Merge pull request #1 from Vahidrostami/first_review

First review

README.md

@@ -1,56 +1,53 @@
 
-### ReScience submission repository
+##  [Re] Spike Synchronization and Rate Modulation Differentially Involved in Motor Cortical Function
 
-This is the submission repository for the [Re**Science** journal](https://rescience.github.io).
+**Authors:** Vahid Rostami, Junji Ito, Michael Denker, Sonja Grün
 
+**Corresponding author:** Vahid Rostami, [email protected]
 
-### How to submit an article ?
+**A reference implementation of:**
 
+Spike synchronization and rate modulation differentially involved in motor cortical function. Alexa Riehle, Sonja Grün, Markus Diesmann, and Ad Aertsen (1997) Science 278:1950-1953. DOI:10.1126/science.278.5345.1950
 
-1. Create a [github](https://github.com) account
 
-2. [Fork](https://help.github.com/articles/fork-a-repo/) the [ReScience submission](https://github.com/ReScience/ReScience-submission) repository
+In this paper we illustrate the successful reproduction of the results shown in Riehle et al (1997) using our new Python implementation of the Unitary Events (UE) method. Our implementation of the UE analysis is available in the `unitary_event_analysis` module of the the Electrophysiology Analysis Toolbox [Elephant](https://github.com/NeuralEnsemble/elephant).
 
-3. Clone this new repository into your desktop environment
+## Dependencies
 
-   ```
-   $ git clone https://github.com/YOUR-USERNAME/ReScience-submission
-   ```
+- Elephant>=0.5.0
+- neo>=0.4.0
+- quantities>=0.9.0
+- numpy>=1.6.2
+- matplotlib>=1.5.1
 
-4. Create a branch (the branch name should be author names separated with dashes)
+## Installation
+### On Ubuntu/Debian:
+- sudo apt-get install python-numpy python-matplotlib python-pip ipython
+- pip install quantities
+- pip install elephant
 
-   ```
-   $ git checkout -b AUTHOR1-AUTHOR2
-   ```
 
 
-5. Add your code & article (see [author guidelines](https://rescience.github.io/write)) and commit your changes:
+## Structure of this repository
 
-   ```
-   $ git commit -a -m "Some comment"
-   ```
+### article
+This folder contains the accompanying text in markdown/pdf/tex format and all the reproduced figures (used in our paper).
 
+### code
+This folder contains all the plotting functions, and the functions for loading and converting (from `gdf` format to `Neo`) the data (provided in `utils.py`). 
 
-6. [Push](https://help.github.com/articles/pushing-to-a-remote/) to github
+The source code of our UE implementation is pull requested and accepted after peer-review [https://github.com/NeuralEnsemble/elephant/pull/64](https://github.com/NeuralEnsemble/elephant/pull/64) in [Elephant](https://github.com/NeuralEnsemble/elephant).
 
-   ```
-   $ git push origin AUTHOR1-AUTHOR2
-   ```
+### data
+This folder contains the preprocessed versions of the spike train data used in the original publication (provided by Dr. Alexa Riehle, CNRS-AMU, Marseille).
 
-7. Issue a [pull request](https://help.github.com/articles/using-pull-requests/) (PR) to Re**Science** with title "Review Request" and insert the following text in the description:
+### notebook
+An jupyter notebook is provided here to plot the figures (Figure 1, Figure 2 and Figure 5) of our paper.
 
-  ```
-  **AUTHOR**
+how to use the jupyter notebook:
+- https://jupyter.readthedocs.io/en/latest/index.html
 
-  Dear @ReScience/editors,
+how to install the jupyter notebook:
+- pip install jupyter
 
-  I request a review for the reproduction of the following paper:
 
-  * References of the paper holding results you're replicating
-
-  I believe the original results have been faithfully reproduced as explained in the accompanying article.
-  ```
-
-8. Assign the PR to an editor from the [editorial board](https://rescience.github.io/board).
-
-9. Answer questions and requests made in the PR conversation page.

article/VRostami_JIto_MDenker_SGruen_2016.bib

@@ -0,0 +1,310 @@
+
+
+@article{Riehle97, 
+  author =       {Riehle, Alexa and Gr{\"u}n, Sonja and Diesmann, Markus and Aertsen, Ad},
+  title =        {Spike Synchronization and Rate Modulation Differentially Involved in Motor Cortical Function},
+  journal =      {Science},
+  year =         1997,
+  volume =       278,
+  pages =        {1950--1953},
+}
+
+
+@ARTICLE{Garcia14, 
+AUTHOR={Garcia, Samuel and Guarino, Domenico and Jaillet, Florent and Jennings, Todd and Pr\"opper, Robert and Rautenberg, Philipp and Rodgers, Chris and Sobolev, Andrey and Wachtler, Thomas and Yger, Pierre and Davison, Andrew},   	 
+TITLE={Neo: an object model for handling electrophysiology data in multiple formats},      
+
+JOURNAL={Frontiers in Neuroinformatics},      
+
+VOLUME={8},      
+
+PAGES={10},     
+
+YEAR={2014},      
+
+}
+
+
+
+
+
+@article{Gruen02a, 
+  author =       {Gr{\"u}n, S. and Diesmann, M. and Aertsen, A.},
+  title =        {{`U}nitary {E}vents' in Multiple Single-Neuron Spiking Activity. {I.} {D}etection and Significance},
+  journal =      {Neural Computation},
+  year =         2002,
+  volume =       14,
+  pages =        {43--80},
+}
+        
+@article{Gruen02b, 
+  author =       {Gr{\"u}n, S. and Diesmann, M. and Aertsen, A.},
+  title =        {{`U}nitary {E}vents' in Multiple Single-Neuron Spiking Activity. {II.} {N}on-{S}tationary Data},
+  journal =      {Neural Computation},
+  year =         2002,
+  volume =       14,
+  pages =        {81--119},
+
+}
+
+
+@article{Gruen03b, 
+  author =       {Gr{\"u}n, S. and Riehle, A. and Diesmann, M.},
+  title =        {Effect of cross-trial nonstationarity on joint-spike events},
+  journal =      {Biological Cybernetics},
+  year =         2003,
+  volume =       88,
+  pages =        {335--351},
+
+}
+
+
+        
+@article{Louis10, 
+  author =       {Louis, S. and Gerstein, G. L. and Gr{\"u}n, S. and Diesmann, M.},
+  title =        {Surrogate spike train generation through dithering in operational time},
+  journal =      {Front. Comput. Neurosci.},
+  year =         {2010},
+  volume =       {4},
+  pages =       {127} 
+}
+
+
+
+
+
+
+@Inbook{GruenRotter10_Chap10,
+  Title                    = {Analysis of Parallel Spike Trains},
+  Author                   = {Gr\"un, Sonja and Diesmann, Markus and Aertsen, Ad},
+  Chapter                  = {Unitary Event Analysis.},
+  Editor                   = {Gr{\"u}n, Sonja and Rotter, Stefan},
+  Publisher                = {Springer},
+  Year                     = {2010},
+}
+
+
+@article{Maldonado08, 
+  author =       {Maldonado, Pedro and Babul, Cecilia and Singer, Wolf and Rodriguez, Eugenio and Berger, Denise and Gr\"{u}n, Sonja},
+  title =        {Synchronization of Neuronal Responses in Primary Visual Cortex of Monkeys Viewing Natural Images},
+  journal =      {Journal of Neurophysiology},
+  year =         2008,
+  volume =       100,
+  pages =        {1523-1532},
+
+}
+
+
+
+@article{Gruen09, 
+  author =       {Gr\"un, Sonja},
+  title =        {Data-driven significance estimation of precise spike correlation.},
+  journal =      {Journal of Neurophysiology},
+  year =         2009,
+  pages =        {1126--1140},
+  number =       101,
+
+}
+
+
+
+
+
+@book{Abeles82, 
+  title =        {{Local Cortical Circuits: An Electrophysiological Study}},
+  publisher =    {Springer-Verlag},
+  year =         1982,
+  author =       {Abeles, Moshe},
+  series =       {Studies of Brain Function},
+  address =      {Berlin, Heidelberg, New York} 
+}
+
+
+@book{GruenPhD, 
+  title =        {{Unitary Joint-Events in Multiple-Neuron Spiking Activity: Detection, Significance, and Interpretation}},
+  publisher =    {Verlag Harri Deutsch},
+  year =         1996,
+  author =       {Gr{\"u}n, S.},
+  series =       {Reihe Physik, Band 60},
+  note =         {ISBN 3-8171-1506-7} 
+}
+
+
+
+@article{Gruen99, 
+  author =       {Gr{\"u}n, S. and Diesmann, M. and Grammont, F. and Riehle, A. and Aertsen, A.},
+  title =        {{Detecting unitary events without discretization of time}},
+  journal =      {Journal of Neuroscience Methods},
+  year =         1999,
+  volume =       94,
+  pages =        {67--79},
+
+}
+    
+
+
+
+@article{Pipa2013,
+author = {Pipa, Gordon and Gr{\"{u}}n, Sonja and Vreeswijk, Carl Van},
+journal = {Neural Computation},
+pages = {1123--1163},
+title = {{Impact of Spike Train Autostructure on Probability Distribution of Joint Spike Events}},
+volume = {1163},
+year = {2013}
+}
+
+
+@article{Grammont99, 
+  author =       {Grammont, Franck and Riehle, Alexa},
+  title =        {Precise spike synchronization in monkey motor cortex involved in preparation for movement},
+  journal =      {Experimental Brain Research},
+  year =         1999,
+  volume =       128,
+  pages =        {118--122} 
+}
+
+@article{Riehle2000, 
+  author =       {Riehle, Alexa and Grammont, Franck and Diesmann, Markus and Gr{\"u}n, Sonja},
+  title =        {Dynamical changes and temporal precision of synchronized spiking activity in monkey motor cortex during movement preparation},
+  journal =      {Journal of Physiology Paris},
+  year =         2000,
+  volume =       94,
+  pages =        {569--582},
+}
+        
+@inproceedings{Riehle00a, 
+  author =       {Riehle, A. and Grammont, F. and Diesmann, M. and Gr{\"u}n, S.},
+  title =        {Dynamical changes of temporal precision of synchronized activity in motor cortical neurons as revealed by using the Multiple-Shift Method},
+  booktitle =    {Computational Neuroscience CNS*00},
+  year =         2000,
+  note =         {Abstract Book} 
+}
+
+
+@article{Kilavik09, 
+  author =       {Kilavik, B. E. and Roux, S. and Ponce-Alvarez, A. and Confais, J. and Gr\"un, S. and Riehle, A.},
+  title =        {Long-term Modifications in Motor Cortical Dynamics induced by intensive practice},
+  journal =      {Journal of Neuroscience},
+  year =         2009,
+  volume =       29,
+  pages =        {12653--12663},
+}
+
+
+@article{Denker10, 
+  author =       {Denker, Michael and Riehle, Alexa and Diesmann, Markus and Gr\"un, Sonja},
+  title =        {Estimating the contribution of assembly activity to cortical dynamics from spike and population measures},
+  journal =      {Journal of Computational Neuroscience},
+  year =         2010,
+  volume =       29,
+  pages =        {599--613},
+
+}
+ 
+@article{Denker11, 
+  title =        {The Local Field Potential Reflects Surplus Spike Synchrony},
+  author =       {Denker, Michael and Roux, S{\'e}bastien and  Lind{\'e}n, Henrik and Diesmann, Markus and Riehle, Alexa and Gr{\"u}n, Sonja},
+  journal =      {Cerebral Cortex},
+  year =         2011,
+  volume =       21,
+  pages =        {2681--2695},
+
+}
+   
+
+@article{Ito11, 
+  author =       {Ito, J and Maldonado, P and Singer, W and Gr{\"u}n, S},
+  title =        {Saccade-related modulations of neuronal excitability support synchrony of visually elicited spikes},
+  journal =      {Cereb Cortex},
+  year =         2011,
+  volume =       21,
+  pages =        {2482--2497},
+
+}
+      
+@article{Pullrequest_UE, 
+  author =       {Vahid Rostami},
+  title = {Pull Request of the Unitary Events method in Elephant},
+  year =         2016,
+  journal =      {Elephant Github},
+  url = 	{https://github.com/NeuralEnsemble/elephant/pull/64}
+}
+
+
+
+@article{Zehl2016,
+author = {Zehl, Lyuba and Jaillet, Florent and Stoewer, Adrian and Grewe, Jan and Sobolev, Andrey and Wachtler, Thomas and Brochier, Thomas G. and Riehle, Alexa and Denker, Michael and Gr{\"{u}}n, Sonja},
+journal = {Frontiers in Neuroinformatics},
+pages = {26},
+title = {{Handling Metadata in a Neurophysiology Laboratory}},
+volume = {10},
+year = {2016}
+}
+
+
+
+@article{Grewe2011,
+author = {Grewe, Jan and Wachtler, Thomas and Benda, Jan},
+journal = {Frontiers in Neuroinformatics},
+title = {{A Bottom-up Approach to Data Annotation in Neurophysiology}},
+volume = {5},
+year = {2011}
+}
+
+
+@article{Adrian2014,
+author = {Adrian, Stoewer and Christian, Kellner and Jan, Benda and Thomas, Wachtler and Jan, Grewe},
+journal = {Frontiers in Neuroinformatics},
+title = {{File format and library for neuroscience data and metadata}},
+volume = {8},
+year = {2014}
+}
+
+
+
+@techreport{badia_incf_2015,
+    type = {Techn. {Report}},
+    title = {{INCF} {Program} on {Standards} for data sharing: new perspectives on workflows and data management for the analysis of electrophysiological data.},
+    author = {Badia, Rosa and Davison, Andrew and Denker, Michael and Giesler, Andre and Gosh, Satra and Goble, Carole and Grewe, Jan and Gr\"un, Sonja and Hatsopoulos, Nicho and LeFranc, Yann and Muller, Jeff and Pr\"opper, Robert and Teeters, Jeff and Wachtler, Thomas and Weeks, Michael and Zehl, Lyuba},
+    year = {2015},
+}
+
+
+@Inbook{Denker2015_000,
+  Title                    = {Brain Inspired Computing},
+  Author                   = {Michael Denker and Sonja Gr\"un},
+  Chapter                  = {Designing Workflows for the Reproducible Analysis of Electrophysiological Data.},
+  Editor                   = {Katrin Amunts and Lucio Grandinetti and Thomas Lippert and Nicolai Petkov},
+  Publisher                = {Springer Series Lecture Notes in Computer Science},
+  Year                     = {in press},
+}
+
+
+
+@article{Nakahara02, 
+  author =       {Nakahara, H. and Amari, S.},
+  title =        {Information-geometric measure for neural spikes},
+  journal =      {Neural Computation},
+  year =         2002,
+  volume =       14,
+  pages =        {2269--2316},
+}
+        
+
+@article{Brown04_456, 
+  author =       {Brown, Emery N. and Kaas, Robert E. and Mitra, Partha P.},
+  title =        {Multiple neural spike train data analysis: state-of-the-art and future challenges},
+  journal =      {Nature Neuroscience},
+  year =         2004,
+  volume =       7,
+  pages =        {456--461},
+}
+
+@article{Diesmann16_personalcomm,
+ author = {Markus Diesmann},
+year = {2016},
+ title = {Report on comparing the IDL and the Matlab implementations of the UE analysis},
+journal = {personal communication}
+
+}
+