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2 X!TANDEM LICENSE AND README ===========================================
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3
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4
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5 X! tandem protein sequence modeler
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6
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7 What is it?
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8 -----------
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9 X! tandem open source software that can model tandem
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10 mass spectra with protein sequences. This software
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11 has a very simple, unsophistocated application programming
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12 interface (API): it simply takes an XML file of instructions
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13 on its command line, and output the results into an XML file,
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14 which has been specified in the input XML file.
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15
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16 The Latest Version
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17 ------------------
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18
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19 Details of the latest version can be found on the X! tandem
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20 project page under http://www.thegpm.org.
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21 This version is the first release the CYCLONE edition (version 2012.10.01.1).
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22
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23
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24 Documentation
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25 -------------
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26
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27 This version of X! tandem is a full release, only including source
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28 level documentation. As more releases occur, better documentation
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29 will be included.
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30
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31 Installation
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32 ------------
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33
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34 (IN this case installation is automatically done by Galaxy's Toolshed).
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35
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36 Licensing
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37 ---------
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38
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39 The Artistic License for all X! software, binaries and documentation
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40
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41 Preamble
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42 The intent of this document is to state the conditions under which a
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43 Package may be copied, such that the Copyright Holder maintains some
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44 semblance of artistic control over the development of the package,
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45 while giving the users of the package the right to use and distribute
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46 the Package in a more-or-less customary fashion, plus the right to
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47 make reasonable modifications.
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48
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49 Definitions
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50 "Package" refers to the collection of files distributed by the Copyright
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51 Holder, and derivatives of that collection of files created through
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52 textual modification.
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53
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54 "Standard Version" refers to such a Package if it has not been modified,
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55 or has been modified in accordance with the wishes of the Copyright
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56 Holder as specified below.
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57
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58 "Copyright Holder" is whoever is named in the copyright or copyrights
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59 for the package.
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60
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61 "You" is you, if you're thinking about copying or distributing this Package.
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62
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63 "Reasonable copying fee" is whatever you can justify on the basis of
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64 media cost, duplication charges, time of people involved, and so on.
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65 (You will not be required to justify it to the Copyright Holder, but
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66 only to the computing community at large as a market that must bear
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67 the fee.)
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68
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69 "Freely Available" means that no fee is charged for the item itself,
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70 though there may be fees involved in handling the item. It also means
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71 that recipients of the item may redistribute it under the same
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72 conditions they received it.
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73
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74 1. You may make and give away verbatim copies of the source form of the
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75 Standard Version of this Package without restriction, provided that
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76 you duplicate all of the original copyright notices and associated
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77 disclaimers.
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78
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79 2. You may apply bug fixes, portability fixes and other modifications
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80 derived from the Public Domain or from the Copyright Holder. A
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81 Package modified in such a way shall still be considered the Standard
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82 Version.
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83
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84 3. You may otherwise modify your copy of this Package in any way, provided
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85 that you insert a prominent notice in each changed file stating how and
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86 when you changed that file, and provided that you do at least ONE of the
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87 following:
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88
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89 a. place your modifications in the Public Domain or otherwise make them
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90 Freely Available, such as by posting said modifications to Usenet
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91 or an equivalent medium, or placing the modifications on a major
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92 archive site such as uunet.uu.net, or by allowing the Copyright Holder
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93 to include your modifications in the Standard Version of the Package.
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94 b. use the modified Package only within your corporation or organization.
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95 c. rename any non-standard executables so the names do not conflict
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96 with standard executables, which must also be provided, and provide
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97 a separate manual page for each non-standard executable that clearly
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98 documents how it differs from the Standard Version.
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99 d. make other distribution arrangements with the Copyright Holder.
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100
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101 4. You may distribute the programs of this Package in object code or
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102 executable form, provided that you do at least ONE of the following:
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103
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104 a. distribute a Standard Version of the executables and library files,
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105 together with instructions (in the manual page or equivalent) on
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106 where to get the Standard Version.
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107 b. accompany the distribution with the machine-readable source of the
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108 Package with your modifications.
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109 c. give non-standard executables non-standard names, and clearly
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110 document the differences in manual pages (or equivalent), together
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111 with instructions on where to get the Standard Version.
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112 d. make other distribution arrangements with the Copyright Holder.
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113
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114 5. You may charge a reasonable copying fee for any distribution of
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115 this Package. You may charge any fee you choose for support of
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116 this Package. You may not charge a fee for this Package itself.
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117 However, you may distribute this Package in aggregate with other
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118 (possibly commercial) programs as part of a larger (possibly
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119 commercial) software distribution provided that you do not a
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120 dvertise this Package as a product of your own. You may embed this
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121 Package's interpreter within an executable of yours (by linking);
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122 this shall be construed as a mere form of aggregation, provided that
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123 the complete Standard Version of the interpreter is so embedded.
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124
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125 6. The scripts and library files supplied as input to or produced as
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126 output from the programs of this Package do not automatically fall
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127 under the copyright of this Package, but belong to whomever generated
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128 them, and may be sold commercially, and may be aggregated with this
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129 Package. If such scripts or library files are aggregated with this
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130 Package via the so-called "undump" or "unexec" methods of producing
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131 a binary executable image, then distribution of such an image shall
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132 neither be construed as a distribution of this Package nor shall it
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133 fall under the restrictions of Paragraphs 3 and 4, provided that you
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134 do not represent such an executable image as a Standard Version of
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135 this Package.
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136
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137 7. C subroutines (or comparably compiled subroutines in other languages)
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138 supplied by you and linked into this Package in order to emulate
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139 subroutines and variables of the language defined by this Package
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140 shall not be considered part of this Package, but are the equivalent
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141 of input as in Paragraph 6, provided these subroutines do not change
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142 the language in any way that would cause it to fail the regression
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143 tests for the language.
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144
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145 8. Aggregation of this Package with a commercial distribution is always
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146 permitted provided that the use of this Package is embedded; that is,
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147 when no overt attempt is made to make this Package's interfaces visible
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148 to the end user of the commercial distribution. Such use shall not be
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149 construed as a distribution of this Package.
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150
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151 9. The name of the Copyright Holder may not be used to endorse or promote
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152 products derived from this software without specific prior written permission.
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153
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154 10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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155 WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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156 MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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157
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158 The End
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159
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160
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161 Contacts
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162 --------
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163
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164 For any questions involving X! tandem, please contact
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165 contact@thegpm.org
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166
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167 Acknowledgments
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168 ----------------
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169
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170 Ron Beavis - system design and implementation
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171 Rob Craig - debugging and LINUX implementation
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172 Jayson Falkner - code for GeeToo LINUX implementation
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173 Patrick Lacasse - initial additions for mzxml and mzdata functionality
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174 Brendan McLean - optimized changes for mzxml and mzdata functionality using expat library
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175
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176
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177
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