11935164613951 0.07 0.0304918969768742 0.999799864971328 0.00156360720906969 "E*" "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" "<NA>: skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" "None"
|
||||
|
||||
# Raw OD values are adjusted and log-transformed before fitting a growth curve as follows: log.OD = log(OD - blank + const) where blank is OD of blank medium and const is specified by the user (1 by default)
|
||||
# Values are reported on the above 'log.OD' scale unless otherwise specified.
|
||||
# .SE columns report standard errors of those values that are estimated directly as parameters of global sigmoid models.
|
||||
# .OD columns report values back-transformed to the linear 'OD - blank' scale.
|
||||
|
||||
# -- Explanation of columns --
|
||||
# - model: Name of the model the well was successfully fit with (if any)
|
||||
# - lag.time: Lag time estimate inferred from the fitted model
|
||||
# - inflection.time: inflection time point of the growth curve when drawn on the log scale
|
||||
# - max.spec.growth.rate: maximum specific growth rate estimate inferred from the fitted model. Estimated as the first derivative of the growth curve at inflection time point
|
||||
# - baseline: growth curve baseline. Global sigmoid model: baseline is parameter 'b' of the model. LOESS: baseline is the same as the lowest predicted log.OD value
|
||||
# - amplitude: difference between upper plateau and baseline values. Global sigmoid model: amplitude is parameter 'A' of the model. LOESS: amplitude = max.log.OD - min.log.OD
|
||||
# - plateau: upper asymptote value of the fitted model. Global sigmoid model: plateau = b + A. LOESS: plateau = max.log.OD
|
||||
# - inoc.log.OD: log.OD value at inoculation. Estimated value from the fitted model is used, rather than the actual measurement
|
||||
# - max.log.OD: maximal log.OD value reached during the experiment. Estimated value from the fitted model is used rather than the actual measurement
|
||||
# - projected.growth: maximal projected growth over inoculation value. Global sigmoid model: projected.growth = plateau - inoc.log.OD. LOESS: not reported
|
||||
# - achieved.growth: maximal growth over inoculation value actually achieved during the experiment. achieved.growth = max.log.OD - inoc.log.OD
|
||||
# - shape.par: shape parameter of the Richard equation
|
||||
# - R.squared: goodness of fit metric. Also known as coefficient of determination. R.squared is usually between 0 and 1. A value close to 1 indicates good fit.
|
||||
# - RSS: residual sum of squares. Another goodness of fit metric. Smaller values indicate better fits.
|
||||
# - empty: (Well indicator)
|
||||
# - an 'E' indicates that the well was empty and no growth was detected.
|
||||
# - an 'I' indicates that the well was inoculated and growth was detected above the threshold.
|
||||
# - an 'E*' indicates that the well was empty and growth was detected (possible contamination).
|
||||
# - an '!' indicates that the well was inoculated and no growth was detected.
|
||||
# - asymp.not.reached: shows “L” if the bottom asymptote (baseline) was not reached and “U” if the upper asymptote (plateau) was not reached.
|
||||
# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index.
|
||||
# - other: Additional flag column. Displays information about whether jumps in OD were detected and what was done about them.
|
||||
# - pdf.file and page.no: location of the figure for this well in the output .pdf files.
|
||||
#
|
||||
# -- Source file information--
|
||||
# YPDAFEXglucoseTests_2-25-10.csv
|
||||
# analyzed using GCAT v 5.0
|
||||
# request sent: 2015-04-07 15:34:27
|
||||
# completed: 2015-04-07 15:34:33
|
||||
#
|
||||
# -- Parameters used in current analysis --
|
||||
# - Constant added to log(OD + n) transformation: 1
|
||||
# - Blank OD value: First timepoint in well
|
||||
# - Index of inoculation timepoint 2
|
||||
# - Minimum growth threshold: 0.05
|
||||
# - Removed points:
|
||||
# - Jump detection: FALSE
|
||||
BIN
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because one or more lines are too long
@@ -1,97 +0,0 @@
|
||||
Destination plate name,Row,Column,Well ID,Plate source,Well Source,Strain,Media Definition
|
||||
Control strain plate,A,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,2,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,3,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,4,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,5,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,6,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,7,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,8,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,9,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,10,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,A,12,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,B,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,B,2,Sample,USDA,,Lab strain,YP
|
||||
Control strain plate,B,3,Sample,USDA,,Wild strain,YP
|
||||
Control strain plate,B,4,Sample,Internal source,,Industrial strain,YP
|
||||
Control strain plate,B,5,Sample,ATCC,,Engineered strain,YP
|
||||
Control strain plate,B,6,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,B,7,Sample,USDA,,Lab strain,AFEX
|
||||
Control strain plate,B,8,Sample,USDA,,Wild strain,AFEX
|
||||
Control strain plate,B,9,Sample,Internal source,,Industrial strain,AFEX
|
||||
Control strain plate,B,10,Sample,ATCC,,Engineered strain,AFEX
|
||||
Control strain plate,B,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,B,12,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,C,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,C,2,Sample,USDA,,Lab strain,YP+0.25% glucose
|
||||
Control strain plate,C,3,Sample,USDA,,Wild strain,YP+0.25% glucose
|
||||
Control strain plate,C,4,Sample,Internal source,,Industrial strain,YP+0.25% glucose
|
||||
Control strain plate,C,5,Sample,ATCC,,Engineered strain,YP+0.25% glucose
|
||||
Control strain plate,C,6,Empty,Empty,Empty,Empty,Empty
|
||||
Control strain plate,C,7,Sample,USDA,,Lab strain,AFEX+0.25% glucose
|
||||
Control strain plate,C,8,Sample,USDA,,Wild strain,AFEX+0.25% glucose
|
||||
Control strain plate,C,9,Sample,Internal source,,Industrial strain,AFEX+0.25% glucose
|
||||
Control strain plate,C,10,Sample,ATCC,,Engineered strain,AFEX+0.25% glucose
|
||||
Control strain plate,C,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,C,12,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,D,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,D,2,Sample,USDA,,Lab strain,YP+0.5% glucose
|
||||
Control strain plate,D,3,Sample,USDA,,Wild strain,YP+0.5% glucose
|
||||
Control strain plate,D,4,Sample,Internal source,,Industrial strain,YP+0.5% glucose
|
||||
Control strain plate,D,5,Sample,ATCC,,Engineered strain,YP+0.5% glucose
|
||||
Control strain plate,D,6,Empty,Empty,Empty,Empty,Empty
|
||||
Control strain plate,D,7,Sample,USDA,,Lab strain,AFEX+0.5% glucose
|
||||
Control strain plate,D,8,Sample,USDA,,Wild strain,AFEX+0.5% glucose
|
||||
Control strain plate,D,9,Sample,Internal source,,Industrial strain,AFEX+0.5% glucose
|
||||
Control strain plate,D,10,Sample,ATCC,,Engineered strain,AFEX+0.5% glucose
|
||||
Control strain plate,D,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,D,12,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,E,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,E,2,Sample,USDA,,Lab strain,YP+1% glucose
|
||||
Control strain plate,E,3,Sample,USDA,,Wild strain,YP+1% glucose
|
||||
Control strain plate,E,4,Sample,Internal source,,Industrial strain,YP+1% glucose
|
||||
Control strain plate,E,5,Sample,ATCC,,Engineered strain,YP+1% glucose
|
||||
Control strain plate,E,6,Empty,Empty,Empty,Empty,Empty
|
||||
Control strain plate,E,7,Sample,USDA,,Lab strain,AFEX+1% glucose
|
||||
Control strain plate,E,8,Sample,USDA,,Wild strain,AFEX+1% glucose
|
||||
Control strain plate,E,9,Sample,Internal source,,Industrial strain,AFEX+1% glucose
|
||||
Control strain plate,E,10,Sample,ATCC,,Engineered strain,AFEX+1% glucose
|
||||
Control strain plate,E,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,E,12,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,F,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,F,2,Sample,USDA,,Lab strain,YP+2% glucose
|
||||
Control strain plate,F,3,Sample,USDA,,Wild strain,YP+2% glucose
|
||||
Control strain plate,F,4,Sample,Internal source,,Industrial strain,YP+2% glucose
|
||||
Control strain plate,F,5,Sample,ATCC,,Engineered strain,YP+2% glucose
|
||||
Control strain plate,F,6,Empty,Empty,Empty,Empty,Empty
|
||||
Control strain plate,F,7,Sample,USDA,,Lab strain,AFEX+2% glucose
|
||||
Control strain plate,F,8,Sample,USDA,,Wild strain,AFEX+2% glucose
|
||||
Control strain plate,F,9,Sample,Internal source,,Industrial strain,AFEX+2% glucose
|
||||
Control strain plate,F,10,Sample,ATCC,,Engineered strain,AFEX+2% glucose
|
||||
Control strain plate,F,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,F,12,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,G,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,G,2,Sample,USDA,,Lab strain,YP+5% glucose
|
||||
Control strain plate,G,3,Sample,USDA,,Wild strain,YP+5% glucose
|
||||
Control strain plate,G,4,Sample,Internal source,,Industrial strain,YP+5% glucose
|
||||
Control strain plate,G,5,Sample,ATCC,,Engineered strain,YP+5% glucose
|
||||
Control strain plate,G,6,Empty,Empty,Empty,Empty,Empty
|
||||
Control strain plate,G,7,Sample,USDA,,Lab strain,AFEX+5% glucose
|
||||
Control strain plate,G,8,Sample,USDA,,Wild strain,AFEX+5% glucose
|
||||
Control strain plate,G,9,Sample,Internal source,,Industrial strain,AFEX+5% glucose
|
||||
Control strain plate,G,10,Sample,ATCC,,Engineered strain,AFEX+5% glucose
|
||||
Control strain plate,G,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,G,12,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,1,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,2,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,3,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,4,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,5,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,6,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,7,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,8,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,9,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,10,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,11,Empty,Empty,Empty,Empty,None
|
||||
Control strain plate,H,12,Empty,Empty,Empty,Empty,None
|
||||
|
Reference in New Issue
Block a user