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@article{Pearson:2017,
Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
Adsurl = {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,
Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
Adsurl = {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 = {\aap},
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},
adsurl = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G},
}
@article{astropy,
author = {{Astropy Collaboration}},
title = "{Astropy: A community Python package for astronomy}",
journal = {\aap},
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},
adsurl = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}
}
@misc{darling_data:2019,
title = {data for The Gene School: Metagenomics workshop},
rights = {Creative Commons Attribution 4.0 International, Open Access},
url = {https://zenodo.org/record/3585993},
shorttitle = {data for The Gene School},
abstract = {Precomputed data including a metagenomic assembly of multiple samples, reads from multiple samples mapped to the coassembly, metagenome-assembled genomes ({MAGs}), and anvio profiles for the {MAGs}. All from timeseries faecal samples of a single porcine host.},
publisher = {Zenodo},
author = {Darling, Aaron E and {DeMaere}, Matthew Z and Gaio, Daniela and Anantanawat, Kay},
urldate = {2021-07-19},
date = {2019-12-19},
doi = {10.5281/ZENODO.3585993},
note = {Type: dataset},
keywords = {metagenomics, pig microbiome},
}
@article{duda_teaching:2021,
title = {Teaching Python for Data Science: Collaborative development of a modular \& interactive curriculum},
url = {http://biorxiv.org/content/early/2021/06/18/2021.06.17.448726.abstract},
doi = {10.1101/2021.06.17.448726},
abstract = {We are bioinformatics trainees at the University of Michigan who started a local chapter of Girls Who Code to provide a fun and supportive environment for high school women to learn the power of coding. Our goal was to cover basic coding topics and data science concepts through live coding and hands-on practice. However, we could not find a resource that exactly met our needs. Therefore, over the past three years, we have developed a curriculum and instructional format using Jupyter notebooks to effectively teach introductory Python for data science. This method, inspired by The Carpentries organization, uses bite-sized lessons followed by independent practice time to reinforce coding concepts, and culminates in a data science capstone project using real-world data. We believe our open curriculum is a valuable resource to the wider education community and hope that educators will use and improve our lessons, practice problems, and teaching best practices. Anyone can contribute to our educational materials on {GitHub}.Competing Interest {StatementThe} authors have declared no competing interest.},
pages = {2021.06.17.448726},
journaltitle = {{bioRxiv}},
author = {Duda, Marlena and Sovacool, Kelly L. and Farzaneh, Negar and Nguyen, Vy Kim and Haynes, Sarah E. and Falk, Hayley and Furman, Katherine L. and Walker, Logan A. and Diao, Rucheng and Oneka, Morgan and Drotos, Audrey C. and Woloshin, Alana and Dotson, Gabrielle A. and Kriebel, April and Meng, Lucy and Thiede, Stephanie N. and Lapp, Zena and Wolford, Brooke N.},
date = {2021-01-01},
}
@article{lapp_developing:2021,
title = {Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research},
url = {http://biorxiv.org/content/early/2021/06/16/2021.06.15.448091.abstract},
doi = {10.1101/2021.06.15.448091},
abstract = {Inspired by well-established material and pedagogy provided by The Carpentries (Wilson 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al. 2019), the Unix shell, version control with git, and {GitHub}. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop. We also felt that the independent nature of the lessons left learners confused about how to integrate the newly acquired programming skills in their own work. Thus, we developed a new curriculum that aims to teach novices how to implement reproducible research principles in their own data analysis. The curriculum integrates live coding lessons with individual-level and group-based practice exercises, and also serves as a succinct resource that learners can reference both during and after the workshop. Moreover, it lowers the entry barrier for new instructors as they do not have to develop their own teaching materials or sift through extensive content. We developed this curriculum during a two-day sprint, successfully used it to host a two-day virtual workshop with almost 40 participants, and updated the material based on instructor and learner feedback. We hope that our new curriculum will prove useful to future instructors interested in teaching workshops with similar learning objectives.Competing Interest {StatementThe} authors have declared no competing interest.},
pages = {2021.06.15.448091},
journaltitle = {{bioRxiv}},
author = {Lapp, Zena and Sovacool, Kelly L. and Lesniak, Nick and King, Dana and Barnier, Catherine and Flickinger, Matthew and Krüger, Jule and Armour, Courtney R. and Lapp, Maya M. and Tallant, Jason and Diao, Rucheng and Oneka, Morgan and Tomkovich, Sarah and Anderson, Jacqueline Moltzau and Lucas, Sarah K. and Schloss, Patrick D.},
date = {2021-01-01},
}
@article{johnston_graduate:2019,
title = {A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching},
volume = {2},
issn = {2577-3569},
url = {https://jose.theoj.org/papers/10.21105/jose.00049},
doi = {10.21105/jose.00049},
shorttitle = {A graduate student-led participatory live-coding quantitative methods course in R},
pages = {49},
number = {16},
journaltitle = {Journal of Open Source Education},
shortjournal = {{JOSE}},
author = {Johnston, Luke and Bonsma-Fisher, Madeleine and Ostblom, Joel and Hasan, Ahmed and Santangelo, James and Coome, Lindsay and Tran, Lina and De Andrade, Elliott and Mahallati, Sara},
urldate = {2021-07-19},
date = {2019-06-06},
langid = {english},
file = {Johnston et al. - 2019 - A graduate student-led participatory live-coding q.pdf:C\:\\Users\\Jose Abel\\Zotero\\storage\\M8BS2JFL\\Johnston et al. - 2019 - A graduate student-led participatory live-coding q.pdf:application/pdf},
}
@article{johnston_graduate:2019-1,
title = {A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching},
volume = {2},
issn = {2577-3569},
pages = {49},
number = {16},
journaltitle = {Journal of Open Source Education},
shortjournal = {Journal of Open Source Education},
author = {Johnston, Luke W and Bonsma-Fisher, Madeleine and Ostblom, Joel and Hasan, Ahmed R and Santangelo, James S and Coome, Lindsay and Tran, Lina and de Andrade, Elliott Sales and Mahallati, Sara},
date = {2019},
}
@article{bolyen_introduction:2018,
title = {An Introduction to Applied Bioinformatics: a free, open, and interactive text.},
volume = {1},
number = {5},
journaltitle = {The Journal of open source education},
shortjournal = {The Journal of open source education},
author = {Bolyen, Evan and Rideout, Jai Ram and Chase, John and Pitman, T Anders and Shiffer, Arron and Mercurio, Willow and Dillon, Matthew R and Caporaso, J Gregory},
date = {2018},
note = {Publisher: {NIH} Public Access},
}
@article{barba_cfd:2018,
title = {{CFD} Python: the 12 steps to Navier-Stokes equations},
volume = {2},
issn = {2577-3569},
pages = {21},
number = {16},
journaltitle = {Journal of Open Source Education},
shortjournal = {Journal of Open Source Education},
author = {Barba, Lorena A and Forsyth, Gilbert F},
date = {2018},
}
@article{kruchten_curricular:2020,
title = {A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R},
volume = {11},
issn = {1664-302X},
pages = {2135},
journaltitle = {Frontiers in microbiology},
shortjournal = {Frontiers in microbiology},
author = {Kruchten, Anne E},
date = {2020},
note = {Publisher: Frontiers},
}
@article{ryder_incubators:2020,
title = {Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education},
volume = {48},
issn = {1470-8175},
pages = {381--390},
number = {4},
journaltitle = {Biochemistry and Molecular Biology Education},
shortjournal = {Biochemistry and Molecular Biology Education},
author = {Ryder, Elizabeth F and Morgan, William R and Sierk, Michael and Donovan, Samuel S and Robertson, Sabrina D and Orndorf, Hayley C and Rosenwald, Anne G and Triplett, Eric W and Dinsdale, Elizabeth and Pauley, Mark A},
date = {2020},
note = {Publisher: Wiley Online Library},
}
@article{david_introducing:2021,
title = {Introducing Python Programming into Undergraduate Biology},
volume = {83},
issn = {0002-7685},
pages = {33--41},
number = {1},
journaltitle = {The American Biology Teacher},
shortjournal = {The American Biology Teacher},
author = {David, Andrew A},
date = {2021},
note = {Publisher: University of California Press},
}
@online{noauthor_zdelrosariodata-science-curriculum_nodate,
title = {zdelrosario/data-science-curriculum},
url = {https://github.com/zdelrosario/data-science-curriculum},
abstract = {Contribute to zdelrosario/data-science-curriculum development by creating an account on {GitHub}.},
titleaddon = {{GitHub}},
urldate = {2021-07-19},
langid = {english},
file = {Snapshot:C\:\\Users\\Jose Abel\\Zotero\\storage\\3TCH2AP2\\paper.html:text/html},
}
@software{rosario_zdelrosariodata-science-curriculum_2021,
title = {zdelrosario/data-science-curriculum},
rights = {{CC}-{BY}-{SA}-4.0},
url = {https://github.com/zdelrosario/data-science-curriculum/blob/d547ff927025ebf2585fd4c86b72b960fab067b3/paper.md},
author = {Rosario, Zachary del},
urldate = {2021-07-19},
date = {2021-07-11},
note = {original-date: 2020-05-15T13:50:52Z},
}
@article{okie_genomic:2020,
title = {Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment},
volume = {9},
issn = {2050-084X},
url = {https://elifesciences.org/articles/49816},
doi = {10.7554/eLife.49816},
abstract = {Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico. This is one of the first whole-ecosystem experiments to involve replicated metagenomic assessment. Mean bacterial genome size, {GC} content, total number of {tRNA} genes, total number of {rRNA} genes, and codon usage bias in ribosomal protein sequences were all higher in the fertilized treatment, as predicted on the basis of the assumption that oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates. Contrasting changes in trait variances also suggested differences between traits in mediating assembly under copiotrophic versus oligotrophic conditions. Trade-offs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly because the major components of metabolism—information, energy, and nutrient requirements—are fine-tuned to an organism’s growth and trophic strategy.},
pages = {e49816},
journaltitle = {{eLife}},
author = {Okie, Jordan G and Poret-Peterson, Amisha T and Lee, Zarraz {MP} and Richter, Alexander and Alcaraz, Luis D and Eguiarte, Luis E and Siefert, Janet L and Souza, Valeria and Dupont, Chris L and Elser, James J},
urldate = {2021-07-19},
date = {2020-01-28},
langid = {english},
file = {Texto completo:C\:\\Users\\Jose Abel\\Zotero\\storage\\KFKTYBPG\\Okie et al. - 2020 - Genomic adaptations in information processing unde.pdf:application/pdf},
}
@article{becker_datacarpentrygenomics-workshop:019,
title = {datacarpentry/genomics-workshop: Data Carpentry: Genomics Workshop Overview, June 2019},
rights = {Creative Commons Attribution 4.0 International, Open Access},
url = {https://zenodo.org/record/3260309},
doi = {10.5281/ZENODO.3260309},
shorttitle = {datacarpentry/genomics-workshop},
abstract = {Workshop overview for the Data Carpentry genomics curriculum.},
author = {Becker, Erin Alison and Teal, Tracy and Michonneau, François and Sane, Maneesha and Reiter, Taylor and Williams, Jason and Charbonneau, Amanda and Kweskin, Matthew and Anwar, Muhammad Zohaib and Cadzow, Murray and Martinez, Paula Andrea},
urldate = {2021-07-19},
date = {2019-06-28},
note = {Publisher: Zenodo
Version Number: v2019.06.1},
}
@online{noauthor_lessons_nodate,
title = {Lessons},
url = {https://datacarpentry.org/lessons/},
urldate = {2021-09-12},
file = {Lessons:C\:\\Users\\Jose Abel\\Zotero\\storage\\XR2N65T8\\lessons.html:text/html},
}
@article{kruchten_curricular:2020-1,
title = {A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R},
volume = {11},
issn = {1664-302X},
url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.578600},
doi = {10.3389/fmicb.2020.578600},
abstract = {Biologists with bioinformatic skills will be better prepared for the job market, but relatively few biology programs require bioinformatics courses. Inclusion in the curriculum may be hindered by several barriers, including lack of faculty expertise, student resistance to computational work, and few examples in the pedagogical literature. An 8-week wet-lab and in silico research experience for undergraduates was implemented. Students performed {DNA} purification and metagenomics analysis to compare the diversity and abundance of microbes in two samples. Students sampled snow from sites in northern Minnesota and purified genomic {DNA} from the microbes, followed by metagenomic analysis. Students used an existing metagenomic dataset to practice analysis skills, including comparing the use of Excel versus R for analysis and visualization of a large dataset. Upon receipt of the snow data, students applied their recently acquired skills to their new dataset and reported their results via a poster. Several outcomes were achieved as a result of this module. First, {YouTube} videos demonstrating hands-on metagenomics and R techniques were used as professional development for faculty, leading to broadened research capabilities and comfort with bioinformatics. Second, students were introduced to computational skills in a manner that was intentional, with time for both introduction and reinforcement of skills. Finally, the module was effectively included in a biology curriculum because it could function as either a stand-alone course or a module within another course such as microbiology. This module, developed with Course-based Undergraduate Research Experience guidelines in mind, introduces students and faculty to bioinformatics in biology research.},
pages = {2135},
journaltitle = {Frontiers in Microbiology},
author = {Kruchten, Anne E.},
urldate = {2021-09-12},
date = {2020},
file = {Full Text PDF:C\:\\Users\\Jose Abel\\Zotero\\storage\\IVGD2I4G\\Kruchten - 2020 - A Curricular Bioinformatics Approach to Teaching U.pdf:application/pdf},
}