JOSS formatting

joss_paper/paper.bib

@@ -57,7 +57,7 @@ @article{H5MD:2014
     pages = {1546-1553},
     year = {2014},
     issn = {0010-4655},
-    doi = {https://doi.org/10.1016/j.cpc.2014.01.018},
+    doi = {10.1016/j.cpc.2014.01.018},
     url = {https://www.sciencedirect.com/science/article/pii/S0010465514000447},
     author = {Pierre {de Buyl} and Peter H. Colberg and Felix Höfling},
     keywords = {Molecular simulation, HDF5},
@@ -89,7 +89,8 @@ @INPROCEEDINGS{MDAKits:2023
   pages      = "76--84",
   year       =  2023,
   conference = "Python in Science Conference",
-  location   = "Austin, Texas"
+  location   = "Austin, Texas",
+  doi = {10.25080/gerudo-f2bc6f59-00a}
 }
 
 
@@ -112,7 +113,7 @@ @article{MDAnalysis:2011
     number = {10},
     pages = {2319-2327},
     keywords = {molecular dynamics simulations, analysis, proteins, object-oriented design, software, membrane systems, Python programming language},
-    doi = {https://doi.org/10.1002/jcc.21787},
+    doi = {10.1002/jcc.21787},
     url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21787},
     eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.21787},
     abstract = {Abstract MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011},
@@ -127,6 +128,7 @@ @misc{MDDB:2024
       archivePrefix={arXiv},
       primaryClass={q-bio.BM},
       url={https://arxiv.org/abs/2407.16584}, 
+      doi={10.48550/arXiv.2407.16584}
 }
 
 @article{MDsrv:2022,
@@ -278,7 +280,7 @@ @article{YiiP:2019
 year = "2019",
 month = "5",
 url = "https://figshare.com/articles/dataset/Molecular_Dynamics_trajectories_of_membrane_protein_YiiP/8202149",
-doi = "10.6084/m9.figshare.8202149.v1"
+doi = {10.6084/m9.figshare.8202149.v1}
 }
 
 @misc{Zarr:2024,
@@ -315,4 +317,6 @@ @article{Liu:2010
 	pages = {1561-1563},
 	title = {Fast determination of the optimal rotational matrix for macromolecular superpositions},
 	volume = 31,
-	year = 2010}
+	year = 2010,
+  doi = {10.1002/jcc.21439},  
+}

joss_paper/paper.md

@@ -9,22 +9,22 @@ tags:
 authors:
   - name: Lawson Woods
     orcid: 0009-0003-0713-4167
-    affiliation: [1, 2]
+    affiliation: "1, 2"
   - name: Hugo MacDermott-Opeskin
     orcid: 0000-0002-7393-7457
-    affiliation: [3]
+    affiliation: "3"
   - name: Edis Jakupovic 
-    affiliation: [4, 5]
+    affiliation: "4, 5"
     orcid: 0000-0001-8813-6356
   - name: Yuxuan Zhuang
     orcid: 0000-0003-4390-8556
-    affiliation: [6, 7]
+    affiliation: "6, 7"
   - name: Richard J Gowers
     orcid: 0000-0002-3241-1846
-    affiliation: [8]
+    affiliation: "8"
   - name: Oliver Beckstein
     orcid: 0000-0003-1340-0831
-    affiliation: [4, 5]
+    affiliation: "4, 5"
 affiliations:
  - name: School of Computing and Augmented Intelligence, Arizona State University, Tempe, Arizona, United States of America
    index: 1