HuttleyLab / DiverseSeq

Tools for analysis of sequence divergence
BSD 3-Clause "New" or "Revised" License
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DOC: manuscript related tasks #22

Open GavinHuttley opened 2 months ago

GavinHuttley commented 2 months ago

Intro

Methods

Results

GavinHuttley commented 2 months ago

Sample paper.md


title: 'Gala: A Python package for galactic dynamics' tags:

Optional fields if submitting to a AAS journal too, see this blog post:

https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing

aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. aas-journal: Astrophysical Journal <- The name of the AAS journal.

Summary

The forces on stars, galaxies, and dark matter under external gravitational fields lead to the dynamical evolution of structures in the universe. The orbits of these bodies are therefore key to understanding the formation, history, and future state of galaxies. The field of "galactic dynamics," which aims to model the gravitating components of galaxies to study their structure and evolution, is now well-established, commonly taught, and frequently used in astronomy. Aside from toy problems and demonstrations, the majority of problems require efficient numerical tools, many of which require the same base code (e.g., for performing numerical orbit integration).

Statement of need

Gala is an Astropy-affiliated Python package for galactic dynamics. Python enables wrapping low-level languages (e.g., C) for speed without losing flexibility or ease-of-use in the user-interface. The API for Gala was designed to provide a class-based and user-friendly interface to fast (C or Cython-optimized) implementations of common operations such as gravitational potential and force evaluation, orbit integration, dynamical transformations, and chaos indicators for nonlinear dynamics. Gala also relies heavily on and interfaces well with the implementations of physical units and astronomical coordinate systems in the Astropy package [@astropy] (astropy.units and astropy.coordinates).

Gala was designed to be used by both astronomical researchers and by students in courses on gravitational dynamics or astronomy. It has already been used in a number of scientific publications [@Pearson:2017] and has also been used in graduate courses on Galactic dynamics to, e.g., provide interactive visualizations of textbook material [@Binney:2008]. The combination of speed, design, and support for Astropy functionality in Gala will enable exciting scientific explorations of forthcoming data releases from the Gaia mission [@gaia] by students and experts alike.

Mathematics

Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$

Double dollars make self-standing equations:

$$\Theta(x) = \left{\begin{array}{l} 0\textrm{ if } x < 0\cr 1\textrm{ else} \end{array}\right.$$

You can also use plain \LaTeX for equations \begin{equation}\label{eq:fourier} \hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx \end{equation} and refer to \autoref{eq:fourier} from text.

Citations

Citations to entries in paper.bib should be in rMarkdown format.

If you want to cite a software repository URL (e.g. something on GitHub without a preferred citation) then you can do it with the example BibTeX entry below for @fidgit.

For a quick reference, the following citation commands can be used:

Figures

Figures can be included like this: Caption for example figure.\label{fig:example} and referenced from text using \autoref{fig:example}.

Figure sizes can be customized by adding an optional second parameter: Caption for example figure.{ width=20% }

Acknowledgements

We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong Oh, and support from Kathryn Johnston during the genesis of this project.

References

GavinHuttley commented 2 months ago

sample paper.bib

@article{Pearson:2017, url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P}, Archiveprefix = {arXiv}, Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.}, Eprint = {1703.04627}, Journal = {ArXiv e-prints}, Keywords = {Astrophysics - Astrophysics of Galaxies}, Month = mar, Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}}, Year = 2017 }

@book{Binney:2008, url = {http://adsabs.harvard.edu/abs/2008gady.book.....B}, Author = {{Binney}, J. and {Tremaine}, S.}, Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.}, Publisher = {Princeton University Press}, Title = {{Galactic Dynamics: Second Edition}}, Year = 2008 }

@article{gaia, author = {{Gaia Collaboration}}, title = "{The Gaia mission}", journal = {Astronomy and Astrophysics}, archivePrefix = "arXiv", eprint = {1609.04153}, primaryClass = "astro-ph.IM", keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes}, year = 2016, month = nov, volume = 595, doi = {10.1051/0004-6361/201629272}, url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G}, }

@article{astropy, author = {{Astropy Collaboration}}, title = "{Astropy: A community Python package for astronomy}", journal = {Astronomy and Astrophysics}, archivePrefix = "arXiv", eprint = {1307.6212}, primaryClass = "astro-ph.IM", keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools}, year = 2013, month = oct, volume = 558, doi = {10.1051/0004-6361/201322068}, url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A} }

@misc{fidgit, author = {A. M. Smith and K. Thaney and M. Hahnel}, title = {Fidgit: An ungodly union of GitHub and Figshare}, year = {2020}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/arfon/fidgit} }