=====================================================================
1. Torrent Suite Software License
=====================================================================
Torrent Suite Software: This software provides for the analysis and storage of data received from the Ion Personal Genome Machine(R) PGM(tm) Sequencer or the Ion Proton(R) Sequencer.
---------------------------------------------------------------------
Copyright (C) 2011 Life Technologies Corporation
All Rights Reserved.
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation; either version 2 of the License, or (at your
option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. You can also find the
GPL on the GNU web site: .
=====================================================================
2. Third Party Software Notices and Licenses.
=====================================================================
The following third party software components are included in the Torrent Suite
Software. These software components are copyrighted and licensed by their respective
owners. Various components require distribution of source code or if a URL is used to
point the end-user to a source-code repository, and the source code is not available at
such site, the distributor must, for a time determined by the license, offer to provide the
source code. In such cases, please contact your Ion Torrent representative. As well,
various licenses require that the end-user receive a copy of the license and such licenses
may be found below. In order to use this Torrent Suite Software, the end-user must
abide by the terms and conditions of these third-party licenses.
lapack
URL: http://www.netlib.org/lapack/
License: BSD
k-means
URL: http://www.cs.umd.edu/~mount/Projects/KMeans/
License: GPL
boost
URL: http://www.boost.org/
License: BSD
atlas
URL: http://math-atlas.sourceforge.net
License: BSD
libgfortran
License: GPL
LAPACK
---------------------------------------------------------------------
Copyright (c) 1992-2008 The University of Tennessee. All rights
reserved.
$COPYRIGHT$
Additional copyrights may follow
$HEADER$
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer listed
in this license in the documentation and/or other materials
provided with the distribution.
- Neither the name of the copyright holders nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
DAMAGE.
K-MEANS
---------------------------------------------------------------------
KMlocal: A testbed for k-means clustering algorithms based on local
search
Version: 1.7
Date: 08/10/2005
Copyright (C) 2004-2005 David M. Mount and University of Maryland
All Rights Reserved.
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation; either version 2 of the License, or (at your
option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
Disclaimer
----------
The University of Maryland and the authors make no representations
about the suitability or fitness of this software for any purpose.
It is provided "as is" without express or implied warranty.
Author
------
David Mount
Dept of Computer Science
University of Maryland,
College Park, MD 20742 USA
mount@cs.umd.edu
http://www.cs.umd.edu/~mount/
BOOST
---------------------------------------------------------------------
Boost Software License - Version 1.0 - August 17th, 2003
Permission is hereby granted, free of charge, to any person or
organization obtaining a copy of the software and accompanying
documentation covered by this license (the "Software") to use,
reproduce, display, distribute, execute, and transmit the Software, and
to prepare derivative works of the Software, and to permit third-parties
to whom the Software is furnished to do so, all subject to the
following:
The copyright notices in the Software and this entire statement,
including the above license grant, this restriction and the following
disclaimer, must be included in all copies of the Software, in whole or
in part, and all derivative works of the Software, unless such copies or
derivative works are solely in the form of machine-executable object
code generated by a source language processor.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-
INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE
DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY,
WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
ATLAS
---------------------------------------------------------------------
Upstream Authors:
R. Clint Whaley atlas@cs.utk.edu
Jack Dongarra atlas@cs.utk.edu
Copyright:
(C) Copyright 1997-2008 All Rights Reserved
Permission to use, copy, modify, and distribute this software and
its documentation for any purpose and without fee is hereby granted
provided that the above copyright notice appear in all copies and
that both the copyright notice and this permission notice appear in
supporting documentation.
Neither the University of Tennessee nor the Author make any
representations about the suitability of this software for any
purpose. This software is provided ``as is'' without express or
implied warranty.
On alpha architectures, the standard builds use K. GOTO's kernels
contributed to the ATLAS project under the LGPL. Therefore on these
platforms, the distributed prebuilt libraries, as well as any user
built library using this kernel, is licensed under the LGPL.
On Debian GNU/Linux systems, the complete text of the GNU Lesser General
Public License can be found in `/usr/share/common-licenses/LGPL'.
=====================================================================
3. GPL v2
=====================================================================
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your freedom to share and
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users. This General Public License applies to most of the Free Software Foundation's
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When we speak of free software, we are referring to freedom, not price. Our General
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To protect your rights, we need to make restrictions that forbid anyone to deny you these
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The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND
MODIFICATION
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This section is intended to make thoroughly clear what is believed to be a consequence of
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NO WARRANTY
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APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE
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PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH
HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
=====================================================================
4. GPL v3
=====================================================================
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (c) 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies of this license document,
but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for software and other kinds
of works.
The licenses for most software and other practical works are designed to take away your
freedom to share and change the works. By contrast, the GNU General Public License is
intended to guarantee your freedom to share and change all versions of a program--to
make sure it remains free software for all its users. We, the Free Software Foundation, use
the GNU General Public License for most of our software; it applies also to any other
work released this way by its authors. You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General
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of free software (and charge for them if you wish), that you receive source code or can
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To protect your rights, we need to prevent others from denying you these rights or asking
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copies of the software, or if you modify it: responsibilities to respect the freedom of
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For example, if you distribute copies of such a program, whether gratis or for a fee, you
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Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright
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TERMS AND CONDITIONS
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copy of the Corresponding Source for all the software in the product that is
covered by this License, on a durable physical medium customarily used for
software interchange, for a price no more than your reasonable cost of physically
performing this conveying of source, or (2) access to copy the Corresponding
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* c) Convey individual copies of the object code with a copy of the written offer to
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in accord with subsection 6b.
* d) Convey the object code by offering access from a designated place (gratis or
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7. Additional Terms.
"Additional permissions" are terms that supplement the terms of this License by making
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entire Program remains governed by this License without regard to the additional
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8. Termination.
You may not propagate or modify a covered work except as expressly provided under
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However, if you cease all violation of this License, then your license from a particular
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Termination of your rights under this section does not terminate the licenses of parties
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the same material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the
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Each time you convey a covered work, the recipient automatically receives a license from
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You may not impose any further restrictions on the exercise of the rights granted or
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11. Patents.
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A contributor's "essential patent claims" are all patent claims owned or controlled by the
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Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under
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In the following three paragraphs, a "patent license" is any express agreement or
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If you convey a covered work, knowingly relying on a patent license, and the
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covered work in a country, or your recipient's use of the covered work in a country,
would infringe one or more identifiable patents in that country that you have reason to
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If, pursuant to or in connection with a single transaction or arrangement, you convey, or
propagate by procuring conveyance of, a covered work, and grant a patent license to
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A patent license is "discriminatory" if it does not include within the scope of its coverage,
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rights that are specifically granted under this License. You may not convey a covered
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extent of your activity of conveying the work, and under which the third party grants, to
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compilations that contain the covered work, unless you entered into that arrangement, or
that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or
other defenses to infringement that may otherwise be available to you under applicable
patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that
contradict the conditions of this License, they do not excuse you from the conditions of
this License. If you cannot convey a covered work so as to satisfy simultaneously your
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you may not convey it at all. For example, if you agree to terms that obligate you to
collect a royalty for further conveying from those to whom you convey the Program, the
only way you could satisfy both those terms and this License would be to refrain entirely
from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have permission to link or
combine any covered work with a work licensed under version 3 of the GNU Affero
General Public License into a single combined work, and to convey the resulting work.
The terms of this License will continue to apply to the part which is the covered work, but
the special requirements of the GNU Affero General Public License, section 13,
concerning interaction through a network will apply to the combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU
General Public License from time to time. Such new versions will be similar in spirit to the
present version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a
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numbered version or of any later version published by the Free Software Foundation. If
the Program does not specify a version number of the GNU General Public License, you
may choose any version ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU
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Later license versions may give you additional or different permissions. However, no
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choosing to follow a later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT
PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN
WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE
THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO
MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE
LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE
OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO
LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES
SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR
OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given
local legal effect according to their terms, reviewing courts shall apply local law that most
closely approximates an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a copy of the Program
in return for a fee.