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Initial check-in of the html manual for converter.py.
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1 clausted 2 <!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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