From 94cbed6c63ad4362547b4cbcc579c63937a780a6 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Mon, 23 Nov 2020 03:00:05 +0000
Subject: First draft of all the points addressed by the referees

A new directory has been added at the top of the project's source called
'peer-review'. The raw reviews of the paper by the editors and referees has
been added there as '1-review.txt'. All the main points raised by the
referees have been listed in a numbered list and addressed (mostly) in
'1-answers.txt'. The text of the paper now also includes all the
implemented answers to the various points.
---
 tex/src/references.tex | 219 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 216 insertions(+), 3 deletions(-)

(limited to 'tex/src/references.tex')

diff --git a/tex/src/references.tex b/tex/src/references.tex
index 1ef3d7d..dc3b816 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -10,6 +10,50 @@
 %% notice and this notice are preserved.  This file is offered as-is,
 %% without any warranty.
 
+
+
+
+
+@ARTICLE{peper20,
+       author = {{Peper}, Marius and {Roukema}, Boudewijn F.},
+        title = "{The role of the elaphrocentre in low surface brightness galaxy formation}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies},
+         year = 2020,
+        month = oct,
+          eid = {arXiv:2010.03742},
+        pages = {arXiv:2010.03742},
+archivePrefix = {arXiv},
+       eprint = {2010.03742},
+ primaryClass = {astro-ph.CO},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv201003742P},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+
+@ARTICLE{roukema20,
+       author = {{Roukema}, Boudewijn F.},
+        title = "{Anti-clustering in the national SARS-CoV-2 daily infection counts}",
+      journal = {arXiv e-prints},
+     keywords = {Quantitative Biology - Populations and Evolution, Physics - Physics and Society, Statistics - Methodology},
+         year = 2020,
+        month = jul,
+          eid = {arXiv:2007.11779},
+        pages = {arXiv:2007.11779},
+archivePrefix = {arXiv},
+       eprint = {2007.11779},
+ primaryClass = {q-bio.PE},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200711779R},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+
 @ARTICLE{aissi20,
      author = {Dylan A\"issi},
       title = {Review for Towards Long-term and Archivable Reproducibility},
@@ -69,6 +113,20 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{nust20,
+     author = {Daniel N\"ust and Vanessa Sochat and Ben Marwick and Stephen J. Eglen and Tim Head and Tony Hirst and Benjamin D. Evans},
+      title = {Ten simple rules for writing Dockerfiles for reproducible data science},
+       year = {2020},
+    journal = {PLOS Computational Biology},
+     volume = {16},
+      pages = {e1008316},
+        doi = {10.1371/journal.pcbi.1008316},
+}
+
+
+
+
+
 @ARTICLE{konkol20,
        author = {{Konkol}, Markus and {N{\"u}st}, Daniel and {Goulier}, Laura},
         title = "{Publishing computational research -- A review of infrastructures for reproducible and transparent scholarly communication}",
@@ -124,6 +182,20 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{lofstead19,
+     author = {Jay Lofstead and Joshua Baker and Andrew Younge},
+      title = {Data Pallets: Containerizing Storage for Reproducibility and Traceability},
+       year = {2019},
+    journal = {High Performance Computing. ISC High Performance 2019},
+     volume = {11887},
+      pages = {1},
+        doi = {10.1007/978-3-030-34356-9\_4},
+}
+
+
+
+
+
 @ARTICLE{clement19,
      author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois},
       title = {Encouraging a wider usage of software derived from research},
@@ -314,11 +386,53 @@ archivePrefix = {arXiv},
 
 
 
-@ARTICLE{brinckman19,
-author = "Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and Matthew B. Jones and Kacper Kowalik and Sivakumar Kulasekaran and Bertram Ludäscher and Bryce D. Mecum and Jarek Nabrzyski and Victoria Stodden and Ian J. Taylor and Matthew J. Turk and Kandace Turner",
+@ARTICLE{kurtzer17,
+     author = {Gregory M. Kurtzer and Vanessa Sochat and Michael W. Bauer},
+      title = {Singularity: Scientific containers for mobility of compute},
+    journal = {PLoS ONE},
+       year = {2017},
+     volume = {12},
+      pages = {e0177459},
+        doi = {10.1371/journal.pone.0177459},
+}
+
+
+
+
+
+@ARTICLE{meng17,
+     author = {Haiyan Meng and Douglas Thain},
+      title = {Facilitating the Reproducibility of Scientific Workflows with Execution Environment Specifications},
+    journal = {Procedia Computer Science},
+       year = {2017},
+     volume = {108},
+      pages = {705},
+        doi = {10.1016/j.procs.2017.05.116},
+}
+
+
+
+
+
+@ARTICLE{tommaso17,
+     author = {Paolo Di Tommaso and Maria Chatzou and Evan W Floden and Pablo Prieto Barja and Emilio Palumbo and Cedric Notredame},
+      title = {Nextflow enables reproducible computational workflows},
+    journal = {Nature Biotechnology},
+       year = 2017,
+     volume = 35,
+      pages = 316,
+        doi = {10.1038/nbt.3820},
+}
+
+
+
+
+
+@ARTICLE{brinckman17,
+     author = {Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and Matthew B. Jones and Kacper Kowalik and Sivakumar Kulasekaran and Bertram Ludäscher and Bryce D. Mecum and Jarek Nabrzyski and Victoria Stodden and Ian J. Taylor and Matthew J. Turk and Kandace Turner},
       title = {Computing environments for reproducibility: Capturing the ``Whole Tale''},
     journal = {Future Generation Computer Systems},
-       year = 2019,
+       year = 2017,
      volume = 94,
       pages = 854,
         doi = {10.1016/j.future.2017.12.029},
@@ -380,6 +494,40 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{oliveira18,
+       author = {Lu\'is Oliveira and David Wilkinson and Daniel Moss\'e and Bruce Robert Childers},
+        title = {Supporting Long-term Reproducible Software Execution},
+      journal = {Proceedings of the First International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS'18)},
+       volume = {1},
+         year = {2018},
+        pages = {6},
+          doi = {10.1145/3214239.3214245},
+}
+
+
+
+
+
+@ARTICLE{rule19,
+       author = {{Rule}, Adam and {Birmingham}, Amanda and {Zuniga}, Cristal and
+                 {Altintas}, Ilkay and {Huang}, Shih-Cheng and {Knight}, Rob and
+                 {Moshiri}, Niema and {Nguyen}, Mai H. and {Brin Rosenthal},
+                 Sara and {P{\'e}rez}, Fernando and {Rose}, Peter W.},
+        title = {Ten Simple Rules for Reproducible Research in Jupyter Notebooks},
+      journal = {PLOS Computational Biology},
+       volume = {15},
+         year = 2019,
+        month = jul,
+        pages = {e1007007},
+archivePrefix = {arXiv},
+       eprint = {1810.08055},
+          doi = {10.1371/journal.pcbi.1007007},
+}
+
+
+
+
+
 @article{tange18,
        author = {Tange, Ole},
         title = {GNU Parallel 2018},
@@ -787,6 +935,20 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{chirigati16,
+       author = {Chirigati, Fernando and Rampin, R{\'e}mi and Shasha, Dennis and Freire, Juliana},
+        title = {ReproZip: Computational Reproducibility With Ease},
+      journal = {Proceedings of the 2016 International Conference on Management of Data (SIGMOD 16)},
+       volume = {2},
+         year = {2016},
+        pages = {2085},
+          doi = {10.1145/2882903.2899401},
+}
+
+
+
+
+
 @ARTICLE{smith16,
        author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer},
         title = {Software citation principles},
@@ -980,6 +1142,20 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{meng15b,
+     author = {Haiyan Meng and Douglas Thain},
+      title = {Umbrella: A Portable Environment Creator for Reproducible Computing on Clusters, Clouds, and Grids},
+    journal = {Proceedings of the 8th International Workshop on Virtualization Technologies in Distributed Computing (VTDC 15)},
+       year = 2015,
+     volume = 1,
+      pages = 23,
+        doi = {10.1145/2755979.2755982},
+}
+
+
+
+
+
 @ARTICLE{meng15,
      author = {Haiyan Meng and Rupa Kommineni and Quan Pham and Robert Gardner and Tanu Malik and Douglas Thain},
       title = {An invariant framework for conducting reproducible computational science},
@@ -1108,6 +1284,28 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{dolfi14,
+       author = {{Dolfi}, M. and {Gukelberger}, J. and {Hehn}, A. and
+                 {Imri{\v{s}}ka}, J. and {Pakrouski}, K. and {R{\o}nnow},
+                 T.~F. and {Troyer}, M. and {Zintchenko}, I. and {Chirigati},
+                 F. and {Freire}, J. and {Shasha}, D.},
+        title = "{A model project for reproducible papers: critical temperature for the Ising model on a square lattice}",
+      journal = {arXiv},
+         year = 2014,
+        month = jan,
+          eid = {arXiv:1401.2000},
+        pages = {arXiv:1401.2000},
+archivePrefix = {arXiv},
+       eprint = {1401.2000},
+ primaryClass = {cs.CE},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2014arXiv1401.2000D},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+
 @ARTICLE{katz14,
      author = {Daniel S. Katz},
       title = {Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products},
@@ -1194,6 +1392,21 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{koster12,
+     author = {Johannes K\"oster and Sven Rahmann},
+      title = {Snakemake—a scalable bioinformatics workflow engine},
+    journal = {Bioinformatics},
+     volume = {28},
+      issue = {19},
+       year = {2012},
+      pages = {2520},
+        doi = {10.1093/bioinformatics/bts480},
+}
+
+
+
+
+
 @ARTICLE{gronenschild12,
      author = {Ed H. B. M. Gronenschild and Petra Habets and Heidi I. L. Jacobs and Ron Mengelers and Nico Rozendaal and Jim van Os and Machteld Marcelis},
       title = {The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements},
-- 
cgit v1.2.1

