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author pieter.lukasse@wur.nl
date Wed, 08 Jan 2014 11:34:51 +0100
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2 X!TANDEM LICENSE AND README ===========================================
3
4
5 X! tandem protein sequence modeler
6
7 What is it?
8 -----------
9 X! tandem open source software that can model tandem
10 mass spectra with protein sequences. This software
11 has a very simple, unsophistocated application programming
12 interface (API): it simply takes an XML file of instructions
13 on its command line, and output the results into an XML file,
14 which has been specified in the input XML file.
15
16 The Latest Version
17 ------------------
18
19 Details of the latest version can be found on the X! tandem
20 project page under http://www.thegpm.org.
21 This version is the first release the CYCLONE edition (version 2012.10.01.1).
22
23
24 Documentation
25 -------------
26
27 This version of X! tandem is a full release, only including source
28 level documentation. As more releases occur, better documentation
29 will be included.
30
31 Installation
32 ------------
33
34 (IN this case installation is automatically done by Galaxy's Toolshed).
35
36 Licensing
37 ---------
38
39 The Artistic License for all X! software, binaries and documentation
40
41 Preamble
42 The intent of this document is to state the conditions under which a
43 Package may be copied, such that the Copyright Holder maintains some
44 semblance of artistic control over the development of the package,
45 while giving the users of the package the right to use and distribute
46 the Package in a more-or-less customary fashion, plus the right to
47 make reasonable modifications.
48
49 Definitions
50 "Package" refers to the collection of files distributed by the Copyright
51 Holder, and derivatives of that collection of files created through
52 textual modification.
53
54 "Standard Version" refers to such a Package if it has not been modified,
55 or has been modified in accordance with the wishes of the Copyright
56 Holder as specified below.
57
58 "Copyright Holder" is whoever is named in the copyright or copyrights
59 for the package.
60
61 "You" is you, if you're thinking about copying or distributing this Package.
62
63 "Reasonable copying fee" is whatever you can justify on the basis of
64 media cost, duplication charges, time of people involved, and so on.
65 (You will not be required to justify it to the Copyright Holder, but
66 only to the computing community at large as a market that must bear
67 the fee.)
68
69 "Freely Available" means that no fee is charged for the item itself,
70 though there may be fees involved in handling the item. It also means
71 that recipients of the item may redistribute it under the same
72 conditions they received it.
73
74 1. You may make and give away verbatim copies of the source form of the
75 Standard Version of this Package without restriction, provided that
76 you duplicate all of the original copyright notices and associated
77 disclaimers.
78
79 2. You may apply bug fixes, portability fixes and other modifications
80 derived from the Public Domain or from the Copyright Holder. A
81 Package modified in such a way shall still be considered the Standard
82 Version.
83
84 3. You may otherwise modify your copy of this Package in any way, provided
85 that you insert a prominent notice in each changed file stating how and
86 when you changed that file, and provided that you do at least ONE of the
87 following:
88
89 a. place your modifications in the Public Domain or otherwise make them
90 Freely Available, such as by posting said modifications to Usenet
91 or an equivalent medium, or placing the modifications on a major
92 archive site such as uunet.uu.net, or by allowing the Copyright Holder
93 to include your modifications in the Standard Version of the Package.
94 b. use the modified Package only within your corporation or organization.
95 c. rename any non-standard executables so the names do not conflict
96 with standard executables, which must also be provided, and provide
97 a separate manual page for each non-standard executable that clearly
98 documents how it differs from the Standard Version.
99 d. make other distribution arrangements with the Copyright Holder.
100
101 4. You may distribute the programs of this Package in object code or
102 executable form, provided that you do at least ONE of the following:
103
104 a. distribute a Standard Version of the executables and library files,
105 together with instructions (in the manual page or equivalent) on
106 where to get the Standard Version.
107 b. accompany the distribution with the machine-readable source of the
108 Package with your modifications.
109 c. give non-standard executables non-standard names, and clearly
110 document the differences in manual pages (or equivalent), together
111 with instructions on where to get the Standard Version.
112 d. make other distribution arrangements with the Copyright Holder.
113
114 5. You may charge a reasonable copying fee for any distribution of
115 this Package. You may charge any fee you choose for support of
116 this Package. You may not charge a fee for this Package itself.
117 However, you may distribute this Package in aggregate with other
118 (possibly commercial) programs as part of a larger (possibly
119 commercial) software distribution provided that you do not a
120 dvertise this Package as a product of your own. You may embed this
121 Package's interpreter within an executable of yours (by linking);
122 this shall be construed as a mere form of aggregation, provided that
123 the complete Standard Version of the interpreter is so embedded.
124
125 6. The scripts and library files supplied as input to or produced as
126 output from the programs of this Package do not automatically fall
127 under the copyright of this Package, but belong to whomever generated
128 them, and may be sold commercially, and may be aggregated with this
129 Package. If such scripts or library files are aggregated with this
130 Package via the so-called "undump" or "unexec" methods of producing
131 a binary executable image, then distribution of such an image shall
132 neither be construed as a distribution of this Package nor shall it
133 fall under the restrictions of Paragraphs 3 and 4, provided that you
134 do not represent such an executable image as a Standard Version of
135 this Package.
136
137 7. C subroutines (or comparably compiled subroutines in other languages)
138 supplied by you and linked into this Package in order to emulate
139 subroutines and variables of the language defined by this Package
140 shall not be considered part of this Package, but are the equivalent
141 of input as in Paragraph 6, provided these subroutines do not change
142 the language in any way that would cause it to fail the regression
143 tests for the language.
144
145 8. Aggregation of this Package with a commercial distribution is always
146 permitted provided that the use of this Package is embedded; that is,
147 when no overt attempt is made to make this Package's interfaces visible
148 to the end user of the commercial distribution. Such use shall not be
149 construed as a distribution of this Package.
150
151 9. The name of the Copyright Holder may not be used to endorse or promote
152 products derived from this software without specific prior written permission.
153
154 10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
155 WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
156 MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
157
158 The End
159
160
161 Contacts
162 --------
163
164 For any questions involving X! tandem, please contact
165 contact@thegpm.org
166
167 Acknowledgments
168 ----------------
169
170 Ron Beavis - system design and implementation
171 Rob Craig - debugging and LINUX implementation
172 Jayson Falkner - code for GeeToo LINUX implementation
173 Patrick Lacasse - initial additions for mzxml and mzdata functionality
174 Brendan McLean - optimized changes for mzxml and mzdata functionality using expat library
175
176
177