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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<HTML>
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<HEAD>
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<META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=windows-1252">
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<TITLE></TITLE>
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<META NAME="AUTHOR" CONTENT="Christopher Lausted, Yuwan Wan">
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</HEAD>
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<BODY LANG="en-US" TEXT="#000000" LINK="#0000ff" DIR="LTR">
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<FONT FACE="Courier New, monospace">converter.py</FONT>
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<H2>Name</H2>
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Converter - Convert the data exported from SPRit, Plexera ICM and Plexera DAM to Clamp and Biosensor format.
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<H2>Details</H2>
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<H3>Requirements</H3>
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Python 2.4+ and the following
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modules: sys, time, os, numpy, matplotlib, xlrd
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<H3>Suggested</H3>
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Ipython, PythonXY (Windows only)
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<H3>License </H3>
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GNU General Public License Version 2
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<H2>For Plexera DAM:</H2>
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<H3>Input files</H3>
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<UL>
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<LI>Spreadsheet exported from DAM software (required)
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<LI>GAL file (optional)
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<LI>Protocol file generated by ICM software (optional)
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</UL>
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<H3>GAL file format</H3>
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<UL>
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<LI>There are eight columns for the gal file.
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<LI>The first three columns identify the position, and (Block, Row, Column) is the unique identity for each ROI.
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<LI>The fourth column (“Name”) is the name of the immobilized protein.
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<LI>The fifth column (“ID”) is the spot number, which is calculated from the first three column, by the formula (Block-1)*blocksize + (Row-1)*rowsize + Column
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<LI>The sixth column (“Set”) indicates the concentration of the immobilized protein.
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<LI>The seventh column (“Family”) is not used by Converter.
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<LI>The eighth column “Group” is filled with the background id for each ROI, in the form of “(Block, Row, Column)”.
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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.
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</UL>
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<BR>
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An example is given below.
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<BR>
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<TABLE WIDTH=591 BORDER=1 BORDERCOLOR="#000000" CELLPADDING=7 CELLSPACING=0>
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<COL WIDTH=40>
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<COL WIDTH=33>
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<COL WIDTH=48>
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<COL WIDTH=54>
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<COL WIDTH=56>
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<COL WIDTH=64>
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<COL WIDTH=57>
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<COL WIDTH=124>
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<TR VALIGN=TOP>
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<TD WIDTH=40> Block </TD>
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<TD WIDTH=33> Row </TD>
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<TD WIDTH=48>Column</TD>
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<TD WIDTH=54>Name</TD>
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<TD WIDTH=56>ID</TD>
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<TD WIDTH=64>Set/Conc</TD>
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<TD WIDTH=57>Family</TD>
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<TD WIDTH=124>Group/Backgroud</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=40>1</TD>
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<TD WIDTH=33>1</TD>
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<TD WIDTH=48>1</TD>
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<TD WIDTH=54>TBA3-2</TD>
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<TD WIDTH=56>Spot1</TD>
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<TD WIDTH=64>100nM</TD>
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<TD WIDTH=57>0</TD>
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<TD WIDTH=124>"1,1,1; 1,1,2"</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=40>1</TD>
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<TD WIDTH=33>1</TD>
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<TD WIDTH=48>2</TD>
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<TD WIDTH=54>Mix2-4</TD>
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<TD WIDTH=56>Spot2</TD>
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<TD WIDTH=64>100nM</TD>
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<TD WIDTH=57>0</TD>
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<TD WIDTH=124>"1,1,2; 1,1,3"</TD>
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</TR>
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</TABLE>
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<BR>
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<H3>Protocol file format</H3>
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The
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protocol file is the same as the analyte table generated by ICM
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software. An example is given below.
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<BR>
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<TABLE WIDTH=591 BORDER=1 BORDERCOLOR="#000000" CELLPADDING=7 CELLSPACING=0>
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<COL WIDTH=43>
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<COL WIDTH=66>
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<COL WIDTH=72>
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<COL WIDTH=44>
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<COL WIDTH=61>
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<COL WIDTH=66>
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<COL WIDTH=39>
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<COL WIDTH=33>
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<COL WIDTH=38>
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<TR VALIGN=TOP>
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<TD WIDTH=43 HEIGHT=2>Location</TD>
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<TD WIDTH=66>Name</TD>
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<TD WIDTH=72>Concentration (mol/L)</TD>
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<TD WIDTH=44>Flow Rate (ul/sec)</TD>
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<TD WIDTH=61>Association Duration (sec)</TD>
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<TD WIDTH=66>Dissociation Duration (sec)
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</TD>
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<TD WIDTH=39>Analyte Series</TD>
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<TD WIDTH=33>Buffer Blank Series</TD>
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<TD WIDTH=38>Working Volume (uL)</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=43 HEIGHT=3>A1</TD>
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<TD WIDTH=66>Calibration1</TD>
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<TD WIDTH=72>1.00E-06</TD>
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<TD WIDTH=44>5</TD>
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<TD WIDTH=61>60</TD>
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<TD WIDTH=66>60</TD>
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<TD WIDTH=39>1</TD>
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<TD WIDTH=33>1</TD>
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<TD WIDTH=38>310</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=43 HEIGHT=3>A2</TD>
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<TD WIDTH=66>Calibration2</TD>
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<TD WIDTH=72>2.00E-06</TD>
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<TD WIDTH=44>5</TD>
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<TD WIDTH=61>60</TD>
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<TD WIDTH=66>60</TD>
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<TD WIDTH=39>1</TD>
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<TD WIDTH=33>1</TD>
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<TD WIDTH=38>310</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=43 HEIGHT=3>A3</TD>
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<TD WIDTH=66>Sample 1</TD>
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<TD WIDTH=72>5.00E-10</TD>
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<TD WIDTH=44>5</TD>
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<TD WIDTH=61>60</TD>
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<TD WIDTH=66>60</TD>
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<TD WIDTH=39>1</TD>
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<TD WIDTH=33>1</TD>
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<TD WIDTH=38>310</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=43 HEIGHT=2>A4</TD>
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<TD WIDTH=66>Sample 2</TD>
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<TD WIDTH=72>2.50E-09</TD>
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<TD WIDTH=44>5</TD>
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<TD WIDTH=61>60</TD>
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<TD WIDTH=66>60</TD>
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<TD WIDTH=39>1</TD>
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<TD WIDTH=33>1</TD>
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<TD WIDTH=38>310</TD>
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</TR>
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</TABLE>
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<BR>
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<H2>For Plexera ICM/ SPRit:</H2>
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<H3>Input files</H3>
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<UL>
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<LI>Tab-delimited text file exported from ICM or SPRit software (required)
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<LI>Tab-delimited Key file (required)
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<LI>Protocol file generated by ICM software (optional)
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</UL>
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<H3>Key file format</H3>
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<UL>
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<LI>Four columns are required in the key file.
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<LI>The first column (“ID”) is the unique identity for each ROI.
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<LI>The second column (“Name”) is the name of the immobilized protein.
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<LI>The third column (“Concentration”) is the concentration of the immobilized protein.
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<LI>The fourth column (“Background”) is the background spot idfor each ROI.
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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.
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<LI>More columns are optional, but are not read by the converter.
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</UL>
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<BR>
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An example is given below.
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<TABLE WIDTH=507 BORDER=1 BORDERCOLOR="#000000" CELLPADDING=7 CELLSPACING=0>
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<COL WIDTH=23>
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<COL WIDTH=75>
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<COL WIDTH=106>
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<COL WIDTH=102>
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<COL WIDTH=46>
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<COL WIDTH=70>
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<TR VALIGN=TOP>
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<TD WIDTH=23>ID</TD>
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<TD WIDTH=75>Name</TD>
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<TD WIDTH=106>Concentration</TD>
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<TD WIDTH=102>Background</TD>
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<TD WIDTH=46>Col</TD>
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<TD WIDTH=70>Row</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=23>1</TD>
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<TD WIDTH=75>TBA2-1</TD>
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<TD WIDTH=106>1uM</TD>
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<TD WIDTH=102>10</TD>
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<TD WIDTH=46>1</TD>
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<TD WIDTH=70>1</TD>
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</TR>
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<TR VALIGN=TOP>
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<TD WIDTH=23>2</TD>
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<TD WIDTH=75>TBA3-1</TD>
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<TD WIDTH=106>1uM</TD>
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<TD WIDTH=102>10; 11</TD>
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<TD WIDTH=46>2</TD>
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<TD WIDTH=70>1</TD>
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</TR>
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</TABLE>
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<BR>
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<H3><B>Protocol file format</B></H3>
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The
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protocol file follows the same instructions as that for Plexera DAM.
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<BR>
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<H2>Output</H2>
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The
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output of the converter/SPRfilereader is a python object that
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contains the data, ROI information, and sample information.
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</BODY>
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</HTML> |
