Difference between revisions of "BioRuby"

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|VCS checkout command=https://github.com/bioruby/bioruby.git
 
|VCS checkout command=https://github.com/bioruby/bioruby.git
 
|Documentation note=http://bioruby.org/rdoc/
 
|Documentation note=http://bioruby.org/rdoc/
 
----
 
----
 
'''[https://www.gezapig.nl/covid.html COronaVIrus Disease 2019 (COVID-19) Special]'''
 
----
 
----
 
 
If you have corrections to this entry or questions about it, please contact: mailto:directory-discuss@gnu.org
 
----
 
 
|Decommissioned or Obsolete=No
 
|Decommissioned or Obsolete=No
 
|IRC general=irc://irc.freenode.org#bioruby
 
|IRC general=irc://irc.freenode.org#bioruby
Line 30: Line 21:
 
|Version download=http://bioruby.org/archive/bioruby-2.0.1.tar.gz
 
|Version download=http://bioruby.org/archive/bioruby-2.0.1.tar.gz
 
|Last review by=Bendikker
 
|Last review by=Bendikker
|Last review date=2020/03/29
+
|Last review date=2020/03/30
 
|Submitted date=2013-03-20
 
|Submitted date=2013-03-20
|Paid support=https://www.fsf.org/resources/service/
 
 
|Accepts cryptocurrency donations=No
 
|Accepts cryptocurrency donations=No
 
|Test entry=No
 
|Test entry=No
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}}
 
}}
 
{{Project license
 
{{Project license
|License=Other
+
|License=GPLv2
 
|License copyright=© Copyright Toshiaki Katayama <k@bioruby.org>
 
|License copyright=© Copyright Toshiaki Katayama <k@bioruby.org>
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2 or Ruby
+
|License note=GPLv2 or Ruby
 
+
}}
GPL-2 or Ruby BioRuby is copyrighted free software by Toshiaki
+
{{Project license
Katayama <k@bioruby.org>. You can redistribute it and/or modify
+
|License=Ruby
it under either the terms of the GPL version 2 (see the file
+
|License copyright=© Copyright Toshiaki Katayama <k@bioruby.org>
GPL), or the conditions below.
+
|License verified by=Debian
 +
|License verified date=2020-03-30
 +
|License note=GPLv2 or Ruby
 
}}
 
}}
 
{{Project license
 
{{Project license
|License=Other
+
|License=LGPLv2.1orlater
 
|License copyright=© 2000-2006 Minero Aoki
 
|License copyright=© 2000-2006 Minero Aoki
 +
/usr/share/common-
 +
licenses/LGPL-2.1
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: LGPL-2.1
 
 
This library is free software; you can redistribute it and/or
 
modify it under the terms of the GNU Lesser General Public
 
License as published by the Free Software Foundation; either
 
version 2.1 of the License, or (at your option) any later
 
version.
 
 
This library 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
 
Lesser General Public License for more details.
 
 
You should have received a copy of the GNU Lesser General Public
 
License along with this library; if not, write to the Free
 
Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
 
Boston, MA 02110-1301 USA
 
 
On Debian systems, the full text of the GNU Lesser General Public
 
License version 2.1 can be found in the file `/usr/share/common-
 
licenses/LGPL-2.1'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
 
|License=GPLv2orlater
 
|License=GPLv2orlater
 
|License copyright=© 2006 Pjotr Prins <p@bioruby.org>
 
|License copyright=© 2006 Pjotr Prins <p@bioruby.org>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
 
|License=GPLv2orlater
 
|License=GPLv2orlater
 
|License copyright=© 2002-2004 KATAYAMA Toshiaki <k@bioruby.org>
 
|License copyright=© 2002-2004 KATAYAMA Toshiaki <k@bioruby.org>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
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|License copyright=© 2006 Pjotr Prins <p@bioruby.org>
 
|License copyright=© 2006 Pjotr Prins <p@bioruby.org>
 
© 2006 Trevor Wennblom <trevor@corevx.com>
 
© 2006 Trevor Wennblom <trevor@corevx.com>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
 
|License=GPLv2orlater
 
|License=GPLv2orlater
 
|License copyright=© 2001 KATAYAMA Toshiaki <k@bioruby.org>
 
|License copyright=© 2001 KATAYAMA Toshiaki <k@bioruby.org>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
Line 181: Line 82:
 
|License copyright=© 2008 KATAYAMA Toshiaki <k@bioruby.org>
 
|License copyright=© 2008 KATAYAMA Toshiaki <k@bioruby.org>
 
© 2008 Pjotr Prins <p@bioruby.org>
 
© 2008 Pjotr Prins <p@bioruby.org>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
Line 207: Line 90:
 
|License copyright=© 2001 KATAYAMA Toshiaki <k@bioruby.org>
 
|License copyright=© 2001 KATAYAMA Toshiaki <k@bioruby.org>
 
© 2002 Yoshinori K. Okuji <o@bioruby.org>
 
© 2002 Yoshinori K. Okuji <o@bioruby.org>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
 
|License=GPLv2orlater
 
|License=GPLv2orlater
 
|License copyright=© 2002 KATAYAMA Toshiaki <k@bioruby.org>
 
|License copyright=© 2002 KATAYAMA Toshiaki <k@bioruby.org>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
Line 260: Line 107:
 
© 2003 Itoshi NIKAIDO <itoshi@gsc.riken.go.jp>
 
© 2003 Itoshi NIKAIDO <itoshi@gsc.riken.go.jp>
 
© 2003 Takeya KASUKAWA <kasukawa@gsc.riken.go.jp>
 
© 2003 Takeya KASUKAWA <kasukawa@gsc.riken.go.jp>
 +
/usr/share/common-licenses/GPL-2
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2+
 
 
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, see
 
<http://www.gnu.org/licenses/>.
 
 
On Debian systems, the full text of the GNU General Public
 
License version 2 can be found in the file `/usr/share/common-
 
licenses/GPL-2'.
 
 
}}
 
}}
 
{{Project license
 
{{Project license
Line 287: Line 116:
 
© These files are marked to be copyrighted by the UniProt Consortium, but this
 
© These files are marked to be copyrighted by the UniProt Consortium, but this
 
© applies to the UniProt database as a whole, not to the individual records.
 
© applies to the UniProt database as a whole, not to the individual records.
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License note=License: not-the-CC-BY-ND-3.0
 
  
 
not-the-CC-BY-ND-3.0 Despite the following statement:
 
not-the-CC-BY-ND-3.0 Despite the following statement:
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The above files, as individual records, are not copyrighted.  The
 
The above files, as individual records, are not copyrighted.  The
 
statement is for the UniProt as a whole.
 
statement is for the UniProt as a whole.
 +
|License verified by=Debian
 +
|License verified date=2013-03-20
 
}}
 
}}
 
{{Project license
 
{{Project license
|License=Other
+
|License=GPLv2orlater
 
|License copyright=© Copyright 2011 Lucas Nussbaum <lucas@debian.org>
 
|License copyright=© Copyright 2011 Lucas Nussbaum <lucas@debian.org>
 
|License verified by=Debian
 
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License note=License: GPL-2 or Ruby
+
|License note=GPLv2orlater or Ruby
 
+
}}
GPL-2:
+
{{Project license
 
+
|License=Ruby
  This program is free software; you can redistribute it and/or
+
|License copyright=© Copyright 2011 Lucas Nussbaum <lucas@debian.org>
  modify it under the terms of the GNU General Public License as
+
|License verified by=Debian
  published by the Free Software Foundation; either version 2 of
+
|License verified date=2020-03-30
  the License, or (at your option) any later version.
+
|License note=GPLv2orlater or Ruby
 
 
  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 package; if not, write to the Free Software
 
  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
 
  02110-1301 USA
 
 
 
  On Debian systems, the full text of the GNU General Public
 
  License version 2 can be found in the file `/usr/share/common-
 
  licenses/GPL-2'.
 
 
 
Ruby:
 
 
 
  BioRuby is copyrighted free software by Toshiaki Katayama
 
  <k@bioruby.org>. You can redistribute it and/or modify it under
 
  either the terms of the GPL version 2 (see the file GPL), or the
 
  conditions below:
 
 
 
  1. You may make and give away verbatim copies of the source form
 
  of the      software without restriction, provided that you
 
  duplicate all of the      original copyright notices and
 
  associated disclaimers.
 
 
 
  2. You may modify your copy of the software in any way, provided
 
  that      you do at least ONE of the following:
 
 
 
  a) place your modifications in the Public Domain or otherwise
 
  make them Freely Available, such as by posting said
 
  modifications to Usenet or an equivalent medium, or by allowing
 
  the author to include your modifications in the software.
 
 
 
  b) use the modified software only within your corporation or
 
  organization.
 
 
 
  c) give non-standard binaries non-standard names, with
 
  instructions on where to get the original software distribution.
 
 
 
  d) make other distribution arrangements with the author.
 
 
 
  3. You may distribute the software in object code or binary form,
 
  provided that you do at least ONE of the following:
 
 
 
  a) distribute the binaries and library files of the software,
 
  together with instructions (in the manual page or equivalent)
 
  on where to get the original distribution.
 
 
 
  b) accompany the distribution with the machine-readable source of
 
  the software.
 
 
 
  c) give non-standard binaries non-standard names, with
 
  instructions on where to get the original software distribution.
 
 
 
  d) make other distribution arrangements with the author.
 
 
 
  4. You may modify and include the part of the software into any
 
  other      software (possibly commercial).  But some files in the
 
  distribution      are not written by the author, so that they are
 
  not under these terms.
 
 
 
  For the list of those files and their copying conditions, see the
 
  file LEGAL.
 
 
 
  5. The scripts and library files supplied as input to or produced
 
  as      output from the software do not automatically fall under
 
  the      copyright of the software, but belong to whomever
 
  generated them,      and may be sold commercially, and may be
 
  aggregated with this      software.
 
 
 
  6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
 
  IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
 
  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 
  PURPOSE.
 
 
}}
 
}}
 
{{Resource
 
{{Resource
Line 414: Line 166:
 
|Programming-language=ruby
 
|Programming-language=ruby
 
|Runs-on=GNU/Linux
 
|Runs-on=GNU/Linux
 +
|Use=fighting-coronavirus
 
}}
 
}}
 
{{Featured}}
 
{{Featured}}

Latest revision as of 14:58, 17 April 2020

[edit]

BioRuby

http://bioruby.org/
Bioinformatics library for Ruby.

BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.

Documentation

http://bioruby.org/rdoc/

"IRC general" IRC general channel
irc://irc.freenode.org#bioruby

Related Projects





Licensing

License

Verified by

Verified on

Notes

License

GPLv2

Verified by

Debian

Verified on

20 March 2013

Notes

GPLv2 or Ruby

License

Ruby

Verified by

Debian

Verified on

30 March 2020

Notes

GPLv2orlater or Ruby

License

Ruby

Verified by

Debian

Verified on

30 March 2020

Notes

GPLv2 or Ruby

Verified by

Debian

Verified on

20 March 2013

Verified by

Debian

Verified on

20 March 2013

License

Other

Verified by

Debian

Verified on

20 March 2013

Verified by

Debian

Verified on

20 March 2013

Notes

GPLv2orlater or Ruby




Leaders and contributors

Resources and communication

AudienceResource typeURI
Ruby (Ref)https://rubygems.org/gems/bio
Debian (Ref) (R)https://tracker.debian.org/pkg/ruby-bio
VCS Repository Webviewhttps://github.com/bioruby/bioruby/
Mailing Listhttps://lists.open-bio.org/mailman/listinfo/bioruby
Mailing Listhttps://lists.open-bio.org/mailman/listinfo/bioruby-ja


Software prerequisites

This entry (in part or in whole) was last reviewed on 30 March 2020.



Entry





Property "Submitted by" (as page type) with input value "{{{Submitted by}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.















































"Ruby (Ref)" is not in the list (General, Help, Bug Tracking, Support, Developer) of allowed values for the "Resource audience" property.


"Debian (Ref) (R)" is not in the list (General, Help, Bug Tracking, Support, Developer) of allowed values for the "Resource audience" property.











Date 2013-03-20
Source Debian import
Source link http://packages.debian.org/sid/ruby-bio

[[Category:]]



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The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.