article.yaml

# 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: "[Rp] Structural flexibility in proteins - impact of the crystal environment"

# List of authors with name, orcid number, email and affiliation
# Affiliation "*" means contact author
authors:
  - name: Konrad Hinsen
    orcid: 0000-0003-0330-9428
    email: konrad.hinsen@cnrs.fr
    affiliations: 1,2,*

# 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:    Centre de Biophysique Moléculaire, CNRS UPR4301
    address: Orléans, France
    
  - code:    2
    name:    Synchrotron SOLEIL, Division Expériences
    address: Gif sur Yvette, France

# List of keywords (adding the programming language might be a good idea)
keywords: protein structure, protein crystals, normal modes, 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/khinsen/rescience-ten-year-challenge-paper-3
  - doi: 
  - swh: swh:1:dir:8a73b8438b411cc8a58a3db7789ff45690808afa

# Data URL and DOI (optional if no data)
data:
  - url:
  - doi:

# Information about the original article that has been replicated
replication:
 - cite: K. Hinsen, Structural flexibility in proteins - impact of the crystal environment, Bioinformatics 24:521 (2008)
 - bib:  HinsenStructuralflexibilityproteins2008
 - url:  https://academic.oup.com/bioinformatics/article-pdf/24/4/521/16884353/btm625.pdf
 - doi:  10.1093/bioinformatics/btm625

# Don't forget to surround abstract with double quotes
abstract: "Reproduction attempt of K. Hinsen, Structural flexibility in proteins: impact
           of the crystal environment, Bioinformatics 24:521 (2008). The code published
           with the original article could be modified to work on a modern computer,
           and produced sufficiently similar results. However, it proved insufficient
           for a complete replication of all the results."

# Bibliography file (yours)
bibliography: bibliography.bib
  
# Type of the article
# Type can be:
#  * Editorial
#  * Letter
#  * Replication
type: Reproduction

# Scientific domain of the article (e.g. Computational Neuroscience)
#  (one domain only & try to be not overly specific)
domain: Biophysics

# 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/submissions/issues/14

contributors:
  - name: Marc André Delsuc
    orcid: 0000-0002-1400-5326
    role: editor
  - name: François-Xavier Coudert
    orcid: 0000-0001-5318-3910
    role: reviewer
  - name:
    orcid:
    role: reviewer

# This information will be provided by the editor
dates:
  - received: January 30, 2020
  - accepted: March 19, 2020
  - published: June 9, 2020

# This information will be provided by the editor
article:
  - number: 5
  - doi:    10.5281/zenodo.3886447
  - url:    https://zenodo.org/record/3886447/files/article.pdf

# This information will be provided by the editor
journal:
  - name:   "ReScience C"
  - issn:   2430-3658
  - volume: 6
  - issue:  1