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Committed: Tue Apr 6 05:35:46 2010 UTC (9 years, 7 months ago) by clausted
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Initial check-in of the html manual for converter.py.
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1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
2 <HTML>
3 <HEAD>
4 <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=windows-1252">
5 <TITLE></TITLE>
6 <META NAME="AUTHOR" CONTENT="Christopher Lausted, Yuwan Wan">
7 </HEAD>
8
9 <BODY LANG="en-US" TEXT="#000000" LINK="#0000ff" DIR="LTR">
10 <FONT FACE="Courier New, monospace">converter.py</FONT>
11
12 <H2>Name</H2>
13 Converter - Convert the data exported from SPRit, Plexera ICM and Plexera DAM to Clamp and Biosensor format.
14
15 <H2>Details</H2>
16 <H3>Requirements</H3>
17 Python 2.4+ and the following
18 modules: sys, time, os, numpy, matplotlib, xlrd
19 <H3>Suggested</H3>
20 Ipython, PythonXY (Windows only)
21 <H3>License </H3>
22 GNU General Public License Version 2
23
24 <H2>For Plexera DAM:</H2>
25 <H3>Input files</H3>
26 <UL>
27 <LI>Spreadsheet exported from DAM software (required)
28 <LI>GAL file (optional)
29 <LI>Protocol file generated by ICM software (optional)
30 </UL>
31
32 <H3>GAL file format</H3>
33 <UL>
34 <LI>There are eight columns for the gal file.
35 <LI>The first three columns identify the position, and (Block, Row, Column) is the unique identity for each ROI.
36 <LI>The fourth column (&ldquo;Name&rdquo;) is the name of the immobilized protein.
37 <LI>The fifth column (&ldquo;ID&rdquo;) is the spot number, which is calculated from the first three column, by the formula (Block-1)*blocksize + (Row-1)*rowsize + Column
38 <LI>The sixth column (&ldquo;Set&rdquo;) indicates the concentration of the immobilized protein.
39 <LI>The seventh column (&ldquo;Family&rdquo;) is not used by Converter.
40 <LI>The eighth column &ldquo;Group&rdquo; is filled with the background id for each ROI, in the form of &ldquo;(Block, Row, Column)&rdquo;.
41 If a ROI has more than one background spots, separate those spots with <B>semicolon plus space</B>, and the average can be taken as the background.
42 </UL>
43 <BR>
44
45 An example is given below.
46 <BR>
47
48 <TABLE WIDTH=591 BORDER=1 BORDERCOLOR="#000000" CELLPADDING=7 CELLSPACING=0>
49 <COL WIDTH=40>
50 <COL WIDTH=33>
51 <COL WIDTH=48>
52 <COL WIDTH=54>
53 <COL WIDTH=56>
54 <COL WIDTH=64>
55 <COL WIDTH=57>
56 <COL WIDTH=124>
57 <TR VALIGN=TOP>
58 <TD WIDTH=40> Block </TD>
59 <TD WIDTH=33> Row </TD>
60 <TD WIDTH=48>Column</TD>
61 <TD WIDTH=54>Name</TD>
62 <TD WIDTH=56>ID</TD>
63 <TD WIDTH=64>Set/Conc</TD>
64 <TD WIDTH=57>Family</TD>
65 <TD WIDTH=124>Group/Backgroud</TD>
66 </TR>
67 <TR VALIGN=TOP>
68 <TD WIDTH=40>1</TD>
69 <TD WIDTH=33>1</TD>
70 <TD WIDTH=48>1</TD>
71 <TD WIDTH=54>TBA3-2</TD>
72 <TD WIDTH=56>Spot1</TD>
73 <TD WIDTH=64>100nM</TD>
74 <TD WIDTH=57>0</TD>
75 <TD WIDTH=124>&quot;1,1,1; 1,1,2&quot;</TD>
76 </TR>
77 <TR VALIGN=TOP>
78 <TD WIDTH=40>1</TD>
79 <TD WIDTH=33>1</TD>
80 <TD WIDTH=48>2</TD>
81 <TD WIDTH=54>Mix2-4</TD>
82 <TD WIDTH=56>Spot2</TD>
83 <TD WIDTH=64>100nM</TD>
84 <TD WIDTH=57>0</TD>
85 <TD WIDTH=124>&quot;1,1,2; 1,1,3&quot;</TD>
86 </TR>
87 </TABLE>
88 <BR>
89
90 <H3>Protocol file format</H3>
91 The
92 protocol file is the same as the analyte table generated by ICM
93 software. An example is given below.
94 <BR>
95
96 <TABLE WIDTH=591 BORDER=1 BORDERCOLOR="#000000" CELLPADDING=7 CELLSPACING=0>
97 <COL WIDTH=43>
98 <COL WIDTH=66>
99 <COL WIDTH=72>
100 <COL WIDTH=44>
101 <COL WIDTH=61>
102 <COL WIDTH=66>
103 <COL WIDTH=39>
104 <COL WIDTH=33>
105 <COL WIDTH=38>
106 <TR VALIGN=TOP>
107 <TD WIDTH=43 HEIGHT=2>Location</TD>
108 <TD WIDTH=66>Name</TD>
109 <TD WIDTH=72>Concentration (mol/L)</TD>
110 <TD WIDTH=44>Flow Rate (ul/sec)</TD>
111 <TD WIDTH=61>Association Duration (sec)</TD>
112 <TD WIDTH=66>Dissociation Duration (sec)
113 </TD>
114 <TD WIDTH=39>Analyte Series</TD>
115 <TD WIDTH=33>Buffer Blank Series</TD>
116 <TD WIDTH=38>Working Volume (uL)</TD>
117 </TR>
118 <TR VALIGN=TOP>
119 <TD WIDTH=43 HEIGHT=3>A1</TD>
120 <TD WIDTH=66>Calibration1</TD>
121 <TD WIDTH=72>1.00E-06</TD>
122 <TD WIDTH=44>5</TD>
123 <TD WIDTH=61>60</TD>
124 <TD WIDTH=66>60</TD>
125 <TD WIDTH=39>1</TD>
126 <TD WIDTH=33>1</TD>
127 <TD WIDTH=38>310</TD>
128 </TR>
129 <TR VALIGN=TOP>
130 <TD WIDTH=43 HEIGHT=3>A2</TD>
131 <TD WIDTH=66>Calibration2</TD>
132 <TD WIDTH=72>2.00E-06</TD>
133 <TD WIDTH=44>5</TD>
134 <TD WIDTH=61>60</TD>
135 <TD WIDTH=66>60</TD>
136 <TD WIDTH=39>1</TD>
137 <TD WIDTH=33>1</TD>
138 <TD WIDTH=38>310</TD>
139 </TR>
140 <TR VALIGN=TOP>
141 <TD WIDTH=43 HEIGHT=3>A3</TD>
142 <TD WIDTH=66>Sample 1</TD>
143 <TD WIDTH=72>5.00E-10</TD>
144 <TD WIDTH=44>5</TD>
145 <TD WIDTH=61>60</TD>
146 <TD WIDTH=66>60</TD>
147 <TD WIDTH=39>1</TD>
148 <TD WIDTH=33>1</TD>
149 <TD WIDTH=38>310</TD>
150 </TR>
151 <TR VALIGN=TOP>
152 <TD WIDTH=43 HEIGHT=2>A4</TD>
153 <TD WIDTH=66>Sample 2</TD>
154 <TD WIDTH=72>2.50E-09</TD>
155 <TD WIDTH=44>5</TD>
156 <TD WIDTH=61>60</TD>
157 <TD WIDTH=66>60</TD>
158 <TD WIDTH=39>1</TD>
159 <TD WIDTH=33>1</TD>
160 <TD WIDTH=38>310</TD>
161 </TR>
162 </TABLE>
163 <BR>
164
165 <H2>For Plexera ICM/ SPRit:</H2>
166 <H3>Input files</H3>
167 <UL>
168 <LI>Tab-delimited text file exported from ICM or SPRit software (required)
169 <LI>Tab-delimited Key file (required)
170 <LI>Protocol file generated by ICM software (optional)
171 </UL>
172 <H3>Key file format</H3>
173 <UL>
174 <LI>Four columns are required in the key file.
175 <LI>The first column (&ldquo;ID&rdquo;) is the unique identity for each ROI.
176 <LI>The second column (&ldquo;Name&rdquo;) is the name of the immobilized protein.
177 <LI>The third column (&ldquo;Concentration&rdquo;) is the concentration of the immobilized protein.
178 <LI>The fourth column (&ldquo;Background&rdquo;) is the background spot idfor each ROI.
179 If a ROI has more than one background spots, separate those spots with <B>semicolon plus space</B>, and the average can be taken as the background.
180 <LI>More columns are optional, but are not read by the converter.
181 </UL>
182 <BR>
183
184 An example is given below.
185 <TABLE WIDTH=507 BORDER=1 BORDERCOLOR="#000000" CELLPADDING=7 CELLSPACING=0>
186 <COL WIDTH=23>
187 <COL WIDTH=75>
188 <COL WIDTH=106>
189 <COL WIDTH=102>
190 <COL WIDTH=46>
191 <COL WIDTH=70>
192 <TR VALIGN=TOP>
193 <TD WIDTH=23>ID</TD>
194 <TD WIDTH=75>Name</TD>
195 <TD WIDTH=106>Concentration</TD>
196 <TD WIDTH=102>Background</TD>
197 <TD WIDTH=46>Col</TD>
198 <TD WIDTH=70>Row</TD>
199 </TR>
200 <TR VALIGN=TOP>
201 <TD WIDTH=23>1</TD>
202 <TD WIDTH=75>TBA2-1</TD>
203 <TD WIDTH=106>1uM</TD>
204 <TD WIDTH=102>10</TD>
205 <TD WIDTH=46>1</TD>
206 <TD WIDTH=70>1</TD>
207 </TR>
208 <TR VALIGN=TOP>
209 <TD WIDTH=23>2</TD>
210 <TD WIDTH=75>TBA3-1</TD>
211 <TD WIDTH=106>1uM</TD>
212 <TD WIDTH=102>10; 11</TD>
213 <TD WIDTH=46>2</TD>
214 <TD WIDTH=70>1</TD>
215 </TR>
216 </TABLE>
217 <BR>
218
219 <H3><B>Protocol file format</B></H3>
220 The
221 protocol file follows the same instructions as that for Plexera DAM.
222 <BR>
223
224 <H2>Output</H2>
225 The
226 output of the converter/SPRfilereader is a python object that
227 contains the data, ROI information, and sample information.
228 </BODY>
229 </HTML>

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