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Port details
MOOSE-neural-simulator Multiphysics Object Oriented Simulation Environment
3.1.2_7 science Deleted on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
3.1.2Version of this port present on the latest quarterly branch.
Deprecated DEPRECATED: Qt4 has been EOL since december 2015
Expired This port expired on: 2019-03-15
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-12-19 16:04:41
Last Update: 2019-03-16 21:55:51
SVN Revision: 495967
Also Listed In: biology
License: GPLv3
MOOSE is designed to simulate neural systems ranging from biochemical signaling
to complex models of single neurons, circuits, and large networks. A typical
use case is to model neural activity-driven synaptic plasticity, in which
network activity to synapses triggers biochemical reaction-diffusion events,
which in turn modulate ion channels to give rise to synaptic plasticity.
MOOSE can operate at many levels of detail, from stochastic chemical
computations, to multicompartment single-neuron models, to spiking neuron
network models.

WWW: http://moose.ncbs.res.in
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (207 items)
  1. /usr/local/share/licenses/MOOSE-neural-simulator-3.1.2_7/catalog.mk
  2. /usr/local/share/licenses/MOOSE-neural-simulator-3.1.2_7/LICENSE
  3. /usr/local/share/licenses/MOOSE-neural-simulator-3.1.2_7/GPLv3
  4. bin/moosegui
  5. lib/moose/gui/.travis.yml
  6. lib/moose/gui/MdiArea.py
  7. lib/moose/gui/PlotWidgetContainer.py
  8. lib/moose/gui/README
  9. lib/moose/gui/README.md
  10. lib/moose/gui/RunWidget.py
  11. lib/moose/gui/SettingsDialog.py
  12. lib/moose/gui/__init__.py
  13. lib/moose/gui/about.html
  14. lib/moose/gui/bioModels/getAllCuratedModelsId.pkl
  15. lib/moose/gui/bioModels/getModelsIdByChEBI.pkl
  16. lib/moose/gui/bioModels/getModelsIdByChEBIId.pkl
  17. lib/moose/gui/biomodelsclient.py
  18. lib/moose/gui/checkcombobox.py
  19. lib/moose/gui/colormaps/fire
  20. lib/moose/gui/colormaps/greenfire
  21. lib/moose/gui/colormaps/grey
  22. lib/moose/gui/colormaps/heat
  23. lib/moose/gui/colormaps/jet
  24. lib/moose/gui/colormaps/rainbow2.pkl
  25. lib/moose/gui/colormaps/redhot
  26. lib/moose/gui/config.py
  27. lib/moose/gui/configwidget.py
  28. lib/moose/gui/defaults.py
  29. lib/moose/gui/global_constants.py
  30. lib/moose/gui/icons/QMdiBackground.png
  31. lib/moose/gui/icons/add.png
  32. lib/moose/gui/icons/add_graph.png
  33. lib/moose/gui/icons/arrow.png
  34. lib/moose/gui/icons/arrow_undo.png
  35. lib/moose/gui/icons/classIcon/BufPool.png
  36. lib/moose/gui/icons/classIcon/CubeMesh.png
  37. lib/moose/gui/icons/classIcon/CylMesh.png
  38. lib/moose/gui/icons/classIcon/Enz.png
  39. lib/moose/gui/icons/classIcon/FuncPool.png
  40. lib/moose/gui/icons/classIcon/Function.png
  41. lib/moose/gui/icons/classIcon/MMenz.png
  42. lib/moose/gui/icons/classIcon/Pool.png
  43. lib/moose/gui/icons/classIcon/Reac.png
  44. lib/moose/gui/icons/classIcon/StimulusTable.png
  45. lib/moose/gui/icons/classIcon/SumFunc.png
  46. lib/moose/gui/icons/clone.svg
  47. lib/moose/gui/icons/connection.png
  48. lib/moose/gui/icons/continue.png
  49. lib/moose/gui/icons/delete.svg
  50. lib/moose/gui/icons/delete_graph.png
  51. lib/moose/gui/icons/grid.png
  52. lib/moose/gui/icons/hand.png
  53. lib/moose/gui/icons/help.png
  54. lib/moose/gui/icons/hopfield.png
  55. lib/moose/gui/icons/list.png
  56. lib/moose/gui/icons/moose_icon.png
  57. lib/moose/gui/icons/moose_icon_64x64.png
  58. lib/moose/gui/icons/moose_icon_large.png
  59. lib/moose/gui/icons/move.svg
  60. lib/moose/gui/icons/plot.svg
  61. lib/moose/gui/icons/reset.png
  62. lib/moose/gui/icons/run.png
  63. lib/moose/gui/icons/runtime.png
  64. lib/moose/gui/icons/squid.png
  65. lib/moose/gui/icons/stop.png
  66. lib/moose/gui/icons/straight_connector_with_filled_circles.png
  67. lib/moose/gui/icons/wrench.png
  68. lib/moose/gui/loaderdialog.py
  69. lib/moose/gui/mexception.py
  70. lib/moose/gui/mgui.py
  71. lib/moose/gui/mload.py
  72. lib/moose/gui/mplot.py
  73. lib/moose/gui/mplugin.py
  74. lib/moose/gui/msearch.py
  75. lib/moose/gui/mtoolbutton.py
  76. lib/moose/gui/mtree.py
  77. lib/moose/gui/mtypes.py
  78. lib/moose/gui/neuroextractor.py
  79. lib/moose/gui/newmodeldialog.py
  80. lib/moose/gui/objectedit.py
  81. lib/moose/gui/plugins/NeuroKit.py
  82. lib/moose/gui/plugins/NeuroKitEditor.py
  83. lib/moose/gui/plugins/NeuroKitRunner.py
  84. lib/moose/gui/plugins/NeuroKitVisualizer.py
  85. lib/moose/gui/plugins/PreferencesPresenter.py
  86. lib/moose/gui/plugins/PreferencesView.py
  87. lib/moose/gui/plugins/README
  88. lib/moose/gui/plugins/Runner.py
  89. lib/moose/gui/plugins/__init__.py
  90. lib/moose/gui/plugins/buildkkit.py
  91. lib/moose/gui/plugins/constants.py
  92. lib/moose/gui/plugins/datastore/preferences.json
  93. lib/moose/gui/plugins/default.py
  94. lib/moose/gui/plugins/defines.py
  95. lib/moose/gui/plugins/kkit.py
  96. lib/moose/gui/plugins/kkitCalcArrow.py
  97. lib/moose/gui/plugins/kkitOrdinateUtil.py
  98. lib/moose/gui/plugins/kkitQGraphics.py
  99. lib/moose/gui/plugins/kkitUtil.py
  100. lib/moose/gui/plugins/kkitViewcontrol.py
  101. lib/moose/gui/plugins/list.txt
  102. lib/moose/gui/plugins/modelBuild.py
  103. lib/moose/gui/plugins/setsolver.py
  104. lib/moose/gui/plugins/test_plotwidget.py
  105. lib/moose/gui/scishell.py
  106. lib/moose/gui/shell.py
  107. lib/moose/gui/sidebar.py
  108. lib/moose/gui/suds/__init__.py
  109. lib/moose/gui/suds/argparser.py
  110. lib/moose/gui/suds/bindings/__init__.py
  111. lib/moose/gui/suds/bindings/binding.py
  112. lib/moose/gui/suds/bindings/document.py
  113. lib/moose/gui/suds/bindings/multiref.py
  114. lib/moose/gui/suds/bindings/rpc.py
  115. lib/moose/gui/suds/builder.py
  116. lib/moose/gui/suds/cache.py
  117. lib/moose/gui/suds/client.py
  118. lib/moose/gui/suds/metrics.py
  119. lib/moose/gui/suds/mx/__init__.py
  120. lib/moose/gui/suds/mx/appender.py
  121. lib/moose/gui/suds/mx/basic.py
  122. lib/moose/gui/suds/mx/core.py
  123. lib/moose/gui/suds/mx/encoded.py
  124. lib/moose/gui/suds/mx/literal.py
  125. lib/moose/gui/suds/mx/typer.py
  126. lib/moose/gui/suds/options.py
  127. lib/moose/gui/suds/plugin.py
  128. lib/moose/gui/suds/properties.py
  129. lib/moose/gui/suds/reader.py
  130. lib/moose/gui/suds/resolver.py
  131. lib/moose/gui/suds/sax/__init__.py
  132. lib/moose/gui/suds/sax/attribute.py
  133. lib/moose/gui/suds/sax/date.py
  134. lib/moose/gui/suds/sax/document.py
  135. lib/moose/gui/suds/sax/element.py
  136. lib/moose/gui/suds/sax/enc.py
  137. lib/moose/gui/suds/sax/parser.py
  138. lib/moose/gui/suds/sax/text.py
  139. lib/moose/gui/suds/servicedefinition.py
  140. lib/moose/gui/suds/serviceproxy.py
  141. lib/moose/gui/suds/soaparray.py
  142. lib/moose/gui/suds/store.py
  143. lib/moose/gui/suds/sudsobject.py
  144. lib/moose/gui/suds/transport/__init__.py
  145. lib/moose/gui/suds/transport/http.py
  146. lib/moose/gui/suds/transport/https.py
  147. lib/moose/gui/suds/transport/options.py
  148. lib/moose/gui/suds/umx/__init__.py
  149. lib/moose/gui/suds/umx/attrlist.py
  150. lib/moose/gui/suds/umx/basic.py
  151. lib/moose/gui/suds/umx/core.py
  152. lib/moose/gui/suds/umx/encoded.py
  153. lib/moose/gui/suds/umx/typed.py
  154. lib/moose/gui/suds/version.py
  155. lib/moose/gui/suds/wsdl.py
  156. lib/moose/gui/suds/wsse.py
  157. lib/moose/gui/suds/xsd/__init__.py
  158. lib/moose/gui/suds/xsd/deplist.py
  159. lib/moose/gui/suds/xsd/doctor.py
  160. lib/moose/gui/suds/xsd/query.py
  161. lib/moose/gui/suds/xsd/schema.py
  162. lib/moose/gui/suds/xsd/sxbase.py
  163. lib/moose/gui/suds/xsd/sxbasic.py
  164. lib/moose/gui/suds/xsd/sxbuiltin.py
  165. lib/moose/gui/utils.py
  166. lib/python2.7/site-packages/moose-3.2.git-py2.7.egg-info
  167. lib/python2.7/site-packages/moose/OrderedDict.py
  168. lib/python2.7/site-packages/moose/SBML/__init__.py
  169. lib/python2.7/site-packages/moose/SBML/readSBML.py
  170. lib/python2.7/site-packages/moose/SBML/validation.py
  171. lib/python2.7/site-packages/moose/SBML/writeSBML.py
  172. lib/python2.7/site-packages/moose/__init__.py
  173. lib/python2.7/site-packages/moose/_moose.so
  174. lib/python2.7/site-packages/moose/alternate.py
  175. lib/python2.7/site-packages/moose/chemMerge/__init__.py
  176. lib/python2.7/site-packages/moose/chemMerge/merge.py
  177. lib/python2.7/site-packages/moose/chemMerge/mtypes.py
  178. lib/python2.7/site-packages/moose/chemUtil/__init__.py
  179. lib/python2.7/site-packages/moose/chemUtil/add_Delete_ChemicalSolver.py
  180. lib/python2.7/site-packages/moose/chemUtil/chemConnectUtil.py
  181. lib/python2.7/site-packages/moose/chemUtil/graphUtils.py
  182. lib/python2.7/site-packages/moose/constants.py
  183. lib/python2.7/site-packages/moose/genesis/__init__.py
  184. lib/python2.7/site-packages/moose/genesis/writeKkit.py
  185. lib/python2.7/site-packages/moose/graph_utils.py
  186. lib/python2.7/site-packages/moose/graphutil.py
  187. lib/python2.7/site-packages/moose/hdfutil.py
  188. lib/python2.7/site-packages/moose/methods_utils.py
  189. lib/python2.7/site-packages/moose/moose.py
  190. lib/python2.7/site-packages/moose/moose_config.py
  191. lib/python2.7/site-packages/moose/moose_constants.py
  192. lib/python2.7/site-packages/moose/moose_test.py
  193. lib/python2.7/site-packages/moose/neuroml/ChannelML.py
  194. lib/python2.7/site-packages/moose/neuroml/MorphML.py
  195. lib/python2.7/site-packages/moose/neuroml/NetworkML.py
  196. lib/python2.7/site-packages/moose/neuroml/NeuroML.py
  197. lib/python2.7/site-packages/moose/neuroml/__init__.py
  198. lib/python2.7/site-packages/moose/neuroml/utils.py
  199. lib/python2.7/site-packages/moose/optimizer_interface.py
  200. lib/python2.7/site-packages/moose/plot_utils.py
  201. lib/python2.7/site-packages/moose/print_utils.py
  202. lib/python2.7/site-packages/moose/recording.py
  203. lib/python2.7/site-packages/moose/utils.py
  204. lib/python2.7/site-packages/rdesigneur/__init__.py
  205. lib/python2.7/site-packages/rdesigneur/rdesigneur.py
  206. lib/python2.7/site-packages/rdesigneur/rdesigneurProtos.py
  207. lib/python2.7/site-packages/rdesigneur/rmoogli.py
  208. Collapse this list.
Dependency lines:
  • MOOSE-neural-simulator>0:science/MOOSE-neural-simulator

No installation instructions: this port has been deleted.

The package name of this deleted port was:

PKGNAME: MOOSE-neural-simulator

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1513628618
SHA256 (BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz) = d338ba3b01b1569603dd5c6f12d47c576daf04323b845263ea968d2ab3bab47d
SIZE (BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz) = 20350741


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. bash : shells/bash
  2. py27-numpy>0 : math/py-numpy@py27
  3. cmake : devel/cmake
  4. gfortran8 : lang/gcc8
  5. python2.7 : lang/python27
  6. as : devel/binutils
Runtime dependencies:
  1. py27-numpy>0 : math/py-numpy@py27
  2. py27-matplotlib>=1.1.0 : math/py-matplotlib@py27
  3. py27-networkx>=1.0 : math/py-networkx@py27
  4. py27-pygraphviz>=0 : graphics/py-pygraphviz@py27
  5. py27-suds-jurko>=0.4 : net/py-suds-jurko@py27
  6. gfortran8 : lang/gcc8
  7. py27-qt4-core>=4.12.1 : devel/py-qt4-core@py27
  8. py27-qt4-gui>=4.12.1 : x11-toolkits/py-qt4-gui@py27
  9. py27-qt4-test>=4.12.1 : devel/py-qt4-test@py27
  10. python2.7 : lang/python27
Library dependencies:
  1. libgsl.so : math/gsl
  2. libhdf5.so : science/hdf5
  3. libsbml.so : biology/libsbml
  4. libsz.so : science/szip
  5. libintl.so : devel/gettext-runtime
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for MOOSE-neural-simulator-3.1.2_7:
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
cmake fortran gettext-runtime pyqt:4 python:2.7

Master Sites:
  1. https://codeload.github.com/BhallaLab/moose/tar.gz/3.1.2-382-gc93d23a?dummy=/
Port Moves
  • port deleted on 2019-03-16
    REASON: Has expired: Qt4 has been EOL since december 2015

Number of commits found: 12

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Mar 2019 21:55:51
Original commit files touched by this commit  3.1.2_7
Revision:495967
tcberner search for other commits by this committer
Qt4 deprecation: Remove Qt4 and its consumes.

2019-03-15 accessibility/qt4-accessible: Qt4 has been EOL since december 2015
2019-03-15 astro/qlandkartegt: Qt4 has been EOL since december 2015
2019-03-15 astro/stellarium-qt4: Qt4 has been EOL since december 2015
2019-03-15 astro/xglobe: Qt4 has been EOL since december 2015
2019-03-15 audio/acoustid-fingerprinter: Qt4 has been EOL since december 2015
2019-03-15 audio/cueplayer: Qt4 has been EOL since december 2015
2019-03-15 audio/esperanza: Qt4 has been EOL since december 2015
2019-03-15 audio/lastfm-desktop: Qt4 has been EOL since december 2015
2019-03-15 audio/minitunes: Qt4 has been EOL since december 2015
2019-03-15 audio/mixxx20: Qt4 has been EOL since december 2015
2019-03-15 audio/mumble: Qt4 has been EOL since december 2015
2019-03-15 audio/murmur: Qt4 has been EOL since december 2015
2019-03-15 audio/puddletag: Qt4 has been EOL since december 2015
(Only the first 15 lines of the commit message are shown above View all of this commit message)
05 Jan 2019 22:46:54
Original commit files touched by this commit  3.1.2_7
Revision:489412
sunpoet search for other commits by this committer
Update science/hdf5 to 1.10.4

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes
PR:		233070
Submitted by:	wen
25 Dec 2018 20:25:40
Original commit files touched by this commit  3.1.2_6
Revision:488341
tcberner search for other commits by this committer
Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine
12 Dec 2018 01:35:36
Original commit files touched by this commit  3.1.2_6
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
02 Dec 2018 15:41:48
Original commit files touched by this commit  3.1.2_5
Revision:486467
rene search for other commits by this committer
Mark QT4 ports/functionality for removal on 2019-03-15

While here, chase some KDE4 ports and functionality, these are scheduled for
removal on 2018-12-31. Change the default option/flavor to QT5 where applicable
or use alternative toolkits like GTK.

Submitted by:	tcberner
Reviewed by:	adridg, jhale, rene, tcberner
Approved by:	portmgr (implicit, flavor hook)
Differential Revision:	https://reviews.freebsd.org/D17741
22 Nov 2018 20:18:37
Original commit files touched by this commit  3.1.2_5
Revision:485614
tcberner search for other commits by this committer
pyqt: Change install directories for Python flavor support

* PyQt could not be installed for multiple Python versions at
  the same time, as there were conflicting files.

  This patch creates Python-version versioned directories for
  all these, and further installs binaries with a version number.

* Note, there might be some hickups for software that depends on
  on of the .so's provided by PyQt5, which might not be found
  anymore autmotically, and maybe need some LD-flaggery.

* Update PyQt5 to 5.10.1

* Mark www/py-qt5-webengine broken. It is unforuntately no longer
  compatible with the old qt5-webengine-5.9.4 we ship.

PR:		232745
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D8714
05 Sep 2018 22:05:23
Original commit files touched by this commit  3.1.2_4
Revision:479046
sunpoet search for other commits by this committer
Update science/hdf5 to 1.10.2

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes
		https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt
PR:		231009
Exp-run by:	antoine
29 Jul 2018 22:18:46
Original commit files touched by this commit  3.1.2_3
Revision:475857
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
23 Jun 2018 08:27:14
Original commit files touched by this commit  3.1.2_2
Revision:473116
tcberner search for other commits by this committer
Update math/gsl to 2.5

PR:		229067
10 Mar 2018 17:46:06
Original commit files touched by this commit  3.1.2_1
Revision:464084
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
30 Jan 2018 21:53:41
Original commit files touched by this commit  3.1.2
Revision:460443
antoine search for other commits by this committer
Fix with DEFAULT_VERSIONS=python=3.x
19 Dec 2017 16:04:34
Original commit files touched by this commit  3.1.2
Revision:456732
yuri search for other commits by this committer
New port: science/MOOSE-neural-simulator: Multiphysics Object Oriented
Simulation Environment

Multiphysics Object Oriented Simulation Environment

MOOSE-neural-simulator allows to simulate
- chemical and biochemical reactions
- networks of neurons
- neural networks

This project is commonly referred to as MOOSE, in the capitalized form.
There is another science project called MOOSE, completely unrelated to this one,
which will also be ported.
MOOSE-neural-simulator is a candidate for the future 'chemistry' category in
case it will be approved.

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13539

Number of commits found: 12

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