| ACADEMIC USER AGREEMENT |
| |
| Please read the entire agreement, fill in the information in the |
| indicated positions (such as "NAME:"), and return the entire document |
| to the indicated people. Please send the document as the message--not |
| as an attachment. |
| |
| Phrap: A program for assembling DNA sequence data. |
| |
| Swat: A program for searching one or more DNA or protein query sequences |
| against a sequence database, using (an efficient implementation of) the |
| Smith-Waterman-Gotoh algorithm. |
| |
| Cross_Match: A general-purpose utility based on Swat for comparing any |
| two sets of (long or short) DNA sequences. |
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| Phred: A program that reads DNA sequencer trace data, calls bases, |
| assigns quality values to the bases, and writes the base calls and quality |
| values to output files. |
| |
| Consed: A program for viewing and editing Phrap assemblies. |
| |
| To receive any of these programs you will need to agree to the following |
| conditions. They should be taken seriously! |
| |
| 1) You agree to read the documentation. We welcome feedback on any |
| inaccuracies. |
| |
| 2) You agree to report any bugs to us. (To fix bugs, we will need |
| from you a dataset and a procedure that reproduces the problem; but do |
| not send datasets without first emailing us to describe the nature of |
| the bug.) |
| |
| 3) You agree not to make the programs (including source code, |
| executables, or any part thereof, in modified or unmodified form) |
| available to anyone outside your group, and not to put them where they |
| may be accessible to outside individuals without your direct knowledge |
| (e.g. on a computer to which people outside your group have login |
| privileges). The documentation however may be freely distributed. |
| Refer any requests for the programs to the authors. If you are |
| operating a computer facility which provides access to several |
| independent investigators, you agree to set the permissions on the |
| executables and source code to allow execute but not read access, so |
| that the programs may not be copied. Investigators who want copies of |
| the software for their own use must return a separate copy of this |
| agreement. |
| |
| 4) You agree not to use the programs for any commercial purpose, |
| including but not limited to commercially restricted sequencing |
| (defined as sequencing for which a company retains patenting or |
| licensing rights regarding the sequence, or the right to restrict or |
| delay dissemination of the sequence; with the sole exception that |
| sequencing is not considered to be commercially restricted if it is |
| federally funded and the investigators adopt the data release policies |
| endorsed at the Wellcome Trust-sponsored Bermuda meeting, |
| i.e. immediate release of data as it is generated). |
| [If you wish to obtain the software for commercially restricted |
| sequencing or any other commercial purposes, you will need to execute |
| a separate licensing agreement with the University of Washington and |
| pay a fee. In that case please contact: |
| |
| Lisa Heinz |
| University of Washington TechTransfer, Digital Ventures |
| Box 354990 |
| 4311-11th Avenue NE, Suite 500 |
| Seattle, WA 98105-4608 |
| |
| http://depts.washington.edu/techtran |
| |
| 206-616-3451 FAX: 206-616-3322 |
| swxfr@u.washington.edu |
| |
| Do not contact her if the academic license applies.] |
| |
| 5) You acknowledge that the software is experimental in nature and is |
| supplied "AS IS", without obligation by the authors or the University |
| of Washington to provide accompanying services or support. The entire |
| risk as to the quality and performance of the Software is with you. |
| UW AND THE AUTHORS EXPRESSLY DISCLAIM ANY AND ALL WARRANTIES |
| REGARDING THE SOFTWARE, WHETHER EXPRESS OR IMPLIED, INCLUDING BUT NOT |
| LIMITED TO WARRANTIES PERTAINING TO MERCHANTABILITY OR FITNESS FOR A |
| PARTICULAR PURPOSE. |
| |
| 6) All members of your group with access to the software agree to the |
| same conditions. |
| |
| |
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| Having read the above, if you are still interested in obtaining the |
| programs, please return a copy of this entire message (which MUST be |
| included so that it is clear what you are agreeing to) by email |
| together with the following information: |
| |
| NAME: Your name in first name/last name order. |
| |
| NAME: |
| |
| |
| Example: |
| NAME: John Dracula |
| (Please do not use all capitals such as John DRACULA) |
| |
| ACKNOWLEDGEMENT: An acknowledgement that you and the members of your |
| group agree to these conditions. |
| |
| ACKNOWLEDGEMENT: |
| |
| Example: |
| ACKNOWLEDGEMENT: I agree to the license. |
| |
| PROGRAMS: Which programs you want (phrap,cross_match, and swat are |
| distributed together). You must cc the message to each appropriate |
| individual (Brent Ewing, David Gordon, and/or Phil Green) at the email |
| addresses below so that they will know to send you the appropriate |
| program. |
| |
| PROGRAMS: |
| |
| Example: |
| PROGRAMS: phred, phrap, consed |
| |
| INSTITUTION: Your academic or government institution (give full name, |
| not abbreviation) |
| |
| INSTITUTION: |
| |
| Example: |
| INSTITUTION: University of Lower Transylvania |
| |
| DEPARTMENT: Your department |
| |
| DEPARTMENT: |
| |
| Example: |
| DEPARTMENT: Department of Hematology |
| |
| EMAIL: Your email address for all future correspondence. Ideally this |
| should be a Unix computer running a generic mail program, since |
| several of the programs are sent as uuencoded files which may be |
| corrupted by some mail programs. |
| If this address is not at the institution & department listed above, |
| please explain the discrepancy. |
| |
| EMAIL: |
| |
| Example: |
| EMAIL: john.dracula@utrans.edu |
| |
| OS: (Consed requestors only) Which platform(s) you want Consed for: |
| solaris 2.5.1, solaris 2.6, solaris 2.7 (solaris 7), solaris 8, |
| solaris 9, digital unix 4.0 (or better), hp-ux 11.x, sgi irix 6.2, |
| 6.3, 6.4, or 6.5, linux (normal 32 bit) (Redhat 7.1-1 or better), |
| linux (Itanium), linux (AMD64), ibm aix 5.2 (or better), macosx 10.2 |
| (Darwin kernel 6.0) (or better), or solaris-intel (2.8 or better). |
| |
| OS: |
| |
| Example: |
| OS: hpux |
| |
| Note: Consed is not available for PC's running Windows, XP, NT, or |
| 2000. |
| |
| IP: (Consed requestors only) The ip address of the computer on which |
| you will be running a web browser to download consed. This does not |
| have to be the same computer as the one on which you will run consed. |
| Please view page |
| http://bozeman.mbt.washington.edu/consed/find_ip_address.html |
| which will tell you what my computer thinks is your ip address. |
| |
| (Even if you think you know your ip address, firewalls and proxies can |
| cause your browser to transmit a different ip address, and thus my |
| webserver would deny you access to consed. So it would be a good idea |
| to view the page above and send me the ip address it shows, even if |
| this isn't your real ip address.) |
| |
| IP: |
| |
| Example: |
| IP: 123.49.74.80 |
| |
| |
| If you want Consed/Autofinish, you must include OS and IP (above). |
| Consed cannot be obtained without them. |
| |
| Please return this entire agreement so it is clear what you are |
| agreeing to. |
| |
| Please send all of this, including the agreement, as part of the |
| email message--not as an attachment. |
| |
| Send it to each of the relevant individuals below: |
| |
| Contacts for obtaining the programs and for questions, bug reports, |
| suggestions: |
| |
| Phrap/cross_match/swat: Phil Green, phg (at) u.washington.edu |
| Phred: Brent Ewing, bge (at) u.washington.edu |
| Consed: David Gordon, gordon (at) genome.washington.edu |
| |
| where the " (at) " is replaced by "@". |
| |
| It can take up to 2 weeks for a license application to be processed, |
| so please be patient. |
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