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61 changes: 20 additions & 41 deletions README.md
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This is the submission repository for the [Re**Science** journal](https://rescience.github.io).


### Reference implementation of:

> The cell-type specific cortical microcircuit: relating structure and activity in a full-scale spiking network model. (2014)

The source code is written in Python (version 2.7.5) Brian (version 2.0.1) using Numpy (version
1.11.1) Pandas (version 0.19.2) and Matplotlib (version 2.0.0).

* **article** -> This folder contains the accompanying text.
* **code** -> Here is the source code.
* **data** -> This folder is empty.
* **notebook** -> There is no notebook for this implementation.


### How to submit an article ?


Expand Down Expand Up @@ -36,56 +50,21 @@ This is the submission repository for the [Re**Science** journal](https://rescie
$ 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:
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:

```
**AUTHOR**

Dear @ReScience/editors,

I request a review for the following replication:

### Original article

**Title:**
**Author(s):**
**Journal (or Conference):**
**Year:**
**DOI:**
**PDF:**
I request a review for the reproduction of the following paper:

### Replication
* References of the paper holding results you're replicating

**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]
I believe the original results have been faithfully reproduced as explained in the accompanying article.
```

8. You can suggest reviewers from [editorial board](https://rescience.github.io/board).
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.

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### Important

Don't forget to change the name of the Name-YEAR file to reflect all the
authors name and the current year.

### Required tools for producing the pdf

You'll need [pandoc](http://pandoc.org) (a universal document converter) and a
full [TeX distribution](https://www.tug.org/texlive/).

For pandoc, you'll also need the
[pandoc-crossref](https://github.com/lierdakil/pandoc-crossref) filter that you can
easily install with:

```
$ cabal update
$ cabal install pandoc-crossref
```

### How to build the PDF ?

In a console, type:

```
pandoc --standalone --filter ~/.cabal/bin/pandoc-crossref --template=rescience-template.tex --latex-engine=xelatex --biblatex --bibliography=bibliography.bib -M "crossrefYaml=crossref.yaml" --output Name-YEAR.tex Name-YEAR.md
xelatex Name-YEAR
biber Name-YEAR
xelatex Name-YEAR
xelatex Name-YEAR
xelatex ShimouraR-KamijiNL-PenaRFO-CordeiroVL-CeballosCC-RomaroC-RoqueAC-2017
biber ShimouraR-KamijiNL-PenaRFO-CordeiroVL-CeballosCC-RomaroC-RoqueAC-2017
xelatex ShimouraR-KamijiNL-PenaRFO-CordeiroVL-CeballosCC-RomaroC-RoqueAC-2017
xelatex ShimouraR-KamijiNL-PenaRFO-CordeiroVL-CeballosCC-RomaroC-RoqueAC-2017
```

Alternativaley, you can also type `make` after having edited the Makefile.
Alternativaley, you can place all files in an Overleaf project.
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