Software Restricted Access

miRTrace v1.0.0

Marc R. Friedländer; Yrin Eldfjell; Wenjing Kang

First release of miRTrace

Github: https://github.com/friedlanderlab/mirtrace/

Restricted Access

You may request access to the files in this upload, provided that you fulfil the conditions below. The decision whether to grant/deny access is solely under the responsibility of the record owner.

This software repository or package consists of the "miRTrace" software and the libraries and databases it depends on. These dependencies may have licences different from the main software.

LICSENSE LISTING:
* The core miRTrace application, which is the software developed by the Friedländer Group. (Each file will contain a copyright header specifying that it is part of "miRTrace".

Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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(a) You must give any other recipients of the Work or
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(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and

(c) You must retain, in the Source form of any Derivative Works
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the Derivative Works; and

(d) If the Work includes a "NOTICE" text file as part of its
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5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
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names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.

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agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
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incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
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has been advised of the possibility of such damages.

9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
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END OF TERMS AND CONDITIONS

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* Artifacts sequences (database "artifact_sequences.fa"). Some or all of the the adapter artifacts sequences are Illumina sequences subject to the following copyright terms:

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* ColorBrewer:

Apache-Style Software License for ColorBrewer software and ColorBrewer Color
Schemes

Copyright (c) 2002 Cynthia Brewer, Mark Harrower, and The Pennsylvania State
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use this file except in compliance with the License. You may obtain a copy of

Unless required by applicable law or agreed to in writing, software
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* D3.js:

Redistribution and use in source and binary forms, with or without modification,
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* FileSaver.js:
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* FileSaver.js
*  A saveAs() & saveTextAs() FileSaver implementation.
*  2014-06-24
*
*  Modify by Brian Chen
*  Author: Eli Grey, http://eligrey.com
*/

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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 AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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* Font Awesome. Minor modifications may have been made to better suit our software. License:

Source: http://scripts.sil.org/OFL

with Reserved Font Name <Reserved Font Name>.
with Reserved Font Name <additional Reserved Font Name>.

This license is copied below, and is also available with a FAQ at:
http://scripts.sil.org/OFL

-----------------------------------------------------------
SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
-----------------------------------------------------------

PREAMBLE
The goals of the Open Font License (OFL) are to stimulate worldwide
development of collaborative font projects, to support the font creation
efforts of academic and linguistic communities, and to provide a free and
open framework in which fonts may be shared and improved in partnership
with others.

The OFL allows the licensed fonts to be used, studied, modified and
redistributed freely as long as they are not sold by themselves. The
fonts, including any derivative works, can be bundled, embedded,
redistributed and/or sold with any software provided that any reserved
names are not used by derivative works. The fonts and derivatives,
however, cannot be released under any other type of license. The
requirement for fonts to remain under this license does not apply
to any document created using the fonts or their derivatives.

DEFINITIONS
"Font Software" refers to the set of files released by the Copyright
Holder(s) under this license and clearly marked as such. This may
include source files, build scripts and documentation.

"Reserved Font Name" refers to any names specified as such after the

"Original Version" refers to the collection of Font Software components as

or substituting -- in part or in whole -- any of the components of the
Original Version, by changing formats or by porting the Font Software to a
new environment.

"Author" refers to any designer, engineer, programmer, technical
writer or other person who contributed to the Font Software.

PERMISSION & CONDITIONS
Permission is hereby granted, free of charge, to any person obtaining
a copy of the Font Software, to use, study, copy, merge, embed, modify,
redistribute, and sell modified and unmodified copies of the Font
Software, subject to the following conditions:

1) Neither the Font Software nor any of its individual components,
in Original or Modified Versions, may be sold by itself.

2) Original or Modified Versions of the Font Software may be bundled,
redistributed and/or sold with any software, provided that each copy
binary files as long as those fields can be easily viewed by the user.

3) No Modified Version of the Font Software may use the Reserved Font
Name(s) unless explicit written permission is granted by the corresponding
Copyright Holder. This restriction only applies to the primary font name as
presented to the users.

4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
Software shall not be used to promote, endorse or advertise any
Modified Version, except to acknowledge the contribution(s) of the
Copyright Holder(s) and the Author(s) or with their explicit written
permission.

5) The Font Software, modified or unmodified, in part or in whole,
must be distributed entirely under this license, and must not be
remain under this license does not apply to any document created
using the Font Software.

TERMINATION
This license becomes null and void if any of the above conditions are
not met.

DISCLAIMER
THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
OTHER DEALINGS IN THE FONT SOFTWARE.
--------------------------------------------------------------------------------
* GSON:

Version 2.0, January 2004

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Definitions.

"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.

"Licensor" shall mean the copyright owner or entity authorized by

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"You" (or "Your") shall mean an individual or Legal Entity
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"Contribution" shall mean any work of authorship, including
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on behalf of whom a Contribution has been received by Licensor and
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2. Grant of Copyright License. Subject to the terms and conditions of
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worldwide, non-exclusive, no-charge, royalty-free, irrevocable
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3. Grant of Patent License. Subject to the terms and conditions of
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use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
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modifications, and in Source or Object form, provided that You
meet the following conditions:

(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and

(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and

(c) You must retain, in the Source form of any Derivative Works
attribution notices from the Source form of the Work,
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the Derivative Works; and

(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
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pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
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wherever such third-party notices normally appear. The contents
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for use, reproduction, or distribution of Your modifications, or
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the conditions stated in this License.

5. Submission of Contributions. Unless You explicitly state otherwise,
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Notwithstanding the above, nothing herein shall supersede or modify
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names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any

8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.

9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
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on Your own behalf and on Your sole responsibility, not on behalf
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defend, and hold each Contributor harmless for any liability
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END OF TERMS AND CONDITIONS

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* Guava:

Version 2.0, January 2004

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Definitions.

"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.

"Licensor" shall mean the copyright owner or entity authorized by

"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.

"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.

"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.

"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.

"Work" shall mean the work of authorship, whether in Source or
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).

"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.

"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."

"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.

2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.

3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.

4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:

(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and

(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and

(c) You must retain, in the Source form of any Derivative Works
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and

(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided

for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.

5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.

names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.

7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any

8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.

9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason

END OF TERMS AND CONDITIONS

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* miRBase (multiple database files):
miRBase is in the public domain. It is not copyrighted.  You may
freely modify, redistribute, or use it for any purpose.  See
http://www.mirbase.org/ for information on how to cite miRBse in
publications.

BECAUSE MIRBASE IS PROVIDED AT NO COST IN THE PUBLIC DOMAIN, IN NO
EVENT SHALL ANY MEMBER OF THE MIRBASE DEVELOPMENT TEAM BE LIABLE TO
ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL
DAMAGES ARISING OUT OF THE USE OF THE MIRBASE DATABASE, EVEN IF THE
MIRBASE TEAM HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

TO THE EXTENT PERMITTED BY LAW, MIRBASE SPECIFICALLY DISCLAIMS ANY
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. MIRBASE IS
PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND.  WE ASSUME NO
OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
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* opencsv:

Version 2.0, January 2004

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Definitions.

"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.

"Licensor" shall mean the copyright owner or entity authorized by

"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.

"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.

"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.

"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.

"Work" shall mean the work of authorship, whether in Source or
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).

"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
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