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Port details
MOOSE-neural-simulator Multiphysics Object Oriented Simulation Environment
3.1.2_2 science 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
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Dec 2017 16:04:41
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 : PortsMon
    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_2/catalog.mk
  2. /usr/local/share/licenses/MOOSE-neural-simulator-3.1.2_2/LICENSE
  3. /usr/local/share/licenses/MOOSE-neural-simulator-3.1.2_2/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.

To install the port: cd /usr/ports/science/MOOSE-neural-simulator/ && make install clean
To add the package: pkg install MOOSE-neural-simulator

PKGNAME: MOOSE-neural-simulator

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. gfortran6 : lang/gcc6
  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. gfortran6 : lang/gcc6
  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_2:
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
cmake:outsource 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=/

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 4

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