Joss paper md files

paper/paper.bib

@@ -0,0 +1,262 @@
+
+@article{radonpy_2022,
+	title = {{RadonPy}: automated physical property calculation using all-atom classical molecular dynamics simulations for polymer informatics},
+	volume = {8},
+	issn = {2057-3960},
+	url = {https://www.nature.com/articles/s41524-022-00906-4},
+	doi = {10.1038/s41524-022-00906-4},
+	shorttitle = {{RadonPy}},
+	pages = {222},
+	number = {1},
+	journaltitle = {npj Computational Materials},
+	shortjournal = {npj Comput Mater},
+	author = {Hayashi, Yoshihiro and Shiomi, Junichiro and Morikawa, Junko and Yoshida, Ryo},
+	urldate = {2023-09-26},
+	date = {2022-11-08},
+	langid = {english},
+	file = {Hayashi et al. - 2022 - RadonPy automated physical property calculation u.pdf:/home/marjan/Zotero/storage/CV4ZA7SU/Hayashi et al. - 2022 - RadonPy automated physical property calculation u.pdf:application/pdf},
+}
+
+@article{TRUE_2020,
+	title = {Towards molecular simulations that are transparent, reproducible, usable by others, and extensible ({TRUE})},
+	volume = {118},
+	issn = {0026-8976, 1362-3028},
+	url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938},
+	doi = {10.1080/00268976.2020.1742938},
+	pages = {e1742938},
+	number = {9},
+	journaltitle = {Molecular Physics},
+	shortjournal = {Molecular Physics},
+	author = {Thompson, Matthew W. and Gilmer, Justin B. and Matsumoto, Ray A. and Quach, Co D. and Shamaprasad, Parashara and Yang, Alexander H. and Iacovella, Christopher R. and {McCabe}, Clare and Cummings, Peter T.},
+	urldate = {2023-09-27},
+	date = {2020-06-01},
+	langid = {english},
+	file = {Thompson et al. - 2020 - Towards molecular simulations that are transparent.pdf:/home/marjan/Zotero/storage/2R32UBC3/Thompson et al. - 2020 - Towards molecular simulations that are transparent.pdf:application/pdf},
+}
+
+@article{biosimspace_2019,
+	title = {{BioSimSpace}: An interoperable Python framework for biomolecular simulation},
+	volume = {4},
+	issn = {2475-9066},
+	url = {https://joss.theoj.org/papers/10.21105/joss.01831},
+	doi = {10.21105/joss.01831},
+	shorttitle = {{BioSimSpace}},
+	pages = {1831},
+	number = {43},
+	journaltitle = {Journal of Open Source Software},
+	shortjournal = {{JOSS}},
+	author = {Hedges, Lester and Mey, Antonia and Laughton, Charles and Gervasio, Francesco and Mulholland, Adrian and Woods, Christopher and Michel, Julien},
+	urldate = {2023-09-27},
+	date = {2019-11-22},
+	langid = {english},
+	file = {Hedges et al. - 2019 - BioSimSpace An interoperable Python framework for.pdf:/home/marjan/Zotero/storage/V89VIW2E/Hedges et al. - 2019 - BioSimSpace An interoperable Python framework for.pdf:application/pdf},
+}
+
+@article{shirts_statistically_2008,
+	title = {Statistically optimal analysis of samples from multiple equilibrium states},
+	volume = {129},
+	issn = {0021-9606, 1089-7690},
+	url = {https://pubs.aip.org/jcp/article/129/12/124105/957527/Statistically-optimal-analysis-of-samples-from},
+	doi = {10.1063/1.2978177},
+	pages = {124105},
+	number = {12},
+	journaltitle = {The Journal of Chemical Physics},
+	author = {Shirts, Michael R. and Chodera, John D.},
+	urldate = {2023-10-02},
+	date = {2008-09-28},
+	langid = {english},
+	file = {Shirts and Chodera - 2008 - Statistically optimal analysis of samples from mul.pdf:/home/marjan/Zotero/storage/8W27U635/Shirts and Chodera - 2008 - Statistically optimal analysis of samples from mul.pdf:application/pdf},
+}
+
+@article{chodera_2007,
+	title = {Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations},
+	volume = {3},
+	issn = {1549-9618, 1549-9626},
+	url = {https://pubs.acs.org/doi/10.1021/ct0502864},
+	doi = {10.1021/ct0502864},
+	pages = {26--41},
+	number = {1},
+	journaltitle = {Journal of Chemical Theory and Computation},
+	shortjournal = {J. Chem. Theory Comput.},
+	author = {Chodera, John D. and Swope, William C. and Pitera, Jed W. and Seok, Chaok and Dill, Ken A.},
+	urldate = {2023-10-02},
+	date = {2007-01-01},
+	langid = {english},
+	file = {Chodera et al. - 2007 - Use of the Weighted Histogram Analysis Method for .pdf:/home/marjan/Zotero/storage/L38UQDMW/Chodera et al. - 2007 - Use of the Weighted Histogram Analysis Method for .pdf:application/pdf},
+}
+
+@misc{hoomd_2019,
+	title = {{HOOMD}-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations},
+	url = {http://arxiv.org/abs/1308.5587},
+	shorttitle = {{HOOMD}-blue},
+	number = {{arXiv}:1308.5587},
+	publisher = {{arXiv}},
+	author = {Anderson, Joshua A. and Glaser, Jens and Glotzer, Sharon C.},
+	urldate = {2023-10-03},
+	date = {2019-10-18},
+	langid = {english},
+	eprinttype = {arxiv},
+	eprint = {1308.5587 [physics]},
+	keywords = {Physics - Computational Physics},
+	file = {Anderson et al. - 2019 - HOOMD-blue A Python package for high-performance .pdf:/home/marjan/Zotero/storage/C6IKKZYP/Anderson et al. - 2019 - HOOMD-blue A Python package for high-performance .pdf:application/pdf},
+}
+
+@article{polyply_2022,
+	title = {Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials},
+	volume = {13},
+	issn = {2041-1723},
+	url = {https://www.nature.com/articles/s41467-021-27627-4},
+	doi = {10.1038/s41467-021-27627-4},
+	pages = {68},
+	number = {1},
+	journaltitle = {Nature Communications},
+	shortjournal = {Nat Commun},
+	author = {Grünewald, Fabian and Alessandri, Riccardo and Kroon, Peter C. and Monticelli, Luca and Souza, Paulo C. T. and Marrink, Siewert J.},
+	urldate = {2023-10-03},
+	date = {2022-01-10},
+	langid = {english},
+	file = {Grünewald et al. - 2022 - Polyply\; a python suite for facilitating simulatio.pdf:/home/marjan/Zotero/storage/BDEA9LQX/Grünewald et al. - 2022 - Polyply\; a python suite for facilitating simulatio.pdf:application/pdf},
+}
+
+@article{gromacs_2013,
+	title = {{GROMACS} 4.5: a high-throughput and highly parallel open source molecular simulation toolkit},
+	volume = {29},
+	issn = {1367-4811, 1367-4803},
+	url = {https://academic.oup.com/bioinformatics/article/29/7/845/253065},
+	doi = {10.1093/bioinformatics/btt055},
+	shorttitle = {{GROMACS} 4.5},
+	pages = {845--854},
+	number = {7},
+	journaltitle = {Bioinformatics},
+	author = {Pronk, Sander and Páll, Szilárd and Schulz, Roland and Larsson, Per and Bjelkmar, Pär and Apostolov, Rossen and Shirts, Michael R. and Smith, Jeremy C. and Kasson, Peter M. and Van Der Spoel, David and Hess, Berk and Lindahl, Erik},
+	urldate = {2023-10-03},
+	date = {2013-04-01},
+	langid = {english},
+	file = {Pronk et al. - 2013 - GROMACS 4.5 a high-throughput and highly parallel.pdf:/home/marjan/Zotero/storage/P3G6GWA3/Pronk et al. - 2013 - GROMACS 4.5 a high-throughput and highly parallel.pdf:application/pdf},
+}
+
+@article{gromacs_2008,
+	title = {{GROMACS} 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation},
+	volume = {4},
+	issn = {1549-9618, 1549-9626},
+	url = {https://pubs.acs.org/doi/10.1021/ct700301q},
+	doi = {10.1021/ct700301q},
+	shorttitle = {{GROMACS} 4},
+	pages = {435--447},
+	number = {3},
+	journaltitle = {Journal of Chemical Theory and Computation},
+	shortjournal = {J. Chem. Theory Comput.},
+	author = {Hess, Berk and Kutzner, Carsten and Van Der Spoel, David and Lindahl, Erik},
+	urldate = {2023-10-03},
+	date = {2008-03-01},
+	langid = {english},
+	file = {Hess et al. - 2008 - GROMACS 4 Algorithms for Highly Efficient, Load-B.pdf:/home/marjan/Zotero/storage/S2YWMFVZ/Hess et al. - 2008 - GROMACS 4 Algorithms for Highly Efficient, Load-B.pdf:application/pdf},
+}
+
+@article{gromacs_1995,
+	title = {{GROMACS}: A message-passing parallel molecular dynamics implementation},
+	volume = {91},
+	issn = {00104655},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/001046559500042E},
+	doi = {10.1016/0010-4655(95)00042-E},
+	shorttitle = {{GROMACS}},
+	pages = {43--56},
+	number = {1},
+	journaltitle = {Computer Physics Communications},
+	shortjournal = {Computer Physics Communications},
+	author = {Berendsen, H.J.C. and Van Der Spoel, D. and Van Drunen, R.},
+	urldate = {2023-10-03},
+	date = {1995-09},
+	langid = {english},
+	file = {Berendsen et al. - 1995 - GROMACS A message-passing parallel molecular dyna.pdf:/home/marjan/Zotero/storage/NQBQTWNV/Berendsen et al. - 1995 - GROMACS A message-passing parallel molecular dyna.pdf:application/pdf},
+}
+
+@article{gromacs_2015,
+	title = {{GROMACS}: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
+	volume = {1-2},
+	issn = {23527110},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/S2352711015000059},
+	doi = {10.1016/j.softx.2015.06.001},
+	shorttitle = {{GROMACS}},
+	pages = {19--25},
+	journaltitle = {{SoftwareX}},
+	shortjournal = {{SoftwareX}},
+	author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and Páll, Szilárd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
+	urldate = {2023-10-03},
+	date = {2015-09},
+	langid = {english},
+	file = {Abraham et al. - 2015 - GROMACS High performance molecular simulations th.pdf:/home/marjan/Zotero/storage/GS2XGYLP/Abraham et al. - 2015 - GROMACS High performance molecular simulations th.pdf:application/pdf},
+}
+
+@incollection{Szilárd_gromacs_2015,
+	title = {Tackling Exascale Software Challenges in Molecular Dynamics Simulations with {GROMACS}},
+	volume = {8759},
+	url = {http://arxiv.org/abs/1506.00716},
+	pages = {3--27},
+	author = {Szilárd, Páll and Abraham, Mark James and Kutzner, Carsten and Hess, Berk and Lindahl, Erik},
+	urldate = {2023-10-03},
+	date = {2015},
+	langid = {english},
+	doi = {10.1007/978-3-319-15976-8_1},
+	eprinttype = {arxiv},
+	eprint = {1506.00716 [cs]},
+	keywords = {Computer Science - Computational Engineering, Finance, and Science, I.6.8, J.2},
+	file = {Szilárd et al. - 2015 - Tackling Exascale Software Challenges in Molecular.pdf:/home/marjan/Zotero/storage/2888WILV/Szilárd et al. - 2015 - Tackling Exascale Software Challenges in Molecular.pdf:application/pdf},
+}
+
+@article{Santana-Bonilla_2023,
+	title = {Modular Software for Generating and Modeling Diverse Polymer Databases},
+	volume = {63},
+	issn = {1549-9596, 1549-960X},
+	url = {https://pubs.acs.org/doi/10.1021/acs.jcim.3c00081},
+	doi = {10.1021/acs.jcim.3c00081},
+	pages = {3761--3771},
+	number = {12},
+	journaltitle = {Journal of Chemical Information and Modeling},
+	shortjournal = {J. Chem. Inf. Model.},
+	author = {Santana-Bonilla, Alejandro and López-Ríos De Castro, Raquel and Sun, Peike and Ziolek, Robert M. and Lorenz, Christian D.},
+	urldate = {2023-10-03},
+	date = {2023-06-26},
+	langid = {english},
+	file = {Santana-Bonilla et al. - 2023 - Modular Software for Generating and Modeling Diver.pdf:/home/marjan/Zotero/storage/AE3GZU56/Santana-Bonilla et al. - 2023 - Modular Software for Generating and Modeling Diver.pdf:application/pdf},
+}
+
+@incollection{mbuild_2016,
+	location = {Singapore},
+	title = {A Hierarchical, Component Based Approach to Screening Properties of Soft Matter},
+	isbn = {978-981-10-1126-9 978-981-10-1128-3},
+	url = {http://link.springer.com/10.1007/978-981-10-1128-3_5},
+	pages = {79--92},
+	booktitle = {Foundations of Molecular Modeling and Simulation},
+	publisher = {Springer Singapore},
+	author = {Klein, Christoph and Sallai, János and Jones, Trevor J. and Iacovella, Christopher R. and {McCabe}, Clare and Cummings, Peter T.},
+	editor = {Snurr, Randall Q and Adjiman, Claire S. and Kofke, David A.},
+	urldate = {2023-10-05},
+	date = {2016},
+	langid = {english},
+	doi = {10.1007/978-981-10-1128-3_5},
+	note = {Series Title: Molecular Modeling and Simulation},
+	file = {Klein et al. - 2016 - A Hierarchical, Component Based Approach to Screen.pdf:/home/marjan/Zotero/storage/FU5HX33B/Klein et al. - 2016 - A Hierarchical, Component Based Approach to Screen.pdf:application/pdf},
+}
+
+@article{lammps_2022,
+	title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
+	volume = {271},
+	issn = {00104655},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/S0010465521002836},
+	doi = {10.1016/j.cpc.2021.108171},
+	pages = {108171},
+	journaltitle = {Computer Physics Communications},
+	shortjournal = {Computer Physics Communications},
+	author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and In 'T Veld, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
+	urldate = {2023-10-05},
+	date = {2022-02},
+	langid = {english},
+	file = {Thompson et al. - 2022 - LAMMPS - a flexible simulation tool for particle-b.pdf:/home/marjan/Zotero/storage/YY2CV6SA/Thompson et al. - 2022 - LAMMPS - a flexible simulation tool for particle-b.pdf:application/pdf},
+}
+
+@software{gmso,
+	title = {{GMSO}: General Molecular Simulation Object.},
+	url = {https://gmso.mosdef.org/en/stable/},
+	publisher = {mosdef-hub, Vanderbilt University},
+}

paper/paper.md

@@ -0,0 +1,134 @@
+---
+title: 'JankFlow: A Flexible Python Library for Organic Workflows'
+tags:
+  - molecular simulation
+  - materials science
+  - molecular dynamics
+  - polymers
+  - HOOMD-blue
+authors:
+  - name: Chris Jones
+    orcid: 0000-0002-6196-5274
+    equal-contrib: true
+    affiliation: 1
+  - name: Marjan Albooyeh
+    orcid: 0009-0001-9565-3076
+    equal-contrib: true
+    affiliation: 1
+  - name: Rainier Barrett
+    orcid: 0000-0002-5728-9074
+    corresponding: true
+    affiliation: 1
+  - name: Eric Jankowski
+    orcid: 0000-0002-3267-1410
+    corresponding: true
+    affiliation: 1
+affiliations:
+ - name: Boise State University, Boise, ID, USA
+   index: 1
+date: 01 January 2001
+bibliography: paper.bib
+
+---
+# Summary
+`JankFlow` is a package for reproducibly performing complex HOOMD-Blue simulation workflows. It enables the programmatic specification of tasks including
+definition of molecular structures, forcefield definition and application, chaining
+together simulation stages (e.g., shrinking, equilibration, simulating a sequence
+of ensembles, tensile testing), and trajectory analysis through an extensible set
+of python classes. Common tasks and forcefields for organic macrmolecular and
+polymer simulations are included, as are tutorials demonstrating customization
+and extensibility.
+
+# Statement of need
+
+High-level programmatic specification of molecular simulation workflows are
+needed for two reasons: First: They provide the information necessary for a
+simulation study to be reproducible, and Second: They minimize the cognitive
+load of getting started with running experiments [?].
+For a researcher new to molecular simulations, building the necessary set
+of computational tools needed to actually perform experiments simultaneously:
+(a) requires skills and knowledge different from those needed to do research,
+(b) involves repeating work that others have already done.
+
+This is a well recognized problem, and recent advances in well-documented
+open-source tools have made the programmatic specification of
+molecular simulation components easier than ever [? ? ? ?].
+Individually, each of these tools lower the cognitive load of one aspect of an
+overall workflow such as representing molecules, building initial structures,
+paramaterizing and applying a forcefield, to running simulations.
+However, the challenge of stitching the pieces together to create a complete
+workflow still contains several barriers.
+
+The computational researcher who follows best practices for accurate,
+accessible and reproducible results may create a programmatic layer over these
+individual software packages (i.e. wrapper) that serves to consolidate and
+automate a complete workflow [?, ?, ?]. However, these efforts often use a bespoke approach
+where the entire workflow design is tailored towards the specific question or
+project. Design choices might include the materials studied, the model used
+(e.g. atomistic or coarse-grained), the source of the forcefield in the model, and
+the simulation protocols followed. As a result, this wrapper is likely unusable
+for the next project where one of the aforementioned choices changes, and the
+process of designing a workflow must begin again from scratch.
+
+Software packages such as Radonpy exist that provide an automated workflow for
+building molecules and bulk structures to calculating physical properties of polymers.
+This doesn't work when modeling complex experimental processes that go beyond measuring
+material properties such as fusion weding of polymer interface, surface wetting, [?, ?, ?]
+
+Jankflow is a python package that consolidates and automates
+end-to-end workflows for modeling such processes with a focus on organic molecules.
+Following the principals of Transparent, Reproducible, Usable by others, and Extensible (TRUE) [?]
+software design, the modular design of `JankFlow` facilitates  building and
+running workflows for specific materials science research applications,
+while reducing the cognitive load and programming demands on the user's part.
+###############
+
+It is extensible; a workflow from beginning to
+end should not depend on the chemistry chosen, whether or not the model is
+atomistic or coarse-grained, or if interaction parameters come from established
+forcefields or from a machine learned model. This tool should be modular,
+allowing workflows to evolve into highly specific applications further down the
+pipeline, without concerns about design choices limiting or interfering with other
+use cases. Moreover, the continuous maintenance, updates, and addition of features to this foundational base permeate throughout the library of workflows.
+If executed thoughtfully and accurately, this enables the creation of a library
+of versatile, open-source, and version-controlled workflows. `JankFlow` is an
+attempt at making this tool by creating a TRUE base and beginning a library of
+workflow modules.
+
+
+# Building Blocks
+`JankFlow` encompasses flexible base classes (building blocks) that lays the
+foundations for constructing segregated workflow recipies. Because of this modular design the recipies are agnostic to choices such as chemistry, model resolution
+(atomistic or coarse grained) or forcefields. This is accomplished by utilizing three base classes:
+
+• Molecule utilizes the mBuild and GMSO packages to initialize chemical
+structures from a variety of input formats. This class provides methods
+for building polymers and copolymer structures and supports straightforward
+coarse-graining process.
+
+• System class serves as an intermediary between molecular initialization
+and simulation setup. This class builds the initial configuration and
+generates the focefield that defines particle interactions.
+
+• Simulation class adds a layer on top of the HOOMD-blue simulation object, which
+adds additional methods and features that simplifies the process of starting and
+resuming a HOOMD-blue simulation.
+
+# Library and Recipes
+.....
+`JankFlow` offers the following two ready-to-go recipes to illustrate how the design creates potential for expanding the library of workflows.
+
+• Welding: What does this recipe do. Simulation to create slabs, building up an interface from slabs, simulation to preform welding.
+• Tensile Testing
+
+# Availability
+`JankFlow` is freely available under the GNU General Public License (version 3)
+on [github](https://github.com/cmelab/JankFlow). For installation instructions,
+and Python API documentation
+please visit the [documentation](https://jankflow.readthedocs.io/en/latest/).
+For examples of how to use `JankFlow`,
+please visit the [tutorials](https://github.com/cmelab/JankFlow/tree/main/tutorials)
+# Acknowledgements
+We acknowledge contributions from [ULI Advisory board, NASA, etc]
+
+# References