references.bib

% UC OSPO Network — shared bibliography
%
% Organisation:
%   1. IASSIST 2026 presentation sources (hettrick2014 … tidelift2024)
%   2. Internet / networking history
%   3. UC project canonical papers (in chapter order)
%   4. Additional UC projects (appendix)
%
% Keys: <firstauthor><year><shortname>  e.g. weil2006ceph
% Used across presentations, history book, and reports.
% Maintained alongside iassist-2026-bibliography.md (annotated validation notes).

@techreport{hettrick2014,
  author      = {Hettrick, Simon and Antonioletti, Mario and Carr, Les and
                 Chue Hong, Neil and Crouch, Stephen and De Roure, David and
                 Emsley, Iain and Goble, Carole and Hay, Alexander and
                 Inupakutika, Devasena and others},
  title       = {{UK Research Software Survey 2014}},
  institution = {Software Sustainability Institute},
  year        = {2014},
  doi         = {10.5281/zenodo.14809},
  url         = {https://zenodo.org/records/14809},
  note        = {92\% of researchers use software; 69\% say research would
                 not be practical without it}
}

@techreport{hoffmann2024,
  author      = {Hoffmann, Manuel and Nagle, Frank and Zhou, Yanuo},
  title       = {The Value of Open Source Software},
  institution = {Harvard Business School},
  year        = {2024},
  number      = {24-038},
  type        = {Working Paper},
  doi         = {10.2139/ssrn.4693148},
  url         = {https://ssrn.com/abstract=4693148},
  note        = {Supply-side value \$4.15B; demand-side value \$8.8T;
                 firms would spend 3.5$\times$ more without OSS}
}

@article{barker2022,
  author      = {Barker, Michelle and Chue Hong, Neil P. and Katz, Daniel S.
                 and Lamprecht, Anna-Lena and Martinez-Ortiz, Carlos and
                 Psomopoulos, Fotis and Harrow, Jennifer and Castro, Leyla Jael
                 and Gruenpeter, Morane and Martinez, Paula Andrea and
                 Honeyman, Tom},
  title       = {Introducing the {FAIR} Principles for research software},
  journal     = {Scientific Data},
  year        = {2022},
  volume      = {9},
  pages       = {622},
  doi         = {10.1038/s41597-022-01710-x}
}

@misc{ruff2026,
  author       = {Ruff, Nick},
  title        = {The Role of Foundations in Advancing Open Collaboration
                  and Innovation},
  howpublished = {UC Open Summit},
  year         = {2026},
  url          = {https://youtu.be/eBriL3CDNeo}
}

@misc{gomez2025,
  author        = {Gomez, Juanita and Lovell, Emily and Lieggi, Stephanie
                   and Cardenas, Alvaro A. and Davis, James},
  title         = {Recipe for Discovery: {A} Pipeline for Institutional
                   Open Source Activity},
  year          = {2025},
  eprint        = {2506.18359},
  archivePrefix = {arXiv},
  primaryClass  = {cs.SE},
  url           = {https://arxiv.org/abs/2506.18359},
  note          = {236,037 repos scanned across 10 UC campuses;
                   81,640 institutionally affiliated after LLM filtering}
}

@misc{scarlett2025,
  author    = {Scarlett, Virginia and Curty, Renata Gonçalves and
               Gomez, Juanita and Langdon, Laura and Jan{\'e}e, Greg and
               Budden, Amber E.},
  title     = {A System-Wide Snapshot: {A} Multi-Campus Survey of Open
               Source Contributors at the {University of California}},
  year      = {2025},
  doi       = {10.31235/osf.io/p8bx6_v1},
  url       = {https://osf.io/preprints/socarxiv/p8bx6},
  publisher = {SocArXiv},
  note      = {294 respondents; 58\% of experienced contributors
               are also maintainers}
}

@techreport{tidelift2024,
  author      = {{Tidelift}},
  title       = {The 2024 {Tidelift} Maintainer Impact Report},
  institution = {Tidelift},
  year        = {2024},
  month       = nov,
  url         = {https://dev.to/tidelift/the-open-source-maintainer-community-is-getting-grayer-1gc2},
  note        = {60\% of maintainers are unpaid hobbyists;
                 nearly two-thirds have quit or considered quitting}
}

% -----------------------------------------------------------------------
% Internet / networking history
% -----------------------------------------------------------------------

@article{cerf1974tcp,
  author  = {Cerf, Vinton G. and Kahn, Robert E.},
  title   = {A protocol for packet network intercommunication},
  journal = {{IEEE} Transactions on Communications},
  year    = {1974},
  volume  = {22},
  number  = {5},
  pages   = {637--648},
  doi     = {10.1109/TCOM.1974.1092259}
}

% -----------------------------------------------------------------------
% UC project canonical papers — in chapter order
% -----------------------------------------------------------------------

% Ch 01: Foundations — Berkeley databases

@article{stonebraker1976ingres,
  author  = {Stonebraker, Michael and Wong, Eugene and Kreps, Peter and Held, Gerald},
  title   = {The design and implementation of {INGRES}},
  journal = {{ACM} Transactions on Database Systems},
  year    = {1976},
  volume  = {1},
  number  = {3},
  pages   = {189--222},
  doi     = {10.1145/320473.320476}
}

@techreport{stonebraker1987postgres,
  author      = {Stonebraker, Michael and Rowe, Lawrence A.},
  title       = {The design of {POSTGRES}},
  institution = {University of California, Berkeley},
  year        = {1987},
  number      = {UCB/ERL M86/85}
}

% Ch 02: Universal Infrastructure

@misc{tzdatabase,
  author       = {Olson, Arthur David and Eggert, Paul},
  title        = {{tz} Database ({IANA} Time Zone Database)},
  year         = {1986},
  howpublished = {IANA},
  url          = {https://www.iana.org/time-zones},
  note         = {Ships with every major operating system;
                  maintained at \url{https://github.com/eggert/tz}}
}

% Ch 03: Open Science

@article{kent2002genome,
  author  = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and
             Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and
             Haussler, David},
  title   = {The human genome browser at {UCSC}},
  journal = {Genome Research},
  year    = {2002},
  volume  = {12},
  number  = {6},
  pages   = {996--1006},
  doi     = {10.1101/gr.229102}
}

@article{delorme2004eeglab,
  author  = {Delorme, Arnaud and Makeig, Scott},
  title   = {{EEGLAB}: An open source toolbox for analysis of single-trial
             {EEG} dynamics including independent component analysis},
  journal = {Journal of Neuroscience Methods},
  year    = {2004},
  volume  = {134},
  number  = {1},
  pages   = {9--21},
  doi     = {10.1016/j.jneumeth.2003.10.009}
}

@article{shannon2003cytoscape,
  author  = {Shannon, Paul and Markiel, Andrew and Ozier, Owen and
             Baliga, Nitin S. and Wang, Jonathan T. and Ramage, Daniel and
             Amin, Nada and Schwikowski, Benno and Ideker, Trey},
  title   = {Cytoscape: A software environment for integrated models of
             biomolecular interaction networks},
  journal = {Genome Research},
  year    = {2003},
  volume  = {13},
  number  = {11},
  pages   = {2498--2504},
  doi     = {10.1101/gr.1239303}
}

% Ch 04: Scientific Computing

@inproceedings{kluyver2016jupyter,
  author    = {Kluyver, Thomas and Ragan-Kelley, Benjamin and P{\'e}rez,
               Fernando and Granger, Brian and Bussonnier, Matthias and
               Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica and
               Grout, Jason and Corlay, Sylvain and Ivanov, Paul and
               Avila, Dami{\'a}n and Abdalla, Safia and Willing, Carol},
  title     = {Jupyter {Notebooks} --- a publishing format for reproducible
               computational workflows},
  booktitle = {Positioning and Power in Academic Publishing: Players, Agents
               and Agendas},
  editor    = {Loizides, Fernando and Schmidt, Birgit},
  year      = {2016},
  pages     = {87--90},
  publisher = {{IOS} Press},
  doi       = {10.3233/978-1-61499-649-1-87}
}

@inproceedings{zaharia2012spark,
  author    = {Zaharia, Matei and Chowdhury, Mosharaf and Das, Tathagata and
               Dave, Ankur and Ma, Justin and McCauly, Murphy and
               Franklin, Michael J. and Shenker, Scott and Stoica, Ion},
  title     = {Resilient distributed datasets: {A} fault-tolerant abstraction
               for in-memory cluster computing},
  booktitle = {9th {USENIX} Symposium on Networked Systems Design and
               Implementation ({NSDI})},
  year      = {2012},
  pages     = {15--28},
  publisher = {{USENIX} Association}
}

% Ch 05: Infrastructure at Scale

@inproceedings{weil2006ceph,
  author    = {Weil, Sage A. and Brandt, Scott A. and Miller, Ethan L. and
               Long, Darrell D. E. and Maltzahn, Carlos},
  title     = {Ceph: A scalable, high-performance distributed file system},
  booktitle = {7th {USENIX} Symposium on Operating Systems Design and
               Implementation ({OSDI})},
  year      = {2006},
  pages     = {307--320},
  publisher = {{USENIX} Association}
}

@misc{riscv2019,
  author       = {Waterman, Andrew and Asanovi{\'c}, Krste},
  title        = {The {RISC-V} Instruction Set Manual, Volume {I}:
                  Unprivileged {ISA}},
  year         = {2019},
  howpublished = {{RISC-V} Foundation},
  url          = {https://github.com/riscv/riscv-isa-manual}
}

@article{zhang2014ndn,
  author  = {Zhang, Lixia and Afanasyev, Alexander and Burke, Jeffrey and
             Jacobson, Van and claffy, kc and Crowley, Patrick and
             Papadopoulos, Christos and Wang, Lan and Zhang, Beichuan},
  title   = {Named data networking},
  journal = {{ACM} {SIGCOMM} Computer Communication Review},
  year    = {2014},
  volume  = {44},
  number  = {3},
  pages   = {66--73},
  doi     = {10.1145/2656877.2656887}
}

@inproceedings{moritz2018ray,
  author    = {Moritz, Philipp and Nishihara, Robert and Wang, Stephanie and
               Tumanov, Alexey and Liaw, Richard and Liang, Eric and
               Elibol, Mehrdad and Yang, Zongheng and Paul, William and
               Jordan, Michael I. and Stoica, Ion},
  title     = {Ray: A distributed framework for emerging {AI} applications},
  booktitle = {13th {USENIX} Symposium on Operating Systems Design and
               Implementation ({OSDI})},
  year      = {2018},
  pages     = {561--577},
  publisher = {{USENIX} Association}
}

% -----------------------------------------------------------------------
% Additional UC projects (appendix)
% -----------------------------------------------------------------------

@article{brown2016sourmash,
  author  = {Brown, C. Titus and Irber, Luiz},
  title   = {sourmash: a library for {MinHash} sketching of {DNA}},
  journal = {Journal of Open Source Software},
  year    = {2016},
  volume  = {1},
  number  = {5},
  pages   = {27},
  doi     = {10.21105/joss.00027}
}

@article{eastman2017openmm,
  author  = {Eastman, Peter and Swails, Jason and Chodera, John D. and
             McGibbon, Robert T. and Zhao, Yutong and Beauchamp, Kyle A. and
             Wang, Lee-Ping and Simmonett, Andrew C. and Harrigan, Matthew P.
             and Stern, Chaya D. and Wiewiora, Rafal P. and Brooks, Bernard R.
             and Pande, Vijay S.},
  title   = {{OpenMM} 7: Rapid development of high performance algorithms for
             molecular dynamics},
  journal = {{PLOS} Computational Biology},
  year    = {2017},
  volume  = {13},
  number  = {7},
  pages   = {e1005659},
  doi     = {10.1371/journal.pcbi.1005659}
}