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Instructions for Authors
-----------------------
<!-- ### Directory-->
1. [Types of submission](#types)
2. [Preparing your submission](#preparing)
    - [The manuscript](#manuscript)
    - [The source code](#source_code)
3. [Submission](#submission)
    - [Pre-submission checklist](#submission_checklist)
4. [Curation](#curation)
5. [Publishing](#publishing)
6. [Copyright of submission](#copyright)

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The model files submitted to <i>Physiome</i> must be <a href="about.html#philosophy">reusable</a>, and associated with at least one article accepted by a peer-reviewed journal in the field of physiological modelling (a Primary Publication). Authors are encouraged to prepare their <i>Physiome</i> submission(s) in parallel to the Primary Publication. Submissions will be curated and evaluated, but not published until the Primary Publication is accepted. 
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For queries, see the <a href="faqs.html">Frequently Asked Questions</a>. Otherwise, <a href = "mailto:<EMAIL>">email the curators</a>. Include the submission identification number if querying a specific submission.

***
<h3 id="types">1. Types of submissions</h3>

The following will be considered for publication in <i>Physiome</i>: 

**2.1 Original submission**

Original submissions are author-initiated submissions directly associated with a primary experimental or modelling paper, aiming to exactly reproduce the published model, using the implementation of the primary paper. While matching authorship between the <i>Physiome</i> submission and the primary publication is not a requirement, it is expected that there is some overlap. The <i>Physiome</i> team can help with reaching out to additional authors if needed.

**2.2 Retrospectives**

[comment]: # (Similar to an original submission, but is associated with a historical Primary Publication which has been judged to be of substantial value to the physiological modelling community, such that a reusable, reproducible, and discoverable version of the study should be made available. Where possible, the authors of retrospective should include authors from the primary publication. Retrospectives may be invited by the <i>Physiome</i> editors or can be author-initiated.)

A retrospective applies to a submission which is a new implementation of the published model, with some changes made that broadly reproduce the primary paper's results. The published model may be a few years old. Therefore, author overlap with the primary publication is not necessary.

When submitting a retrospective, it is best to first submit an expression of interest to the editors outlining why the original primary publication should be considered a suitable contribution to <i>Physiome</i>.

**2.3 Reviews**
<commit_msg>Update instructions-to-authors.md<commit_after><html>
    <head>
        <title>Instructions to Authors</title>
    </head>
</html>
<!-- Title: Instructions to Authors -->
<!-- Slug: instructions-to-authors -->

<h3 id="instructions"> </h3>

Instructions for Authors
-----------------------
<!-- ### Directory-->
1. [Types of submission](#types)
2. [Preparing your submission](#preparing)
    - [The manuscript](#manuscript)
    - [The source code](#source_code)
3. [Submission](#submission)
    - [Pre-submission checklist](#submission_checklist)
4. [Curation](#curation)
5. [Publishing](#publishing)
6. [Copyright of submission](#copyright)

<!-- <details> -->
<!-- <summary>Click</summary> -->
The model files submitted to <i>Physiome</i> must be <a href="about.html#philosophy">reusable</a>, and associated with at least one article accepted by a peer-reviewed journal in the field of physiological modelling (a Primary Publication). Authors are encouraged to prepare their <i>Physiome</i> submission(s) in parallel to the Primary Publication. Submissions will be curated and evaluated, but not published until the Primary Publication is accepted. 
<!-- </details> -->

For queries, see the <a href="faqs.html">Frequently Asked Questions</a>. Otherwise, <a href = "mailto:<EMAIL>">email the curators</a>. Include the submission identification number if querying a specific submission.

***
<h3 id="types">1. Types of submissions</h3>

The following will be considered for publication in <i>Physiome</i>: 

**2.1 Original submission**

Original submissions are author-initiated submissions directly associated with a primary experimental or modelling paper, aiming to reproduce the published model using the implementation used in producing the primary paper. While matching authorship between the <i>Physiome</i> submission and the primary publication is not a requirement, it is expected that there is some overlap. The <i>Physiome</i> team can help with reaching out to additional authors if needed.

In cases where the original implementation is not able to be made available with the <i>Physiome</i> submission or if it in a non-standard format, authors may supplement their <i>Physiome</i> submission with a new implementation, perferably in a standard format, which demonstrates reproducibility of the primary paper.

**2.2 Retrospectives**

[comment]: # (Similar to an original submission, but is associated with a historical Primary Publication which has been judged to be of substantial value to the physiological modelling community, such that a reusable, reproducible, and discoverable version of the study should be made available. Where possible, the authors of retrospective should include authors from the primary publication. Retrospectives may be invited by the <i>Physiome</i> editors or can be author-initiated.)

A retrospective is a submission which is a new implementation of a published model that broadly reproduces the results presented in the primary paper. Where possible, the authors of retrospective should include authors from the primary publication. Retrospectives may include additional aspects that help put the primary paper in a current context.

When submitting a retrospective, it is best to first submit an expression of interest to the editors outlining why the original primary publication should be considered a suitable contribution to <i>Physiome</i>.

**2.3 Reviews**

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