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Revision 1.1 - (show annotations) (download)
Wed Dec 31 00:20:14 2008 UTC (5 years, 8 months ago) by weaver
Branch: MAIN
CVS Tags: HEAD
New license phrap for sci-biology/phrap

1 ACADEMIC USER AGREEMENT
2
3 Please read the entire agreement, fill in the information in the
4 indicated positions (such as "NAME:"), and return the entire document
5 to the indicated people. Please send the document as the message--not
6 as an attachment.
7
8 Phrap: A program for assembling DNA sequence data.
9
10 Swat: A program for searching one or more DNA or protein query sequences
11 against a sequence database, using (an efficient implementation of) the
12 Smith-Waterman-Gotoh algorithm.
13
14 Cross_Match: A general-purpose utility based on Swat for comparing any
15 two sets of (long or short) DNA sequences.
16
17 Phred: A program that reads DNA sequencer trace data, calls bases,
18 assigns quality values to the bases, and writes the base calls and quality
19 values to output files.
20
21 Consed: A program for viewing and editing Phrap assemblies.
22
23 To receive any of these programs you will need to agree to the following
24 conditions. They should be taken seriously!
25
26 1) You agree to read the documentation. We welcome feedback on any
27 inaccuracies.
28
29 2) You agree to report any bugs to us. (To fix bugs, we will need
30 from you a dataset and a procedure that reproduces the problem; but do
31 not send datasets without first emailing us to describe the nature of
32 the bug.)
33
34 3) You agree not to make the programs (including source code,
35 executables, or any part thereof, in modified or unmodified form)
36 available to anyone outside your group, and not to put them where they
37 may be accessible to outside individuals without your direct knowledge
38 (e.g. on a computer to which people outside your group have login
39 privileges). The documentation however may be freely distributed.
40 Refer any requests for the programs to the authors. If you are
41 operating a computer facility which provides access to several
42 independent investigators, you agree to set the permissions on the
43 executables and source code to allow execute but not read access, so
44 that the programs may not be copied. Investigators who want copies of
45 the software for their own use must return a separate copy of this
46 agreement.
47
48 4) You agree not to use the programs for any commercial purpose,
49 including but not limited to commercially restricted sequencing
50 (defined as sequencing for which a company retains patenting or
51 licensing rights regarding the sequence, or the right to restrict or
52 delay dissemination of the sequence; with the sole exception that
53 sequencing is not considered to be commercially restricted if it is
54 federally funded and the investigators adopt the data release policies
55 endorsed at the Wellcome Trust-sponsored Bermuda meeting,
56 i.e. immediate release of data as it is generated).
57 [If you wish to obtain the software for commercially restricted
58 sequencing or any other commercial purposes, you will need to execute
59 a separate licensing agreement with the University of Washington and
60 pay a fee. In that case please contact:
61
62 Lisa Heinz
63 University of Washington TechTransfer, Digital Ventures
64 Box 354990
65 4311-11th Avenue NE, Suite 500
66 Seattle, WA 98105-4608
67
68 http://depts.washington.edu/techtran
69
70 206-616-3451 FAX: 206-616-3322
71 swxfr@u.washington.edu
72
73 Do not contact her if the academic license applies.]
74
75 5) You acknowledge that the software is experimental in nature and is
76 supplied "AS IS", without obligation by the authors or the University
77 of Washington to provide accompanying services or support. The entire
78 risk as to the quality and performance of the Software is with you.
79 UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES
80 REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT
81 LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A
82 PARTICULAR PURPOSE.
83
84 6) All members of your group with access to the software agree to the
85 same conditions.
86
87
88
89 Having read the above, if you are still interested in obtaining the
90 programs, please return a copy of this entire message (which MUST be
91 included so that it is clear what you are agreeing to) by email
92 together with the following information:
93
94 NAME: Your name in first name/last name order.
95
96 NAME:
97
98
99 Example:
100 NAME: John Dracula
101 (Please do not use all capitals such as John DRACULA)
102
103 ACKNOWLEDGEMENT: An acknowledgement that you and the members of your
104 group agree to these conditions.
105
106 ACKNOWLEDGEMENT:
107
108 Example:
109 ACKNOWLEDGEMENT: I agree to the license.
110
111 PROGRAMS: Which programs you want (phrap,cross_match, and swat are
112 distributed together). You must cc the message to each appropriate
113 individual (Brent Ewing, David Gordon, and/or Phil Green) at the email
114 addresses below so that they will know to send you the appropriate
115 program.
116
117 PROGRAMS:
118
119 Example:
120 PROGRAMS: phred, phrap, consed
121
122 INSTITUTION: Your academic or government institution (give full name,
123 not abbreviation)
124
125 INSTITUTION:
126
127 Example:
128 INSTITUTION: University of Lower Transylvania
129
130 DEPARTMENT: Your department
131
132 DEPARTMENT:
133
134 Example:
135 DEPARTMENT: Department of Hematology
136
137 EMAIL: Your email address for all future correspondence. Ideally this
138 should be a Unix computer running a generic mail program, since
139 several of the programs are sent as uuencoded files which may be
140 corrupted by some mail programs.
141 If this address is not at the institution & department listed above,
142 please explain the discrepancy.
143
144 EMAIL:
145
146 Example:
147 EMAIL: john.dracula@utrans.edu
148
149 OS: (Consed requestors only) Which platform(s) you want Consed for:
150 solaris 2.5.1, solaris 2.6, solaris 2.7 (solaris 7), solaris 8,
151 solaris 9, digital unix 4.0 (or better), hp-ux 11.x, sgi irix 6.2,
152 6.3, 6.4, or 6.5, linux (normal 32 bit) (Redhat 7.1-1 or better),
153 linux (Itanium), linux (AMD64), ibm aix 5.2 (or better), macosx 10.2
154 (Darwin kernel 6.0) (or better), or solaris-intel (2.8 or better).
155
156 OS:
157
158 Example:
159 OS: hpux
160
161 Note: Consed is not available for PC's running Windows, XP, NT, or
162 2000.
163
164 IP: (Consed requestors only) The ip address of the computer on which
165 you will be running a web browser to download consed. This does not
166 have to be the same computer as the one on which you will run consed.
167 Please view page
168 http://bozeman.mbt.washington.edu/consed/find_ip_address.html
169 which will tell you what my computer thinks is your ip address.
170
171 (Even if you think you know your ip address, firewalls and proxies can
172 cause your browser to transmit a different ip address, and thus my
173 webserver would deny you access to consed. So it would be a good idea
174 to view the page above and send me the ip address it shows, even if
175 this isn't your real ip address.)
176
177 IP:
178
179 Example:
180 IP: 123.49.74.80
181
182
183 If you want Consed/Autofinish, you must include OS and IP (above).
184 Consed cannot be obtained without them.
185
186 Please return this entire agreement so it is clear what you are
187 agreeing to.
188
189 Please send all of this, including the agreement, as part of the
190 email message--not as an attachment.
191
192 Send it to each of the relevant individuals below:
193
194 Contacts for obtaining the programs and for questions, bug reports,
195 suggestions:
196
197 Phrap/cross_match/swat: Phil Green, phg (at) u.washington.edu
198 Phred: Brent Ewing, bge (at) u.washington.edu
199 Consed: David Gordon, gordon (at) genome.washington.edu
200
201 where the " (at) " is replaced by "@".
202
203 It can take up to 2 weeks for a license application to be processed,
204 so please be patient.

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