Review Request : R. Larisch

.gitignore

@@ -0,0 +1,8 @@
+*.pyc
+*.aux
+*.bbl
+*.bcf
+*.blg
+*.log
+*.out
+*.run.xml

README.md

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 This is the submission repository for the [Re**Science** journal](https://rescience.github.io).
 
-### How to submit an article ?
+**Author:** René Larisch ([email protected])
 
+This is a replication of:
 
-1. Create a [github](https://github.com) account
+Connectivity reflects coding: a model of voltage-based STDP with homeostasis,
+C. Clopath, L. Büsing, E. Vasilaki and W. Gerstner, In: Nature Neuroscience 13.3
+(2010), pp. 344–352, doi= 10.1038/nn.2479
 
-2. [Fork](https://help.github.com/articles/fork-a-repo/) the [ReScience submission](https://github.com/ReScience/ReScience-submission) repository
+The reimplementation is written in Python (v2.7 and tested on v3.6) with the help of the neuro-simulator ANNarchy (v4.6.8.1),
+Numpy (v1.11.0) and Matplotlib (v1.5.1).
 
-3. Clone this new repository into your desktop environment
+#### Data
 
-   ```
-   $ git clone https://github.com/YOUR-USERNAME/ReScience-submission
-   ```
+The experiment for the emergence of V1 simple-cell-like receptive fields needs the dataset of 10 natural scenes from Olshausen and Field (1996).
+Dataset can be found on the webpage of Olshausen (http://www.rctn.org/bruno/sparsenet/). Please note, that the whitened natural scenes are required.
 
-4. Create a branch (the branch name should be author names separated with dashes)
+#### Model
 
-   ```
-   $ git checkout -b AUTHOR1-AUTHOR2
-   ```
+The implementation of the model can be found in the **code** directory.
+It exists a model version with a fixed and static homeostasic mechanisms (can be found in *code/net_fix.py*),
+and a model version with a dynamic homeostasic mechanisms (can be found in *code/net_homeostatic.py*).
 
 
-5. Add your code & article (see [author guidelines](https://rescience.github.io/write)) and commit your changes:
-
-   ```
-   $ git commit -a -m "Some comment"
-   ```
-
-
-6. [Push](https://help.github.com/articles/pushing-to-a-remote/) to github
-
-   ```
-   $ git push origin AUTHOR1-AUTHOR2
-   ```
-
-7. Issue a [pull request](https://help.github.com/articles/using-pull-requests/) (PR) to Re**Science** with title containing author(s) name and follow the template that will appear once you opened the pull request:
-
-  ```
-  **AUTHOR**
-
-  Dear @ReScience/editors,
-
-  I request a review for the following replication:
-
-  ### Original article
-
-  **Title:**  
-  **Author(s):**  
-  **Journal (or Conference):**  
-  **Year:**  
-  **DOI:**  
-  **PDF:**   
-
-  ### Replication
-
-  **Author(s)**:   
-  **Repository**:  
-  **PDF**:  
-  **Keywords**:  
-  **Language**:  
-  **Domain**:  
-
-  ### Results
-
-  * [ ] Article has been fully replicated
-  * [ ] Article has been partially replicated
-  * [ ] Article has not been replicated
-
-  ### Potential reviewers
-  <!-- If you know potential reviewers, you can tell us here -->
-  <!-- You can look at http://rescience.github.io/board for the -->
-  <!-- list of registered reviewers (but you can propose others) -->
-
-  ---
-
-  **EDITOR**
-
-  * [ ] Editor acknowledgment
-  * [ ] Reviewer 1 
-  * [ ] Reviewer 2
-  * [ ] Review 1 decision [accept/reject]
-  * [ ] Review 2 decision [accept/reject]
-  * [ ] Editor decision [accept/reject]
-  ```
-
-8. You can suggest reviewers from [editorial board](https://rescience.github.io/board).
-
-9. Answer questions and requests made in the PR conversation page.
+#### Results
+![Weight change in the Voltage clamp experiment. The blue line presents the weight change with the parameter set for the visual cortex.
+The red line presents the weight change with the parameter set for the hippocampus.](article/figures/Fig1_clamp.png)
+![Classic STDP learning window. On the x-axis is the time of a postsynaptic spike in relation to the presynaptic spike presented.](article/figures/Fig1_window.png)
+![Weight changes as a function of pair frequency repetition.](article/figures/Fig1_pairing.png)
+![**Upper left**, weight change as a function of the numbers of postsynaptic spikes.
+**Upper right**, weight change as a function of the frequency between three postsynaptic spikes.
+**Down**, weight change as a function of the time between the first of three postsynaptic spikes and one presynaptic spike.](article/figures/Fig2_burst.png)
+![Neurons with similar high firing rates develop strong bidirectional connections (a). Temporal order of activity is mirrored in the connectivity structure (c). The same as (a) for a standard STDP rule (b). The same as (c) for a standard STDP rule (d).](article/figures/Fig3.png)
+![Weight value at the end of the current epoch from the presynaptic neuron to a single postsynaptic neuron by presenting a Gaussian curve input. Black are weight values around zero and weight are weight values around the maximum weight (a). Four different receptive fields by presenting natural scenes as input (b). Higher input firing rate on natural scene input leads to a smaller receptive field (c).](article/figures/Fig4_W.png)