Software

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2021-07-22
13:35
[FZJ-2021-03060] Software
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LiberTEM/LiberTEM: 0.7.1
<div class='document'> <strong>Homepage: <a href='https://libertem.github.io/LiberTEM/'>https://libertem.github.io/LiberTEM/</a><br></strong><strong>GitHub repository: <a href='https://github.com/LiberTEM/LiberTEM/'>https://github.com/LiberTEM/LiberTEM/</a><br></strong><strong>PyPI: <a href='https://pypi.org/project/libertem/'>https://pypi.org/project/libertem/</a><br></strong><p>LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets and live data streams using a modified <a class='reference external' href='https://en.wikipedia.org/wiki/MapReduce'>MapReduce programming model</a>. The current focus is <a class='reference external' href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy#Universal_detectors_(4D_STEM)'>pixelated</a> scanning transmission electron microscopy (<a class='reference external' href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy'>STEM</a>) and scanning electron beam diffraction data.</p> <p>MapReduce-like processing allows to specify an algorithm through two functions: One function that is mapped on portions of the input data, and another function that merges (reduces) a partial result from this mapping step into the complete result [...]

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2021-07-22
13:17
[FZJ-2021-03059] Software
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LiberTEM/LiberTEM: 0.7.0
<div class='document'> <strong>Homepage: <a href='https://libertem.github.io/LiberTEM/'>https://libertem.github.io/LiberTEM/</a><br></strong><strong>GitHub repository: <a href='https://github.com/LiberTEM/LiberTEM/'>https://github.com/LiberTEM/LiberTEM/</a><br></strong><strong>PyPI: <a href='https://pypi.org/project/libertem/'>https://pypi.org/project/libertem/</a><br></strong><p>LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets and live data streams using a modified <a class='reference external' href='https://en.wikipedia.org/wiki/MapReduce'>MapReduce programming model</a>. The current focus is <a class='reference external' href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy#Universal_detectors_(4D_STEM)'>pixelated</a> scanning transmission electron microscopy (<a class='reference external' href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy'>STEM</a>) and scanning electron beam diffraction data.</p> <p>MapReduce-like processing allows to specify an algorithm through two functions: One function that is mapped on portions of the input data, and another function that merges (reduces) a partial result from this mapping step into the complete result [...]

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2021-07-22
12:06
[FZJ-2021-03058] Software
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LiberTEM/LiberTEM: 0.6.0
<p><strong>Homepage: <a href='https://libertem.github.io/LiberTEM/'>https://libertem.github.io/LiberTEM/</a></strong><br> <strong>GitHub repository: <a href='https://github.com/LiberTEM/LiberTEM/'>https://github.com/LiberTEM/LiberTEM/</a></strong><br> <strong>PyPI: <a href='https://pypi.org/project/libertem/'>https://pypi.org/project/libertem/</a></strong></p> <p>LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets using a simplified <a href='https://en.wikipedia.org/wiki/MapReduce'>MapReduce programming model</a>. The current focus is <a href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy#Universal_detectors_(4D_STEM)'>pixelated</a> scanning transmission electron microscopy (<a href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy'>STEM</a>) and scanning electron beam diffraction data.</p> <p>It is <a href='https://libertem.github.io/LiberTEM/architecture.html'>designed for high throughput and scalability</a> on PCs, single server nodes, clusters and cloud services [...]

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2021-07-02
07:48
[FZJ-2021-02823] Software
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LiberTEM/LiberTEM-live: 0.1.0
<div class='document'> <strong>Homepage: <a href='https://libertem.github.io/LiberTEM-live'>https://libertem.github.io/LiberTEM-live</a><br></strong><strong>GitHub repository: <a href='https://github.com/LiberTEM/LiberTEM-live'>https://github.com/LiberTEM/LiberTEM-live</a><br></strong><strong>PyPI: <a href='https://pypi.org/project/libertem-live/'>https://pypi.org/project/libertem-live/</a><br></strong><p>LiberTEM-live is an extension module for <a class='reference external' href='https://libertem.github.io/LiberTEM/'>LiberTEM</a> that allows live data processing.</p> <div class='admonition note'> <p class='first admonition-title'>Note</p> <p>LiberTEM-live is still experimental and under active development, including the overall architecture. New releases can include changes that break backwards compatibility until the code and architecture are proven in practical application and stabilized sufficiently.</p> <p class='last'>That being said, we encourage early experimental use, are happy to support real-world application and appreciate feedback! You can contact us by <a class='reference external' href='https://github.com/LiberTEM/LiberTEM-live/issues'>creating or commenting on an Issue on GitHub</a> or in the <a class='reference external' href='https://gitter.im/LiberTEM/Lobby'>LiberTEM Gitter chat</a>.</p> </div> <p>LiberTEM <a class='reference external' href='https://libertem.github.io/LiberTEM/udf.html'>user-defined functions (UDFs)</a> are designed to work without modification on both offline data and live data streams [...]

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2021-07-02
07:43
[FZJ-2021-02822] Software
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Ptychography 4.0: 0.1.0
<div class='document'> <strong>Homepage: <a href='https://ptychography-4-0.github.io/ptychography/'>https://ptychography-4-0.github.io/ptychography/</a><br></strong><strong>GitHub repository: <a href='https://github.com/Ptychography-4-0/ptychography/'>https://github.com/Ptychography-4-0/ptychography/</a><br></strong><strong>PyPI: <a href='https://pypi.org/project/ptychography40/'>https://pypi.org/project/ptychography40/</a><br></strong><div class='admonition note'> <p class='first admonition-title'>Note</p> <p class='last'>The Ptychography 4.0 repository and documentation are currently under construction.</p> </div> <p>This repository collects implementations for ptychography that result from the work of the <a class='reference external' href='https://ptychography.helmholtz-muenchen.de/'>Ptychography 4.0 project</a>.</p> <div class='section'> <p><strong>Installation</strong></p><p>The short version:</p> <pre class='code shell literal-block'>$ virtualenv -p python3.8 ~/ptychography-venv/ $ <span class='name builtin'>source</span> ~/ptychography-venv/bin/activate <span class='operator'>(</span>ptychography-venv<span class='operator'>)</span> $ git clone https://github.com/Ptychography-4-0/ptychography <span class='operator'>(</span>ptychography-venv<span class='operator'>)</span> $ <span class='name builtin'>cd</span> ptychography <span class='operator'>(</span>ptychography-venv<span class='operator'>)</span> $ python -m pip install -e . </pre> <p>Please see <a class='reference external' href='https://ptychography-4-0.github.io/ptychography/'>our documentation</a> for details!</p> </div> <div class='section'> <p><strong>Applications</strong></p><ul class='simple'> <li>Scalable, parallel implementation of the Single Side Band method that is suitable for live data processing.</li> </ul> <p>Please see <a class='reference external' href='https://ptychography-4-0.github.io/ptychography/algorithms.html'>the algorithms section</a> of our documentation for details!</p> <p>Ptychography 4.0 is evolving rapidly and prioritizes features following user demand and contributions [...]

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2021-06-28
11:22
[FZJ-2021-02728] Software
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Code and data for:Keup et al. (2021) Transient Chaotic Dimensionality Expansion by Recurrent Networks. PRX 11, 021064
Simulation data, python code and figures used in the publicationKeup, Kühn, Dahmen, Helias (2021) Transient chaotic dimensionality expansion by recurrent networks. Physical Review X 11, 021064, doi: 10.1103/PhysRevX.11.021064.Please see README.md for a detailed description and execution instructions..
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2021-06-11
15:54
[FZJ-2021-02602] Software
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ODE-toolbox 2.3
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2021-06-11
15:43
[FZJ-2021-02601] Software
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NESTML 4.0
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2021-02-17
15:39
[FZJ-2021-01074] Software
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Arbor Library v0.5
()
<p>Since v0.4 there have been some major features, and many small fixes and improvements.</p> <p>Core API features:</p> <ul> <li>[C++/Python] Numerous small bug fixes, optimizations and improvements.</li> <li>[C++/Python] Refactor cable cell interface to be read only, and be constructed from<br> descriptions of morphology, labels, and decorations.</li> <li>[C++/Python]Expose diverse probes and rich interface for describing where and<br> what to sample on cable cells.</li> <li>[C++/Python] Support for querying names in mechanism catalogues</li> <li>[Python] Wrapper for existing C++ <code>pw_lin</code> functionality</li> <li>[C++] Improved validation of recipe definitions during model building</li> </ul> <p>Documentation:</p> <ul> <li>Added new Python examples</li> <li>Many small fixes for links, spelling, grammar and clarity.</li> <li>Add extensive guide for contributions and coding polices.</li> </ul> <p>Build:</p> <ul> <li>Allow CMake configuration to use system copies of C++ dependencies<br> (nlohmann/json and pybind11), and makes this the default option.</li> <li>Added GitHub Actions support for automated testing of a wider range of tests<br> and features than are run on our Travis CI (which will be removed soon)</li> <li>More robust Python detection and consistent use of the same Python<br> interpreter in CMake configure and build steps.</li> </ul> <p>Contributions by, in no specific order, <a href='https://github.com/brenthuisman'>@brenthuisman</a>, <a href='https://github.com/noraabiakar'>@noraabiakar</a>,<br> <a href='https://github.com/thorstenhater'>@thorstenhater</a>, <a href='https://github.com/halfflat'>@halfflat</a>, <a href='https://github.com/schmitts'>@schmitts</a> and <a href='https://github.com/bcumming'>@bcumming</a></p> <p>Since v0.3, the following changes can be reported:</p> <p>Library</p> <ul> <li>Moved from C++14 to C++17 <ul> <li>Removed our hand-rolled versions of <code>any</code>, <code>optional</code> and <code>variant</code>.</li> </ul> </li> <li>Added <code>std::expected</code> equivalent for error handling.</li> </ul> <p>Features</p> <ul> <li>Added mechanism catalogues with mechanisms used by Allen and BBP models.</li> <li>Removed support for spherical segments at the root of cable morphologies, and<br> replaced the sample-based representation with a segment-based representation: <ul> <li>Morphologies are defined in terms of two-point segments.</li> <li>Gaps are allowed between segments anywhere in a morphology.</li> </ul> </li> <li>Exposed the current <code>time</code> inside mechanisms.</li> <li>Added support for NeuroML2 morphology descriptions.</li> <li>Added a "stitch" morphology builder for constructing morphologies with<br> cable sections that can connect to any location on their parent cable.</li> <li>Replaced recipe probe API with more flexible API that allows for sampling<br> not only voltages at single locations, but currents, ion species properties,<br> and mechanism state variables at single locations or across an entire cell.</li> <li>Added support for querying probe metadata from the simulation object.</li> <li>Added new &#39;place_pwlin&#39; C++ API for cell geometry queries.</li> <li>Added support for loading Allen SDK cell model morphologies from SWC.</li> <li>Added support for composing policies for creating compartments over sub-regions.</li> </ul> <p>Documentation</p> <ul> <li>Restructured documentation to have cleaner separation between high level descriptions<br> of concepts and the C++ and Python APIs.</li> <li>Added high level documentation for morphology descriptions, labels and cable cell<br> construction.</li> </ul> <p>Optimizations</p> <ul> <li>Implemented memory optimizations for GPU matrix solver.</li> <li>Added support for ARM SVE intrinsics in the vectorized CPU back end.</li> </ul> <p>Bug Fixes</p> <ul> <li>Fixed various modcc code generation errors.</li> </ul> <p>Since v0.2, the following changes can be reported:</p> <ul> <li>Python wrapper with pip installation.</li> <li>Replace the morphology specification API for more flexible cell building.</li> <li>Flat descriptions of ion channel distribution and synapse placement.</li> <li>Multi-compartment back end support for sub-branch mechanism distributions.</li> <li>Improved NMODL support: <ul> <li>nonlinear kinetic schemes</li> <li>linear system solution in initial conditions</li> <li>many small features and bug fixes</li> </ul> </li> <li>Generic ion species.</li> <li>Many optimizations and bug fixes.</li> </ul>
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2021-01-14
21:15

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