The Arbor multi-compartment neural network simulation library.
BSD-3-CLAUSE License
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Published by thorstenhater 3 months ago
example/brunel
)modcc
no longer allows internal variables (v
, celsius
, ...) as ASSIGNED
simulation::inject_events
, use a generator instead.Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.9.0...v0.10.0
Published by brenthuisman almost 2 years ago
** 2022 11 15 **
Welcome to another installment of the Arbor simulator!
In this release we add a CHANGELOG, where major new features and breaking changes will be mentioned specifically.
arbor.cable_cell
has the labels and decor arguments swapped. I.e.: (tree, labels, decor)
(tree, decor, label)
. Labels are now optional. https://github.com/arbor-sim/arbor/pull/1978
generate-catalogue
script. modcc
accepts now a list of NMODL files and is able to spit out a catalogue.cpp file. https://github.com/arbor-sim/arbor/pull/1975
t
in NMODL. https://github.com/arbor-sim/arbor/pull/1967
time
by @thorstenhater in https://github.com/arbor-sim/arbor/pull/1967
arbor_exception
by @thorstenhater in https://github.com/arbor-sim/arbor/pull/1945
mpoint
s hashable. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/1950
/ext
by @brenthuisman in https://github.com/arbor-sim/arbor/pull/1968
VERSION
except on version tag. by @brenthuisman in https://github.com/arbor-sim/arbor/pull/1931
Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.7...v0.8-rc
Published by brenthuisman over 2 years ago
create_polygon
function in lfpykit example by @espenhgn in https://github.com/arbor-sim/arbor/pull/1881
lfpykit
intersphinx mapping by @Helveg in https://github.com/arbor-sim/arbor/pull/1878
node_index
read needed for reading time t
in the mechanisms by @noraabiakar in https://github.com/arbor-sim/arbor/pull/1866
pyproject.toml
, bump Python minver to 3.7, fix macos wheel generation by @brenthuisman in https://github.com/arbor-sim/arbor/pull/1916
ubenches
compilation errors by @noraabiakar in https://github.com/arbor-sim/arbor/pull/1828
Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.6...v0.7
Published by brenthuisman over 2 years ago
Core API:
dim3
to gridDim constructor in generated mechanism code by @noraabiakar in https://github.com/arbor-sim/arbor/pull/1630
build-catalogue
by @Helveg in https://github.com/arbor-sim/arbor/pull/1686
stdout
and stderr
by @Helveg in https://github.com/arbor-sim/arbor/pull/1679
domain_decomposition
given a list of group_descriptions
. by @noraabiakar in https://github.com/arbor-sim/arbor/pull/1788
CI/build/testing:
cibuildwheel
action repo's. by @Helveg in https://github.com/arbor-sim/arbor/pull/1703
make VERBOSE=1
in verbose mode by @Helveg in https://github.com/arbor-sim/arbor/pull/1715
Documentation:
arbor.mechanism_catalogue.extend()
documentation added. by @brenthuisman in https://github.com/arbor-sim/arbor/pull/1597
config()
flags by @Helveg in https://github.com/arbor-sim/arbor/pull/1708
nernst
application rules to the docs. by @noraabiakar in https://github.com/arbor-sim/arbor/pull/1638
get_probes
to probes
by @Helveg in https://github.com/arbor-sim/arbor/pull/1763
probe_sample.rst
by @Helveg in https://github.com/arbor-sim/arbor/pull/1761
Fixes/optimization:
-fvisibility=hidden
by @noraabiakar in https://github.com/arbor-sim/arbor/pull/1599
setup.py
by @Helveg in https://github.com/arbor-sim/arbor/pull/1672
peer_index
and v_peer
by @noraabiakar in https://github.com/arbor-sim/arbor/pull/1735
Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.5.2...v0.6
Published by brenthuisman over 3 years ago
This release fixes an error in the CI generated Python wheels, which are as of this release available on PyPI. Other than those fixes, this release is identical to v0.5.1.
Published by bcumming over 3 years ago
Since v0.5 there have been some major features, and many small fixes and improvements.
Core API features:
Documentation:
Build / CI:
Contributions by, in no specific order, @haampie, @clinssen, @espenhgn, @Helveg, @brenthuisman, @noraabiakar,
@thorstenhater, @halfflat, @schmitts and @bcumming
Published by bcumming almost 4 years ago
Since v0.4 there have been some major features, and many small fixes and improvements.
Core API features:
pw_lin
functionalityDocumentation:
Build:
Contributions by, in no specific order, @brenthuisman, @noraabiakar,
@thorstenhater, @halfflat, @schmitts and @bcumming
Published by bcumming about 4 years ago
any
, optional
and variant
.std::expected
equivalent for error handling.time
inside mechanisms.Published by bcumming over 4 years ago
Arbor library version 0.3, tagged as v0.3
Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.
An installation guide and library documentation are available online at Read the Docs.
Submit a ticket if you have any questions or want help.
Changes since v0.2:
Published by bcumming about 5 years ago
Arbor library version 0.2.1, tagged as v0.2.1
Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.
An installation guide and library documentation are available online at Read the Docs.
Submit a ticket if you have any questions or want help.
Minor Update.
Published by bcumming over 5 years ago
Arbor library version 0.2, tagged as v0.2
Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.
An installation guide and library documentation are available online at Read the Docs.
Submit a ticket if you have any questions or want help.
Some key features include:
Changes since v0.1:
libarborenv
is now installed with usefullibarborenv
. See #659 and #654.Nora Abi Akar
John Biddiscombe
Benjamin Cumming
Felix Huber
Marko Kabic
Vasileios Karakasis
Wouter Klijn
Anne Küsters
Alexander Peyser
Stuart Yates
Nora Abi Akar, John Biddiscombe, Benjamin Cumming, Felix Huber, Marko Kabic, Vasileios Karakasis, Wouter Klijn, Anne Küsters, Alexander Peyser, Stuart Yates. (2019, March 4). arbor-sim/arbor: Arbor Library v0.2 (Version v0.2). Zenodo. http://doi.org/10.5281/zenodo.2583709
Published by apeyser about 6 years ago
Arbor library version 0.1, tagged as v0.1
Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.
An installation guide and library documentation are available online at Read the Docs.
Submit a ticket if you have any questions or want help.
Some key features include:
* Optimized back ends for CUDA, KNL and AVX2 intrinsics.
* Asynchronous spike exchange that overlaps compute and communication.
* Efficient sampling of voltage and current on all back ends.
* Efficient implementation of all features on GPU.
* Reporting of memory and energy consumption (when available on platform).
* An API for addition of new cell types, e.g. LIF and Poisson spike generators.
* Validation tests against numeric/analytic models and NEURON.
Nora Abi Akar
John Biddiscombe
Benjamin Cumming
Marko Kabic
Vasileios Karakasis
Wouter Klijn
Anne Küsters
Ivan Martinez
Alexander Peyser
Stuart Yates
If you use this version of Arbor, please cite it as Nora Abi Akar, John Biddiscombe, Benjamin Cumming, Marko Kabic, Vasileios Karakasis, Wouter Klijn, Anne Küsters, Ivan Martinez, Alexander Peyser, Stuart Yates. (2018, October 12). arbor-sim/arbor: Version 0.1: First release (Version v0.1). Zenodo. http://doi.org/10.5281/zenodo.1459679. The full citation is available in different formats on Zenodo.