@article{fuegi_lovelace_2003,
    title = {Lovelace \& babbage and the creation of the 1843 'notes'},
    volume = {25},
    issn = {1058-6180},
    url = {https://ieeexplore.ieee.org/document/1253887/},
    doi = {10.1109/MAHC.2003.1253887},
    language = {en},
    number = {4},
    urldate = {2024-05-10},
    journal = {IEEE Annals of the History of Computing},
    author = {Fuegi, J. and Francis, J.},
    month = oct,
    year = {2003},
    pages = {16--26},
}

@book{herbert_dune_2010,
    address = {New York},
    edition = {Ace premium edition},
    series = {The {Dune} chronicles},
    title = {Dune},
    isbn = {978-0-441-17271-9},
    abstract = {Follows the adventures of Paul Atreides, the son of a betrayed duke given up for dead on a treacherous desert planet and adopted by its fierce, nomadic people, who help him unravel his most unexpected destiny},
    language = {eng},
    publisher = {Ace},
    author = {Herbert, Frank and Herbert, Brian},
    year = {2010},
    annote = {bk. 1. Dune -- bk. 2. Muad'Dib -- bk. 3. The prophet},
}

@article{nath_managing_2015,
    title = {Managing woody bamboos for carbon farming and carbon trading},
    volume = {3},
    issn = {23519894},
    url = {https://linkinghub.elsevier.com/retrieve/pii/S2351989415000281},
    doi = {10.1016/j.gecco.2015.03.002},
    language = {en},
    urldate = {2024-05-12},
    journal = {Global Ecology and Conservation},
    author = {Nath, Arun Jyoti and Lal, Rattan and Das, Ashesh Kumar},
    month = jan,
    year = {2015},
    pages = {654--663},
}

@book{kimmerer_braiding_2013,
    address = {Minneapolis, Minn},
    edition = {First paperback edition},
    title = {Braiding sweetgrass: indigenous wisdom, scientific knowledge and the teachings of plants},
    isbn = {978-1-57131-356-0},
    shorttitle = {Braiding sweetgrass},
    language = {eng},
    publisher = {Milkweed Editions},
    author = {Kimmerer, Robin Wall},
    year = {2013},
    annote = {"As a leading researcher in the field of biology, Robin Wall Kimmerer understands the delicate state of our world. But as an active member of the Potawatomi nation, she senses and relates to the world through a way of knowing far older than any science. In Braiding Sweetgrass, she intertwines these two modes of awareness--the analytic and the emotional, the scientific and the cultural--to ultimately reveal a path toward healing the rift that grows between people and nature. The woven essays that construct this book bring people back into conversation with all that is green and growing; a universe that never stopped speaking to us, even when we forgot how to listen"-- "An inspired weaving of indigenous knowledge, plant science, and personal narrative from a distinguished professor of science and a Native American whose previous book, Gathering Moss, was awarded the John Burroughs Medal for outstanding nature writing. As a botanist and professor of plant ecology, Robin Wall Kimmerer has spent a career learning how to ask questions of nature using the tools of science. As a Potawatomi woman, she learned from elders, family, and history that the Potawatomi, as well as a majority of other cultures indigenous to this land, consider plants and animals to be our oldest teachers. In Braiding Sweetgrass, Kimmerer brings these two lenses of knowing together to reveal what it means to see humans as "the younger brothers of creation." As she explores these themes she circles toward a central argument: the awakening of a wider ecological consciousness requires the acknowledgement and celebration of our reciprocal relationship with the world. Once we begin to listen for the languages of other beings, we can begin to understand the innumerable life-giving gifts the world provides us and learn to offer our thanks, our care, and our own gifts in return"--},
}

@book{hart_forest_1996,
    address = {White River Junction, Vt},
    title = {Forest gardening: cultivating an edible landscape},
    isbn = {978-0-930031-84-8},
    shorttitle = {Forest gardening},
    publisher = {Chelsea Green Pub. Co},
    author = {Hart, Robert A. de J.},
    year = {1996},
    keywords = {Agroforestry, Edible forest gardens, Permaculture},
    annote = {"Originally published in 1991 in the United Kingdom by Green Books, Ltd. Revised and expanded Green Books edition published in 1996"--T.p. verso},
}

@article{kagawa_fujisaki_3d_farming,
author={Kagawa, T., and S. Fujisaki.},
year={1935},
title={Rittai Nogyo no riron to jissen (Theory and practice of three-dimensional structural farming)},
journal={Tokyo, Japan: Nihonhyoronsya}
}

@article{foote1997big,
  title={Big ball of mud},
  author={Foote, Brian and Yoder, Joseph},
  journal={Pattern languages of program design},
  volume={4},
  pages={654--692},
  year={1997}
}

@article{mcdonough1998waste,
  title={Waste equals food: our future and the making of things},
  author={McDonough, William},
  journal={Awakening--The Upside of Y2k, The Printed Word, Spokane},
  year={1998}
}

@book{stappmanns_garden_2023,
    key = {SVK23},
    address = {Weil am Rhein},
    title = {Garden futures: designing with nature},
    isbn = {978-3-945852-53-8},
    shorttitle = {Garden futures},
    language = {eng},
    publisher = {Vitra Design Museum},
    editor = {Stappmanns, Viviane and Kries, Mateo and {Vitra Design Museum} and {Wüstenrot Stiftung}},
    year = {2023},
    file = {Table of Contents PDF:/Users/dabu5788/Zotero/storage/ZFGM58ZY/Stappmanns et al. - 2023 - Garden futures designing with nature.pdf:application/pdf},
}

@misc{image_gimmel_lattice,
  author = {Benjamin Gimmel},
  title = {Round window with lattice},
  year = {2005},
  url = {https://commons.wikimedia.org/wiki/File:Rundes_Fenster_mit_Gitter.jpg},
  urldate = {2024-05-17},
}

@misc{image_burnett_forestgarden,
  author = {Graham Burnett},
  title = {Forest garden diagram to replace the one that currently exists on the article.},
  year = {2006},
  url = {https://commons.wikimedia.org/wiki/File:Forgard2-003.gif},
  urldate = {2024-05-17},
}

@article{gramling2020tree,
  title={‘Tree Story’ explores what tree rings can tell us about the past},
  author={Gramling, Carolyn},
  journal={Science News},
  year={2020},
  month={June},
  url={https://www.sciencenews.org/article/tree-story-book-explores-what-tree-rings-can-tell-us-about-past},
  note={Accessed: 2024-05-18}
}

@book{morton2013hyperobjects,
  title={Hyperobjects: Philosophy and Ecology after the End of the World},
  author={Morton, Timothy},
  year={2013},
  publisher={University of Minnesota Press},
  address={Minneapolis},
  isbn={9780816689231}
}

@misc{image_elfward_sundial,
  author = {Elfward},
  title = {Garden sundial in an Epping garden},
  year = {2015},
  url = {https://commons.wikimedia.org/wiki/File:Sundial_2916_HDR.jpg},
  urldate = {2024-05-18},
}

@inproceedings{hassan_predicting_2009,
  address = {Vancouver, BC, Canada},
  title = {Predicting faults using the complexity of code changes},
  isbn = {978-1-4244-3453-4},
  url = {http://ieeexplore.ieee.org/document/5070510},
  doi = {10.1109/ICSE.2009.5070510},
  urldate = {2024-07-15},
  booktitle = {2009 IEEE 31st International Conference on Software Engineering},
  publisher = {IEEE},
  author = {Hassan, Ahmed E.},
  year = {2009},
  pages = {78--88},
}

@article{lee_ten_2018,
  title = {Ten simple rules for documenting scientific software},
  volume = {14},
  issn = {1553-7358},
  url = {https://dx.plos.org/10.1371/journal.pcbi.1006561},
  doi = {10.1371/journal.pcbi.1006561},
  language = {en},
  number = {12},
  urldate = {2024-12-31},
  journal = {PLOS Computational Biology},
  author = {Lee, Benjamin D.},
  editor = {Markel, Scott},
  month = dec,
  year = {2018},
  pages = {e1006561},
}


@inproceedings{coelho_why_2017,
  address = {Paderborn Germany},
  title = {Why modern open source projects fail},
  isbn = {978-1-4503-5105-8},
  url = {https://dl.acm.org/doi/10.1145/3106237.3106246},
  doi = {10.1145/3106237.3106246},
  language = {en},
  urldate = {2024-12-31},
  booktitle = {Proceedings of the 2017 11th {Joint} {Meeting} on {Foundations} of {Software} {Engineering}},
  publisher = {ACM},
  author = {Coelho, Jailton and Valente, Marco Tulio},
  month = aug,
  year = {2017},
  pages = {186--196},
}


@misc{treude_towards_2024,
  title = {Towards the {First} {Code} {Contribution}: {Processes} and {Information} {Needs}},
  copyright = {arXiv.org perpetual, non-exclusive license},
  shorttitle = {Towards the {First} {Code} {Contribution}},
  url = {https://arxiv.org/abs/2404.18677},
  doi = {10.48550/ARXIV.2404.18677},
  abstract = {Newcomers to a software project must overcome many barriers before they can successfully place their first code contribution, and they often struggle to find information that is relevant to them. In this work, we argue that much of the information needed by newcomers already exists, albeit scattered among many different sources, and that many barriers can be addressed by automatically identifying, extracting, generating, summarizing, and presenting documentation that is specifically aimed and customized for newcomers. To gain a detailed understanding of the processes followed by newcomers and their information needs before making their first code contribution, we conducted an empirical study. Based on a survey with about 100 practitioners, grounded theory analysis, and validation interviews, we contribute a 16-step model for the processes followed by newcomers to a software project and we identify relevant information, along with individual and project characteristics that influence the relevancy of information types and sources. Our findings form an essential step towards automated tool support that provides relevant information to project newcomers in each step of their contribution processes.},
  urldate = {2024-12-31},
  publisher = {arXiv},
  author = {Treude, Christoph and Gerosa, Marco A. and Steinmacher, Igor},
  year = {2024},
  note = {Version Number: 1},
  keywords = {FOS: Computer and information sciences, Software Engineering (cs.SE)},
}


@incollection{damian_codes_2024,
  address = {Berkeley, CA},
  title = {Codes of {Conduct} in {Open} {Source}},
  isbn = {978-1-4842-9650-9 978-1-4842-9651-6},
  url = {https://link.springer.com/10.1007/978-1-4842-9651-6_17},
  abstract = {Abstract
            Hana Frluckaj, James Howison, Qiwei Li, and Laura Dabbish},
  language = {en},
  urldate = {2025-01-02},
  booktitle = {Equity, {Diversity}, and {Inclusion} in {Software} {Engineering}},
  publisher = {Apress},
  author = {Frluckaj, Hana and Howison, James},
  editor = {Damian, Daniela and Blincoe, Kelly and Ford, Denae and Serebrenik, Alexander and Masood, Zainab},
  year = {2024},
  doi = {10.1007/978-1-4842-9651-6_17},
  pages = {295--308},
}

@misc{choosealicense_nopermission,
  author       = {GitHub, Inc.},
  title        = {No License},
  url          = {https://choosealicense.com/no-permission/},
  note         = {Accessed: 2025-01-02},
}


@misc{deekshitha_rsmm_2024,
  title = {{RSMM}: {A} {Framework} to {Assess} {Maturity} of {Research} {Software} {Project}},
  shorttitle = {{RSMM}},
  url = {http://arxiv.org/abs/2406.01788},
  abstract = {The organizations and researchers producing research software face a common problem of making their software sustainable beyond funding provided by a single research project. This is addressed by research software engineers through building communities around their software, providing appropriate licensing, creating reliable and reproducible research software, making it sustainable and impactful, promoting, and ensuring that the research software is easy to adopt in research workflows, etc. As a result, numerous practices and guidelines exist to enhance research software quality, reusability, and sustainability. However, there is a lack of a unified framework to systematically integrate these practices and help organizations and research software developers refine their development and management processes. Our paper aims at bridging this gap by introducing a novel framework: RSMM. It is designed through systematic literature review and insights from interviews with research software project experts. In short, RSMM offers a structured pathway for evaluating and refining research software project management by categorizing 79 best practices into 17 capabilities across 4 focus areas. From assessing code quality and security to measuring impact, sustainability, and reproducibility, the model provides a complete evaluation of a research software project maturity. With RSMM, individuals as well as organizations involved in research software development gain a systematic approach to tackling various research software engineering challenges. By utilizing RSMM as a comprehensive checklist, organizations can systematically evaluate and refine their project management practices and organizational structure.},
  urldate = {2024-10-02},
  publisher = {arXiv},
  author = {Deekshitha and Bakhshi, Rena and Maassen, Jason and Ortiz, Carlos Martinez and van Nieuwpoort, Rob and Jansen, Slinger},
  month = jun,
  year = {2024},
  note = {arXiv:2406.01788 [cs]},
  keywords = {Computer Science - Software Engineering, D.2, K.6.3},
  annote = {Comment: 10 pages, 6 figures, 1 table. Submitted to IEEE eScience 2024 Conference},
}


@article{naur_programming_1985,
  title = {Programming as theory building},
  volume = {15},
  copyright = {https://www.elsevier.com/tdm/userlicense/1.0/},
  issn = {01656074},
  url = {https://linkinghub.elsevier.com/retrieve/pii/0165607485900328},
  doi = {10.1016/0165-6074(85)90032-8},
  language = {en},
  number = {5},
  urldate = {2025-01-02},
  journal = {Microprocessing and Microprogramming},
  author = {Naur, Peter},
  month = may,
  year = {1985},
  pages = {253--261},
}


@misc{afiaz_evaluation_2023,
  title = {Evaluation of software impact designed for biomedical research: {Are} we measuring what's meaningful?},
  shorttitle = {Evaluation of software impact designed for biomedical research},
  url = {http://arxiv.org/abs/2306.03255},
  abstract = {Software is vital for the advancement of biology and medicine. Analysis of usage and impact metrics can help developers determine user and community engagement, justify additional funding, encourage additional use, identify unanticipated use cases, and help define improvement areas. However, there are challenges associated with these analyses including distorted or misleading metrics, as well as ethical and security concerns. More attention to the nuances involved in capturing impact across the spectrum of biological software is needed. Furthermore, some tools may be especially beneficial to a small audience, yet may not have compelling typical usage metrics. We propose more general guidelines, as well as strategies for more specific types of software. We highlight outstanding issues regarding how communities measure or evaluate software impact. To get a deeper understanding of current practices for software evaluations, we performed a survey of participants in the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We also investigated software among this community and others to assess how often infrastructure that supports such evaluations is implemented and how this impacts rates of papers describing usage of the software. We find that developers recognize the utility of analyzing software usage, but struggle to find the time or funding for such analyses. We also find that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seem to be associated with increased usage rates. Our findings can help scientific software developers make the most out of evaluations of their software.},
  urldate = {2024-10-02},
  publisher = {arXiv},
  author = {Afiaz, Awan and Ivanov, Andrey and Chamberlin, John and Hanauer, David and Savonen, Candace and Goldman, Mary J. and Morgan, Martin and Reich, Michael and Getka, Alexander and Holmes, Aaron and Pati, Sarthak and Knight, Dan and Boutros, Paul C. and Bakas, Spyridon and Caporaso, J. Gregory and Del Fiol, Guilherme and Hochheiser, Harry and Haas, Brian and Schloss, Patrick D. and Eddy, James A. and Albrecht, Jake and Fedorov, Andrey and Waldron, Levi and Hoffman, Ava M. and Bradshaw, Richard L. and Leek, Jeffrey T. and Wright, Carrie},
  month = jun,
  year = {2023},
  note = {arXiv:2306.03255 [cs, q-bio]},
  keywords = {Computer Science - Software Engineering, Quantitative Biology - Other Quantitative Biology},
  annote = {Comment: 25 total pages (17 pages for manuscript and 8 pages for the supplement). There are 2 figures},
}

@incollection{henney_97_2010,
  address = {Sebastopol, Calif},
  edition = {1st ed},
  title = {Comment Only What the Code Cannot Say},
  booktitle = {97 things every programmer should know: collective wisdom from the experts},
  isbn = {978-0-596-80948-5 978-0-596-80951-5},
  shorttitle = {97 things every programmer should know},
  abstract = {Tap into the wisdom of experts to learn what every programmer should know, no matter what language you use. With the 97 short and extremely useful tips for programmers in this book, you'll expand your skills by adopting new approaches to old problems, learning appropriate best practices, and honing your craft through sound advice. With contributions from some of the most experienced and respected practitioners in the industry--including Michael Feathers, Pete Goodliffe, Diomidis Spinellis, Cay Horstmann, Verity Stob, and many more--this book contains practical knowledge and principles that you can apply to all kinds of projects. A few of the 97 things you should know: "Code in the Language of the Domain" by Dan North "Write Tests for People" by Gerard Meszaros "Convenience Is Not an -ility" by Gregor Hohpe "Know Your IDE" by Heinz Kabutz "A Message to the Future" by Linda Rising "The Boy Scout Rule" by Robert C. Martin (Uncle Bob) "Beware the Share" by Udi Dahan},
  language = {eng},
  publisher = {O'Reilly Media},
  editor = {Henney, Kevlin},
  year = {2010},
  annote = {Description based on print version record. - Includes index},
}
