1 | <%@ page import="net.sf.basedb.core.*"%> |
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2 | <%@ page import="net.sf.basedb.clients.web.*"%> |
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3 | <%@ page import="net.sf.basedb.util.*"%> |
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4 | <%@ page import="java.util.*"%> |
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5 | |
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6 | <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" /> |
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7 | <!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name --> |
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8 | <jsp:setProperty name="inputDataBean" property="*" /> |
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9 | |
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10 | <% |
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11 | final SessionControl sc = Base.getExistingSessionControl(pageContext, true); |
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12 | final String ID = sc.getId(); |
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13 | final String requestID = request.getParameter("requestId"); |
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14 | %> |
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15 | |
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16 | |
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17 | <html> |
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18 | |
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19 | <head> |
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20 | |
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21 | <link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" /> |
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22 | <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css"> |
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23 | <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css"> |
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24 | |
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25 | <script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script> |
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26 | |
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27 | <script language="JavaScript" type="text/javascript"> |
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28 | //submits form |
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29 | function submit() |
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30 | { |
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31 | document.hybridizations.submit(); |
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32 | } |
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33 | function getRoot() |
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34 | { |
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35 | return '/base/'; |
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36 | } |
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37 | function getScale() |
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38 | { |
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39 | return 1.0; |
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40 | } |
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41 | function doImport() |
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42 | { |
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43 | var frm = document.forms['hybridizations']; |
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44 | if (Main.trimString(frm.path.value) == '') |
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45 | { |
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46 | alert("You must select a file to import from"); |
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47 | frm.path.focus(); |
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48 | } |
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49 | else |
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50 | { |
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51 | frm.submit(); |
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52 | } |
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53 | } |
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54 | function browseOnClick() |
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55 | { |
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56 | var frm = document.forms['hybridizations']; |
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57 | var url = '<%= request.getContextPath()%>/filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&title=Select+file+to+import&callback=setFileCallback'; |
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58 | url += '&filter:INT:location=1'; |
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59 | Main.openPopup(url, 'SelectFile', 1000, 700); |
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60 | } |
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61 | function setFileCallback(fileId, path) |
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62 | { |
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63 | var frm = document.forms['hybridizations']; |
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64 | frm.file_id.value = fileId; |
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65 | frm.path.value = path; |
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66 | document.getElementById('zipFile').value = path; |
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67 | } |
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68 | function recentFileOnChange() |
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69 | { |
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70 | var frm = document.forms['hybridizations']; |
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71 | var selected = frm.recentFile[frm.recentFile.selectedIndex]; |
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72 | setFileCallback(selected.value, selected.text); |
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73 | frm.recentFile.selectedIndex = 0; |
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74 | } |
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75 | |
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76 | |
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77 | </script> |
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78 | |
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79 | </head> |
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80 | |
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81 | <body> |
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82 | |
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83 | |
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84 | |
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85 | |
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86 | |
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87 | <form name="hybridizations"action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/mappings.jsp" method="post"> |
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88 | <input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters"> |
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89 | <input type="hidden"name="requestID" value="<%=requestID%>"> |
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90 | |
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91 | <input type="hidden" name="file_id" value=""> |
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92 | <input type="hidden" name="zipFile" value="" id="zipFile"> |
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93 | |
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94 | <h1>Tab2MAGE Importer -- Your Hybridizations</h1> |
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95 | Page 3 of 4 |
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96 | <p> |
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97 | <!-- table with the input form --> |
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98 | <table cellpadding="15"> |
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99 | |
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100 | <!-- question 1 --> |
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101 | <tr > |
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102 | <td class="boldText">Microarray platform:</td> |
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103 | <td class="input"> |
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104 | <select name="platform"> |
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105 | <option >Affymetrix</option> |
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106 | <option >Agilent</option> |
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107 | <option >AIDA</option> |
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108 | <option >BZScan</option> |
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109 | <option >ChipSkipper</option> |
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110 | <option >GenePix</option> |
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111 | <option >GeneTAC</option> |
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112 | <option >Illumina</option> |
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113 | <option >Imagene</option> |
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114 | <option >QuantArray Biotin</option> |
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115 | <option >QuantArray Cy</option> |
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116 | <option >Spotfinder</option> |
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117 | <option ><i>Custom</i></option> |
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118 | </select></td> |
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119 | <td>The manufacturer of the microarray chip used.</td> |
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120 | </tr> |
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121 | |
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122 | <!-- question 2 --> |
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123 | <tr> |
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124 | <td class="boldText">Experimental organism:</td> |
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125 | <td class="input"><input type="text" size="50" name="organism" value="Solanum tuberosum"/></td> |
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126 | <td>The full scientific name of the experimental organism used.</td> |
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127 | </tr> |
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128 | |
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129 | <!-- question 3 --> |
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130 | <tr> |
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131 | <td class="boldText">Number of different arrays designs used:</td> |
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132 | <td class="input"><input type="text" size="3" name="numDesigns" value="1"/></td> |
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133 | <td>If more than one array design was used in parallel, please specify the number here. |
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134 | We assume that all samples are applied once to each array design</td> |
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135 | </tr> |
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136 | |
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137 | <!-- question 4 --> |
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138 | <tr> |
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139 | <td class="boldText">Dye-swap</td> |
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140 | <td class="input">yes <input type="radio" name="dyeSwap" value="yes"> no <input type="radio" |
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141 | name="parameter:dyeSwap" value="no" checked="checked"> <br> |
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142 | |
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143 | </td> |
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144 | <td>If you used a dye-swap design please indicate this here.</td> |
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145 | </tr> |
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146 | |
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147 | <!-- question 5 --> |
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148 | <tr> |
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149 | <td class="boldText">Reference sample</td> |
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150 | <td class="input">yes <input type="radio" name="refSample" value="yes" > no <input type="radio" |
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151 | name="parameter:refSample" value="no" checked="checked"></td> |
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152 | <td>If you used a reference sample please indicate this here.</td> |
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153 | </tr> |
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154 | |
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155 | <!-- question 6 --> |
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156 | <tr> |
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157 | <td class="boldText">Number of treatment groups:</td> |
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158 | <td class="input"><input type="text" size="3" name="numTreatmentGroups" value="2"/></td> |
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159 | <td>The number of permutations of factor values. <p> |
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160 | Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3). |
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161 | </td> |
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162 | </tr> |
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163 | |
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164 | <!-- question 7 --> |
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165 | <tr> |
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166 | <td class="boldText">Experimental factors: |
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167 | </td> |
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168 | <td class="input"><textarea rows="7" cols="32" name="expFactors">Strain(mutant,wildtype)</textarea></td> |
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169 | <td>Please list all experimental factors and value ranges using the following format (one per |
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170 | line):<br> |
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171 | <i>Factor 1(value1,value2,...valueN)<br></i> |
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172 | <p>Example: <i><br> |
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173 | Compound(aspirin,ibuprofen) <br> |
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174 | Dose(control,low,medium,high)</i></td> |
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175 | </tr> |
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176 | |
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177 | <!-- question 8 --> |
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178 | <tr> |
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179 | <td class="boldText">Number of subjects per group:</td> |
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180 | <td class="input"><input type="text" size="3" name="numReplicates" value="2"/></td> |
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181 | <td>This is the number of biological replicates in each treatment group.</td> |
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182 | </tr> |
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183 | |
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184 | <!-- question 9 --> |
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185 | <tr> |
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186 | <td class="boldText">Target tissues:</td> |
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187 | <td class="input"><textarea rows="2" cols="32" name="tissues">stem</textarea></td> |
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188 | <td>List all target tissues (as a comma separated list).<br> |
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189 | Example: liver,heart</td> |
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190 | </tr> |
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191 | |
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192 | <!-- question 10 --> |
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193 | <tr> |
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194 | <td class="boldText">Sample pooling:</td> |
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195 | <td class="input">yes <input type="radio" name="pooling" value="yes"> no <input type="radio" |
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196 | name="parameter:pooling" value="no" checked="checked"></td> |
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197 | <td>If the samples were pooled please indicate this here.</td> |
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198 | </tr> |
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199 | |
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200 | |
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201 | <!-- file upload --> |
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202 | <tr> |
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203 | <td class="boldText">Zip file:</td> |
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204 | |
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205 | <td class="input"> |
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206 | <table class="noBorder" border="0" cellspacing="0" cellpadding="5"> |
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207 | <tr class="noBorder" > |
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208 | |
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209 | <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td> |
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210 | |
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211 | <td style="vertical-align: middle;border-style: none;"> |
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212 | <div class="buttons" |
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213 | onmouseover="this.className='buttons_hover';" |
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214 | onmouseout="this.className='buttons';" |
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215 | onclick="browseOnClick()"> |
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216 | <div class="buttons_inner"> |
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217 | |
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218 | <table class="noBorder" cellspacing="0" cellpadding="0"> |
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219 | <tr class="noBorder"> |
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220 | <td style="border-style: none;"> <img src="/base/images/browse.png" border="0"></td> |
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221 | <td style="border-style: none;">Browse…</td> |
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222 | </tr> |
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223 | </table> |
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224 | |
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225 | </div> |
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226 | </div> |
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227 | </td> |
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228 | |
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229 | </tr> |
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230 | </table> |
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231 | </td> |
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232 | |
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233 | <td>Please select the zip file on your local disk that contains the data files for import. |
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234 | All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td> |
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235 | </tr> |
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236 | |
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237 | </table> |
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238 | |
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239 | <p> |
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240 | |
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241 | <table align="center" class="noBorder" cellspacing="5" cellpadding="5"> |
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242 | <tr class="noBorder"> |
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243 | <td id="next" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Next</td></tr></table></div></div></td> |
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244 | <td id="close" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table class="noBorder" cellspacing="0" cellpadding="0"><tr class="noBorder"><td style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td> </tr> |
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245 | </table> |
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246 | |
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247 | |
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248 | </form> |
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249 | |
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250 | </body> |
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251 | </html> |
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