Added entry 10_5281_zenodo.3538217

gdetor · gdetor · commit beb0c0148c40 · 2019-11-13T12:09:16.000-08:00
diff --git a/10_5281_zenodo.3538217/article.bib b/10_5281_zenodo.3538217/article.bib
@@ -0,0 +1,180 @@
+@misc{markdown,
+    author    = "John Gruber and Aaron Swartz",
+    title     = "The Markdown format",
+    year      = "2004",
+    url       = "http://daringfireball.net/projects/markdown/syntax"
+}
+
+@article{Artola1990,
+author = {Artola, Alain and Br{\"{o}}cher, Susanne and Singer, Wolf},
+doi = {10.1038/347069a0},
+journal = {Nature},
+pages = {69–72},
+title = {Different voltage-dependent thresholds for inducing long-term depression and long-term potentiation in slices of rat visual cortex},
+url = {http://dx.doi.org/10.1038/347069a0},
+volume = {347},
+year = {1990}
+}
+
+@article{Brette2005,
+author = {Brette, Romain and Gerstner, Wulfram},
+title = {Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activity},
+journal = {Journal of Neurophysiology},
+volume = {94},
+number = {5},
+pages = {3637-3642},
+year = {2005},
+doi = {10.1152/jn.00686.2005},
+note ={PMID: 16014787},
+URL = { https://doi.org/10.1152/jn.00686.2005},
+eprint = {https://doi.org/10.1152/jn.00686.2005}
+}
+@article{Clopath2010,
+author = {Clopath, Claudia and B{\"{u}}sing, Lars and Vasilaki, Eleni and Gerstner, Wulfram},
+doi = {10.1038/nn.2479},
+isbn = {1546-1726 (Electronic){\$}\backslash{\$}n1097-6256 (Linking)},
+issn = {1097-6256},
+journal = {Nature Neuroscience},
+number = {3},
+pages = {344--352},
+pmid = {20098420},
+title = {{Connectivity reflects coding: a model of voltage-based STDP with homeostasis}},
+url = {http://www.nature.com/doifinder/10.1038/nn.2479},
+volume = {13},
+year = {2010}
+}
+
+@Article{Brette2007,
+author="Brette, Romain
+and Rudolph, Michelle
+and Carnevale, Ted
+and Hines, Michael
+and Beeman, David
+and Bower, James M.
+and Diesmann, Markus
+and Morrison, Abigail
+and Goodman, Philip H.
+and Harris, Frederick C.
+and Zirpe, Milind
+and Natschl{\"a}ger, Thomas
+and Pecevski, Dejan
+and Ermentrout, Bard
+and Djurfeldt, Mikael
+and Lansner, Anders
+and Rochel, Olivier
+and Vieville, Thierry
+and Muller, Eilif
+and Davison, Andrew P.
+and El Boustani, Sami
+and Destexhe, Alain",
+title="Simulation of networks of spiking neurons: A review of tools and strategies",
+journal="Journal of Computational Neuroscience",
+year="2007",
+month="Dec",
+day="01",
+volume="23",
+number="3",
+pages="349--398",
+issn="1573-6873",
+doi="10.1007/s10827-007-0038-6",
+url="https://doi.org/10.1007/s10827-007-0038-6"
+}
+
+@article{Bi1998,
+	author = {Bi, Guo-Qiang and Poo, Mu-Ming},
+	title = {Synaptic Modifications in Cultured Hippocampal Neurons: Dependence on Spike Timing, Synaptic Strength, and Postsynaptic Cell Type},
+	volume = {18},
+	number = {24},
+	pages = {10464--10472},
+	year = {1998},
+	publisher = {Society for Neuroscience},
+	abstract = {In cultures of dissociated rat hippocampal neurons, persistent potentiation and depression of glutamatergic synapses were induced by correlated spiking of presynaptic and postsynaptic neurons. The relative timing between the presynaptic and postsynaptic spiking determined the direction and the extent of synaptic changes. Repetitive postsynaptic spiking within a time window of 20 msec after presynaptic activation resulted in long-term potentiation (LTP), whereas postsynaptic spiking within a window of 20 msec before the repetitive presynaptic activation led to long-term depression (LTD). Significant LTP occurred only at synapses with relatively low initial strength, whereas the extent of LTD did not show obvious dependence on the initial synaptic strength. Both LTP and LTD depended on the activation of NMDA receptors and were absent in cases in which the postsynaptic neurons were GABAergic in nature. Blockade of L-type calcium channels with nimodipine abolished the induction of LTD and reduced the extent of LTP. These results underscore the importance of precise spike timing, synaptic strength, and postsynaptic cell type in the activity-induced modification of central synapses and suggest that Hebb{\textquoteright}s rule may need to incorporate a quantitative consideration of spike timing that reflects the narrow and asymmetric window for the induction of synaptic modification.},
+	issn = {0270-6474},
+	URL = {http://www.jneurosci.org/content/18/24/10464},
+	eprint = {http://www.jneurosci.org/content/18/24/10464.full.pdf},
+	journal = {Journal of Neuroscience}
+}
+
+@article {Ngezahayo2000,
+	author = {Ngezahayo, Anaclet and Schachner, Melitta and Artola, Alain},
+	title = {Synaptic Activity Modulates the Induction of Bidirectional Synaptic Changes in Adult Mouse Hippocampus},
+	volume = {20},
+	number = {7},
+	pages = {2451--2458},
+	year = {2000},
+	doi = {10.1523/JNEUROSCI.20-07-02451.2000},
+	publisher = {Society for Neuroscience},
+	abstract = {Activity-dependent synaptic plasticity is critical for learning and memory. Considerable attention has been paid to mechanisms that increase or decrease synaptic efficacy, referred to as long-term potentiation (LTP) and long-term depression (LTD), respectively. It is becoming apparent that synaptic activity also modulates the ability to elicit subsequent synaptic changes. We provide direct experimental evidence that this modulation is attributable, at least in part, to variations in the level of postsynaptic depolarization required for inducing plasticity. In slices from adult hippocampal CA1, a brief pairing protocol known to produce LTP can also induce LTD. The voltage{\textendash}response function for the induction of LTD and LTP in naive synapses exhibits three parts: at a postsynaptic membrane potential during pairing (Vm) <= -40 mV, no synaptic modification is obtained; at Vmbetween -40 and -20 mV, LTD is induced; and, finally, atVm \&gt; -20 mV, LTP is generated. This function varies with initial synaptic efficacy. In depressed synapses, Θ-, the Vm above which LTD is generated, is shifted toward more depolarizedVms and Θ+, the LTD{\textendash}LTP crossover point or, equivalently, the Vmabove which LTP is induced, toward more polarizedVms. Conversely in potentiated synapses, Θ- is shifted toward more polarizedVms. Therefore synaptic activity changes synaptic efficacy and accordingly adjusts the voltages for eliciting subsequent synaptic modifications. The concomitant shifts in the voltages for inducing LTD and LTP in opposite directions promote synaptic potentiation and inhibit synaptic depression in depressed synapses and vice versa in potentiated synapses.},
+	issn = {0270-6474},
+	URL = {http://www.jneurosci.org/content/20/7/2451},
+	eprint = {http://www.jneurosci.org/content/20/7/2451.full.pdf},
+	journal = {Journal of Neuroscience}
+}
+
+@article {Nevian2006,
+    author = {Nevian, Thomas and Sakmann, Bert},
+    title = {Spine Ca2+ Signaling in Spike-Timing-Dependent Plasticity},
+    volume = {26},
+    number = {43},
+    pages = {11001--11013},
+    year = {2006},
+    doi = {10.1523/JNEUROSCI.1749-06.2006},
+    publisher = {Society for Neuroscience},
+    journal = {Journal of Neuroscience}
+}
+@article {Olshausen1996,
+    author = {Olshausen, Bruno A., and Field, David J.},
+    title = {Emergence of simple-cell receptive field properties by learning a sparse code for natural images},
+    journal = {Nature},
+    year = {1996},
+    number ={6},
+    volume ={381},
+    pages ={607--609},
+    doi ={10.1038/381607a0}
+}
+
+@article{Pfister2006,
+title = {Beyond Pair-Based STDP: a Phenomenological Rule for Spike Triplet and Frequency Effects},
+author = {Jean-Pascal Pfister and Gerstner, Wulfram},
+booktitle = {Advances in Neural Information Processing Systems 18},
+editor = {Y. Weiss and B. Sch\"{o}lkopf and J. C. Platt},
+pages = {1081--1088},
+year = {2006},
+publisher = {MIT Press},
+url = {http://papers.nips.cc/paper/2923-beyond-pair-based-stdp-a-phenomenological-rule-for-spike-triplet-and-frequency-effects.pdf}
+}
+@ARTICLE{Vitay2015,
+AUTHOR={Vitay, Julien and Dinkelbach, Helge and Hamker, Fred},
+TITLE={ANNarchy: a code generation approach to neural simulations on parallel hardware},
+JOURNAL={Frontiers in Neuroinformatics},
+VOLUME={9},
+PAGES={19},
+YEAR={2015},
+URL={https://www.frontiersin.org/article/10.3389/fninf.2015.00019},
+DOI={10.3389/fninf.2015.00019},
+ISSN={1662-5196}
+}
+@article{Sjoestroem2001,
+title = "Rate, Timing, and Cooperativity Jointly Determine Cortical Synaptic Plasticity",
+journal = "Neuron",
+volume = "32",
+number = "6",
+pages = "1149 - 1164",
+year = "2001",
+issn = "0896-6273",
+doi = "https://doi.org/10.1016/S0896-6273(01)00542-6",
+url = "http://www.sciencedirect.com/science/article/pii/S0896627301005426",
+author = "Per Jesper Sjöström and Gina G Turrigiano and Sacha B Nelson"
+}
+@article{Song2001,
+title = "Cortical Development and Remapping through Spike Timing-Dependent Plasticity",
+journal = "Neuron",
+volume = "32",
+number = "2",
+pages = "339 - 350",
+year = "2001",
+issn = "0896-6273",
+doi = "https://doi.org/10.1016/S0896-6273(01)00451-2",
+url = "http://www.sciencedirect.com/science/article/pii/S0896627301004512",
+author = "Sen Song and L.F. Abbott"
+}
diff --git a/10_5281_zenodo.3538217/article.pdf b/10_5281_zenodo.3538217/article.pdf
diff --git a/10_5281_zenodo.3538217/article.yaml b/10_5281_zenodo.3538217/article.yaml
@@ -0,0 +1,112 @@
+# To be filled by the author(s) at the time of submission
+# -------------------------------------------------------
+
+# Title of the article:
+#  - For a successful replication, it shoudl be prefixed with "[Re]"
+#  - For a failed replication, it should be prefixed with "[¬Re]"
+#  - For other article types, no instruction (but please, not too long)
+title: "[Re] Connectivity reflects coding a model of voltage-based STDP with
+        homeostasis"
+
+# List of authors with name, orcid number, email and affiliation
+# Affiliation "*" means contact author
+authors:
+  - name: Rene Larisch
+    orcid:
+    email: rene.larisch@informatik.tu-chemnitz.de
+    affiliations: 1,*
+
+# List of affiliations with code (corresponding to author affiliations), name
+# and address. You can also use these affiliations to add text such as "Equal
+# contributions" as name (with no address).
+affiliations:
+  - code:    1
+    name:    Professorship for Artificial Intelligence, Department of Computer Science, Chemnitz University of Technology
+    address: D-09107 Chemnitz, Germany
+
+
+# List of keywords (adding the programming language might be a good idea)
+keywords: Spike Timing-Dependent Plasticity (STDP), Computational Neuroscience, Unsupervised Learning, Python
+
+# Code URL and DOI (url is mandatory for replication, doi after acceptance)
+# You can get a DOI for your code from Zenodo,
+#   see https://guides.github.com/activities/citable-code/
+code:
+  - url: https://github.com/rLarisch/ReScience-submission/tree/Larisch-2019/code
+  - doi:
+
+# Date URL and DOI (optional if no data)
+data:
+  - url:
+  - doi:
+
+# Information about the original article that has been replicated
+replication:
+ - cite: Connectivity reflects coding a model of voltage-based STDP with homeostasis,
+         C.Clopath, L. Buesing, E.Vasilaki and W. Gerstner, Nature Neuroscience 13.3 (2010), pp. 344-352 # Full textual citation
+ - bib:  # Bibtex key (if any) in your bibliography file
+ - url:   https://www.nature.com/articles/nn.2479 # URL to the PDF, try to link to a non-paywall version
+ - doi:  10.1038/nn.2479 # Regular digital object identifier
+
+# Don't forget to surround abstract with double quotes
+abstract: "Since the first description of spike timing-dependent plasticity (STDP), different models
+            of STDP have been published to reproduce different experimental findings.
+            Clopath et al. (2010) introduced a STDP model which is able to reproduce the experimental findings of triplet studies.
+            They implemented a homeostatic mechanism to control the level of generated LTD, based on the relationship between the average postsynaptic membrane
+potential and a reference value. With this voltage-based STDP rule thei reproduce a wide range of physiological experiments.
+We here present a reimplementation of the Clopath et al . (2010) learning rule in Python with the help of the neuro-simulator ANNarchy."
+
+# Bibliography file (yours)
+bibliography: bibliography.bib
+
+# Type of the article
+# Type can be:
+#  * Editorial
+#  * Letter
+#  * Replication
+type: Replication
+
+# Scientific domain of the article (e.g. Computational Neuroscience)
+#  (one domain only & try to be not overly specific)
+domain: Computational Neuroscience
+
+# Coding language (main one only if several)
+language: Python
+
+
+# To be filled by the author(s) after acceptance
+# -----------------------------------------------------------------------------
+
+# For example, the URL of the GitHub issue where review actually occured
+review:
+  - url: https://github.com/ReScience/ReScience-submission/pull/57#issuecomment-549728501
+
+contributors:
+  - name: Georgios Detorakis
+    orcid: 0000-0001-5891-1702 
+    role: editor
+  - name: Christian Jarvers 
+    orcid: 0000-0003-0062-9776
+    role: reviewer
+  - name: Andrew P. Davison
+    orcid: 0000-0002-4793-7541
+    role: reviewer
+
+# This information will be provided by the editor
+dates:
+  - received:  November 1, 2018
+  - accepted:  November 4, 2019
+  - published: November 12, 2019
+
+# This information will be provided by the editor
+article:
+  - number: 2
+  - doi: 10.5281/zenodo.3538217 
+  - url: https://zenodo.org/record/3538217/files/article.pdf
+
+# This information will be provided by the editor
+journal:
+  - name:   "ReScience C"
+  - issn:   2430-3658
+  - volume: 5
+  - issue:  3
