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Research Toolkit, the bibliography: every source cited, with identifiers and check notes (tpm_toolkit 0.1.0)
 
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''Every source the [[The Principia Machina/Research Toolkit|Research Toolkit]] cites: 284 entries in three groups, one per part, then further reading. Each entry carries its key (the label the toolkit's pages link to), its citation as the research passes recorded it, its identifiers as links, and a note of how it was checked: what was fetched, on 2026-10-05 or 2026-10-06, and what could not be confirmed (marked UNVERIFIED). An entry is a pointer to a source, not a claim that the source is right.''
''Every source the [[The Principia Machina/Research Toolkit|Research Toolkit]] cites: 284 entries in three groups, one per part, then further reading. Each entry carries its key (the label the toolkit's pages link to), its citation as the research passes recorded it, its identifiers as links, and a note of how it was checked: what was fetched, on 2026-10-05 or 2026-10-06, and what could not be confirmed (marked UNVERIFIED). An entry is a pointer to a source, not a claim that the source is right.''


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[[Category:Research Toolkit]] [[Category:The Principia Machina]]
[[Category:Research Toolkit]] [[Category:The Principia Machina]]

Latest revision as of 19:33, 15 October 2026

Research Toolkit: map
Reading the toolkit
Arriving as an AI? The manual
Agent flow control
Research methods
Research tools
Bibliography
The physics tools
The survey
In plain language
The operator's guide
The primer
For AI agents
The toolkit as a card
The tools, machine-optimized
Related
The Principia Machina

Every source the Research Toolkit cites: 284 entries in three groups, one per part, then further reading. Each entry carries its key (the label the toolkit's pages link to), its citation as the research passes recorded it, its identifiers as links, and a note of how it was checked: what was fetched, on 2026-10-05 or 2026-10-06, and what could not be confirmed (marked UNVERIFIED). An entry is a pointer to a source, not a claim that the source is right.

How to read an entry

KEY – authors (year). Title. Venue, volume, pages. Identifiers: a DOI links through doi.org, an arXiv identifier to its abstract page. Checked: the research pass's own note.

Before relying on any entry in a register record, resolve its identifier yourself and look for retraction or correction notices (the manual's checklist); on this site a record cites literature only through its container's bibliography, by BIB ID (TPS 5.21). This page is not such a bibliography: it lies outside every container.

Agent flow control

Cited on agent flow control. 73 entries.

Practices and evidence

  • ADAPTIVE – Nasr, M., Carlini, N., Sitawarin, C., Schulhoff, S. V., Hayes, J., Ilie, M., Pluto, J., Song, S., Chaudhari, H., Shumailov, I., Thakurta, A., Xiao, K. Y., Terzis, A., Tramèr, F. (2025). The Attacker Moves Second: Stronger Adaptive Attacks Bypass Defenses Against LLM Jailbreaks and Prompt Injections. arXiv. arXiv:2510.09023. Checked: arXiv abs page fetched
  • AGENTS-MATTER – Kapoor, S., Stroebl, B., Siegel, Z. S., Nadgir, N., Narayanan, A. (2024). AI Agents That Matter. arXiv. arXiv:2407.01502. Checked: arXiv abs page fetched
  • ANTH-BEA – Schluntz, E. [byline "Erik S."], Zhang, B. (2024). Building effective agents. Anthropic Engineering, 19 Dec 2024. www.anthropic.com/engineering/building-effective-agents. Checked: page fetched
  • ANTH-CE – Rajasekaran, P., Dixon, E., Ryan, C., Hadfield, J. (2025). Effective context engineering for AI agents. Anthropic Engineering, 29 Sep 2025. www.anthropic.com/engineering/effective-context-engineering-.... Checked: page fetched
  • ANTH-EVALS – Grace, M., Hadfield, J., Olivares, R., De Jonghe, J. (2026). Demystifying evals for AI agents. Anthropic Engineering, 9 Jan 2026. www.anthropic.com/engineering/demystifying-evals-for-ai-agen.... Checked: page fetched
  • ANTH-HARNESS – Young, J. (2025). Effective harnesses for long-running agents. Anthropic Engineering, 26 Nov 2025. www.anthropic.com/engineering/effective-harnesses-for-long-r.... Checked: page fetched
  • ANTH-HDESIGN – Rajasekaran, P. (2026). Harness design for long-running application development. Anthropic Engineering, 24 Mar 2026. www.anthropic.com/engineering/harness-design-long-running-ap.... Checked: page fetched
  • ANTH-MA – Hadfield, J., Zhang, B., Lien, K., Scholz, F., Fox, J., Ford, D. (2025). How we built our multi-agent research system. Anthropic Engineering, 13 Jun 2025. www.anthropic.com/engineering/multi-agent-research-system. Checked: page fetched
  • AUTOBIAS – Skitka, L. J., Mosier, K. L., Burdick, M. (1999). Does automation bias decision-making? International Journal of Human-Computer Studies 51(5):991–1006. doi:10.1006/ijhc.1999.0252. Checked: Crossref metadata only; abstract not fetched (cited for the construct only)
  • BACKOFF – Brooker, M. (2015, updated 2023). Exponential Backoff And Jitter. AWS Architecture Blog. aws.amazon.com/blogs/architecture/exponential-backoff-and-ji.... Checked: page fetched | full-jitter formula
  • BREAKER – Fowler, M. (2014). CircuitBreaker. martinfowler.com bliki, 6 Mar 2014. martinfowler.com/bliki/CircuitBreaker.html. Checked: page fetched
  • CHECKLIST – Haynes, A. B., Weiser, T. G., Berry, W. R., et al. (2009). A Surgical Safety Checklist to Reduce Morbidity and Mortality in a Global Population. New England Journal of Medicine 360(5):491–499. doi:10.1056/NEJMsa0810119. Checked: Crossref metadata and full-text PDF abstract fetched
  • COMPLACENCY – Parasuraman, R., Manzey, D. H. (2010). Complacency and Bias in Human Use of Automation: An Attentional Integration. Human Factors 52(3):381–410. doi:10.1177/0018720810376055. Checked: Crossref metadata and SAGE abstract fetched | TU Berlin repository copy
  • COVE – Dhuliawala, S., Komeili, M., Xu, J., Raileanu, R., Li, X., Celikyilmaz, A., Weston, J. (2024). Chain-of-Verification Reduces Hallucination in Large Language Models. Findings of ACL 2024, 3563–3578. doi:10.18653/v1/2024.findings-acl.212; arXiv:2309.11495. Checked: arXiv abs and ACL Anthology pages fetched
  • CRITIC – Gou, Z., Shao, Z., Gong, Y., Shen, Y., Yang, Y., Duan, N., Chen, W. (2023; ICLR 2024). CRITIC: Large Language Models Can Self-Correct with Tool-Interactive Critiquing. ICLR 2024. arXiv:2305.11738. Checked: arXiv abs page fetched
  • ERRORBARS – Miller, E. (2024). Adding Error Bars to Evals: A Statistical Approach to Language Model Evaluations. arXiv. arXiv:2411.00640. Checked: arXiv abs page fetched
  • GCP-PATTERNS – He, S. (author) et al. (2026). Choose a design pattern for your agentic AI system. Google Cloud Architecture Center, last updated 2026-05-28. docs.cloud.google.com/architecture/choose-design-pattern-age.... Checked: page fetched (first 100,000 characters read)
  • HALLUC – Kalai, A. T., Nachum, O., Vempala, S. S., Zhang, E. (2025). Why Language Models Hallucinate. arXiv. arXiv:2509.04664. Checked: arXiv abs page fetched
  • HIERARCHY – Wallace, E., Xiao, K., Leike, R., Weng, L., Heidecke, J., Beutel, A. (2024). The Instruction Hierarchy: Training LLMs to Prioritize Privileged Instructions. arXiv. arXiv:2404.13208. Checked: arXiv abs page fetched
  • HORIZON – Sinha, A., Arun, A., Goel, S., Staab, S., Geiping, J. (2025). The Illusion of Diminishing Returns: Measuring Long Horizon Execution in LLMs. arXiv. arXiv:2509.09677. Checked: arXiv abs page fetched
  • HUANG – Huang, J., Chen, X., Mishra, S., Zheng, H. S., Yu, A. W., Song, X., Zhou, D. (2023; ICLR 2024). Large Language Models Cannot Self-Correct Reasoning Yet. ICLR 2024. arXiv:2310.01798. Checked: arXiv abs page fetched
  • IDEMPOTENT – Featonby, M. (n.d.). Making retries safe with idempotent APIs. Amazon Builders' Library. aws.amazon.com/builders-library/making-retries-safe-with-ide.... Checked: page fetched
  • INDIRECT – Greshake, K., Abdelnabi, S., Mishra, S., Endres, C., Holz, T., Fritz, M. (2023). Not What You've Signed Up For: Compromising Real-World LLM-Integrated Applications with Indirect Prompt Injection. Proc. 16th ACM Workshop on Artificial Intelligence and Security, 79–90. doi:10.1145/3605764.3623985; arXiv:2302.12173. Checked: arXiv abs page and Crossref record fetched
  • IRONIES – Bainbridge, L. (1983). Ironies of automation. Automatica 19(6):775–779. doi:10.1016/0005-1098(83)90046-8. Checked: Crossref metadata only; content summarized from prior knowledge, not re-read in the research pass
  • JUDGE – Zheng, L., Chiang, W.-L., Sheng, Y., Zhuang, S., Wu, Z., et al. (13 authors) (2023). Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena. NeurIPS 2023 Datasets and Benchmarks. arXiv:2306.05685. Checked: arXiv abs page fetched
  • KAMOI – Kamoi, R., Zhang, Y., Zhang, N., Han, J., Zhang, R. (2024). When Can LLMs Actually Correct Their Own Mistakes? A Critical Survey of Self-Correction of LLMs. TACL 2024. arXiv:2406.01297. Checked: arXiv abs page fetched
  • L2M – Zhou, D., Schärli, N., Hou, L., Wei, J., Scales, N., Wang, X., Schuurmans, D., Cui, C., Bousquet, O., Le, Q., Chi, E. (2022; ICLR 2023). Least-to-Most Prompting Enables Complex Reasoning in Large Language Models. ICLR 2023. arXiv:2205.10625. Checked: arXiv abs page fetched
  • LOSTMID – Liu, N. F., Lin, K., Hewitt, J., Paranjape, A., Bevilacqua, M., Petroni, F., Liang, P. (2024). Lost in the Middle: How Language Models Use Long Contexts. TACL 12:157–173. doi:10.1162/tacl_a_00638; arXiv:2307.03172. Checked: arXiv abs and ACL Anthology pages fetched | arXiv abstract; TACL volume UNVERIFIED
  • MAST – Cemri, M., Pan, M. Z., Yang, S., Agrawal, L. A., Chopra, B., Tiwari, R., Keutzer, K., Parameswaran, A., Klein, D., Ramchandran, K., Zaharia, M., Gonzalez, J. E., Stoica, I. (2025). Why Do Multi-Agent LLM Systems Fail? arXiv. arXiv:2503.13657. Checked: arXiv abs page fetched
  • MONKEYS – Brown, B., Juravsky, J., Ehrlich, R., Clark, R., Le, Q. V., Ré, C., Mirhoseini, A. (2024). Large Language Monkeys: Scaling Inference Compute with Repeated Sampling. arXiv. arXiv:2407.21787. Checked: arXiv abs page fetched
  • MW-ETIQUETTE – MediaWiki.org contributors (n.d.; accessed 2026-10-05). API:Etiquette. MediaWiki.org. www.mediawiki.org/wiki/API:Etiquette. Checked: page fetched | serial requests, combined requests, maxlag, User-Agent
  • MW-MAXLAG – MediaWiki.org contributors (n.d.; accessed 2026-10-05). Manual:Maxlag parameter. MediaWiki.org. www.mediawiki.org/wiki/Manual:Maxlag_parameter. Checked: page fetched | maxlag=5; Retry-After; wait at least 5 s
  • OPENAI-GUIDE – OpenAI (2025). A practical guide to building agents. OpenAI (PDF). cdn.openai.com/business-guides-and-resources/a-practical-gui.... Checked: PDF fetched; no date in the PDF; April 2025 release per secondary coverage (MarkTechPost, 17 Apr 2025)
  • OTEL-GENAI – OpenTelemetry (2026). Semantic conventions for generative AI: agent spans (stability: Development). GitHub, open-telemetry/semantic-conventions-genai. github.com/open-telemetry/semantic-conventions-genai. Checked: repo page, agent-spans document, and the "Moved" notice on opentelemetry.io (semconv 1.44.0) fetched | move notice on old docs page and raw README; stability label not stated
  • OWASP – OWASP Gen AI Security Project (2025). OWASP Top 10 for LLM Applications 2025 (LLM01–LLM10). OWASP. genai.owasp.org/llm-top-10/. Checked: list page and the LLM01, LLM05 and LLM06 risk pages fetched
  • PAL – Gao, L., Madaan, A., Zhou, S., Alon, U., Liu, P., Yang, Y., Callan, J., Neubig, G. (2022). PAL: Program-aided Language Models. arXiv. arXiv:2211.10435. Checked: arXiv abs page fetched (conference venue not confirmed)
  • PI-PATTERNS – Beurer-Kellner, L., Buesser, B., Creţu, A.-M., Debenedetti, E., Dobos, D., Fabian, D., Fischer, M., Froelicher, D., Grosse, K., Naeff, D., Ozoani, E., Paverd, A., Tramèr, F., Volhejn, V. (2025). Design Patterns for Securing LLM Agents against Prompt Injections. arXiv. arXiv:2506.08837. Checked: arXiv abs page fetched; the six pattern names from S. Willison's write-up (simonwillison.net/2025/Jun/13/prompt-injection-design-patterns/), fetched
  • PLANSOLVE – Wang, L., Xu, W., Lan, Y., Hu, Z., Lan, Y., Lee, R. K.-W., Lim, E.-P. (2023). Plan-and-Solve Prompting: Improving Zero-Shot Chain-of-Thought Reasoning by Large Language Models. ACL 2023. arXiv:2305.04091. Checked: arXiv abs page fetched
  • REACT – Yao, S., Zhao, J., Yu, D., Du, N., Shafran, I., Narasimhan, K., Cao, Y. (2022; ICLR 2023). ReAct: Synergizing Reasoning and Acting in Language Models. ICLR 2023. doi:10.48550/arXiv.2210.03629, arXiv:2210.03629. Checked: arXiv abs page fetched (ICLR camera-ready per Comments)
  • REFLEXION – Shinn, N., Cassano, F., Berman, E., Gopinath, A., Narasimhan, K., Yao, S. (2023). Reflexion: Language Agents with Verbal Reinforcement Learning. NeurIPS 2023. arXiv:2303.11366. Checked: arXiv abs page fetched; venue from authors' GitHub README
  • RFC9110 – Fielding R., Nottingham M., Reschke J. (2022). HTTP Semantics, RFC 9110 / STD 97. IETF. doi:10.17487/RFC9110. Checked: §10.2.3 read on rfc-editor.org; DOI not resolved. | §9.2.2 (idempotent methods) and §10.2.3 (Retry-After) read
  • RULEOF2 – Meta AI (2025). Agents Rule of Two: A Practical Approach to AI Agent Security. Meta AI blog, 31 Oct 2025. ai.meta.com/blog/practical-ai-agent-security/. Checked: page fetched (no individual author shown)
  • SELFCONS – Wang, X., Wei, J., Schuurmans, D., Le, Q., Chi, E., Narang, S., Chowdhery, A., Zhou, D. (2022; ICLR 2023). Self-Consistency Improves Chain of Thought Reasoning in Language Models. ICLR 2023. arXiv:2203.11171. Checked: arXiv abs page fetched
  • SELFPREF – Panickssery, A., Bowman, S. R., Feng, S. (2024). LLM Evaluators Recognize and Favor Their Own Generations. arXiv. arXiv:2404.13076. Checked: arXiv abs page fetched
  • SELFREFINE – Madaan, A., Tandon, N., Gupta, P., Hallinan, S., Gao, L., Wiegreffe, S., Alon, U., Dziri, N., Prabhumoye, S., Yang, Y., Gupta, S., Majumder, B. P., Hermann, K., Welleck, S., Yazdanbakhsh, A., Clark, P. (2023). Self-Refine: Iterative Refinement with Self-Feedback. arXiv. arXiv:2303.17651. Checked: arXiv abs page fetched (venue not confirmed)
  • SPOTLIGHT – Hines, K., Lopez, G., Hall, M., Zarfati, F., Zunger, Y., Kiciman, E. (2024). Defending Against Indirect Prompt Injection Attacks With Spotlighting. arXiv. arXiv:2403.14720. Checked: arXiv abs page fetched
  • SRE-RISK – Alvidrez, M. (2016). Embracing Risk. In Beyer, B., Jones, C., Petoff, J., Murphy, N. R. (eds.), Site Reliability Engineering: How Google Runs Production Systems. O'Reilly. sre.google/sre-book/embracing-risk/. Checked: chapter page fetched (year is the book edition's, not shown on the page)
  • STATEFLOW – Wu, Y., Yue, T., Zhang, S., Wang, C., Wu, Q. (2024). StateFlow: Enhancing LLM Task-Solving through State-Driven Workflows. arXiv. arXiv:2403.11322. Checked: arXiv abs page fetched
  • STPA – Leveson, N. G., Thomas, J. P. (2018). STPA Handbook. MIT (PDF, March 2018). www.flighttestsafety.org/images/STPA_Handbook.pdf. Checked: PDF fetched (mirror copy; first 100,000 characters read)
  • SWEBENCH – Jimenez, C. E., Yang, J., Wettig, A., Yao, S., Pei, K., Press, O., Narasimhan, K. (2023; ICLR 2024). SWE-bench: Can Language Models Resolve Real-World GitHub Issues? ICLR 2024. arXiv:2310.06770. Checked: arXiv abs page fetched
  • SWEV-RETIRED – OpenAI (2026). Why SWE-bench Verified no longer measures frontier coding capabilities. OpenAI, 23 Feb 2026. openai.com/index/why-we-no-longer-evaluate-swe-bench-verifie.... Checked: page fetched
  • SWISS – Reason, J. (2000). Human error: models and management. BMJ 320(7237):768–770. doi:10.1136/bmj.320.7237.768. Checked: Crossref metadata only; content (Swiss cheese model) from prior knowledge
  • TAU – Yao, S., Shinn, N., Razavi, P., Narasimhan, K. (2024). τ-bench: A Benchmark for Tool-Agent-User Interaction in Real-World Domains. arXiv. arXiv:2406.12045. Checked: arXiv abs page fetched
  • TEMPORAL – Temporal Technologies (n.d.; accessed 2026-10-05). Activity Definition: idempotency, retries, timeouts. Temporal Documentation. docs.temporal.io/activity-definition. Checked: page fetched
  • TIMEOUTS – Brooker, M. [byline "Marc"] (n.d.; page dated 12 Jun 2026). Timeouts, retries, and backoff with jitter. Amazon Builders' Library (now on builder.aws.com). builder.aws.com/content/3EumjoZascWd1oZiEgL8ORlv3qE/timeouts.... Checked: page fetched after redirect from aws.amazon.com/builders-library/
  • TOT – Yao, S., Yu, D., Zhao, J., Shafran, I., Griffiths, T. L., Cao, Y., Narasimhan, K. (2023). Tree of Thoughts: Deliberate Problem Solving with Large Language Models. NeurIPS 2023. arXiv:2305.10601. Checked: arXiv abs page fetched
  • TPI – NIST Computer Security Resource Center (n.d.). Glossary: two-person integrity (TPI), citing CNSSI 4009-2022 and NIST IR 8401. NIST CSRC. csrc.nist.gov/glossary/term/two_person_integrity. Checked: page fetched
  • TRIFECTA – Willison, S. (2025). The lethal trifecta for AI agents: private data, untrusted content, and external communication. simonwillison.net, 16 Jun 2025. simonwillison.net/2025/Jun/16/the-lethal-trifecta/. Checked: page fetched
  • UNFAITHFUL – Turpin, M., Michael, J., Perez, E., Bowman, S. R. (2023). Language Models Don't Always Say What They Think: Unfaithful Explanations in Chain-of-Thought Prompting. NeurIPS 2023. arXiv:2305.04388. Checked: arXiv abs page fetched

LLM self-knowledge

  • KADAVATH22 – Kadavath S. et al. (2022). Language Models (Mostly) Know What They Know. arXiv:2207.05221. Checked: arXiv abstract
  • SHARMA23 – Sharma M. et al. (2023). Towards Understanding Sycophancy in Language Models. arXiv:2310.13548. Checked: arXiv abstract
  • WW23 – Walters W.H., Wilder E.I. (2023). Fabrication and errors in the bibliographic citations generated by ChatGPT. Scientific Reports 13, 14045. doi:10.1038/s41598-023-41032-5. Checked: article page, rates

Machine discipline: digests, Unicode, time

Wiki and API etiquette

Research methods

Cited on research methods. 106 entries.

Problem solving, verification and philosophy of science

  • AE25 – Novikov, A., Vũ, N., Eisenberger, M., Dupont, E., Huang, P.-S., et al. (2025). AlphaEvolve: A coding agent for scientific and algorithmic discovery. arXiv:2506.13131. Checked: arXiv abstract page
  • AG24 – Trinh, T. H., Wu, Y., Le, Q. V., He, H., Luong, T. (2024). Solving olympiad geometry without human demonstrations. Nature 625, 476–482. doi:10.1038/s41586-023-06747-5. Checked: Nature page and abstract; an author correction exists (doi:10.1038/s41586-024-07115-7)
  • AIAA98 – AIAA (1998; reaffirmed 2002). Guide for the Verification and Validation of Computational Fluid Dynamics Simulations, G-077-1998(2002). AIAA. doi:10.2514/4.472855. Checked: AIAA ARC book page
  • AIF20 – Udrescu, S.-M., Tegmark, M. (2020). AI Feynman: A physics-inspired method for symbolic regression. Science Advances 6, eaay2631. doi:10.1126/sciadv.aay2631; arXiv:1905.11481. Checked: arXiv page (journal reference; 100/100 vs 71 result); science.org DOI URL
  • AP26 – Hubert, T., Mehta, R., Sartran, L., et al. (2026; online 2025). Olympiad-level formal mathematical reasoning with reinforcement learning. Nature 651(8106), 607–613. doi:10.1038/s41586-025-09833-y. Checked: Nature page (AlphaProof, Lean, IMO 2024 result)
  • ASME20 – ASME (2009; reaffirmed 2021). V&V 20-2009, Standard for Verification and Validation in Computational Fluid Dynamics and Heat Transfer. ASME. ISBN 9780791832097. Checked: ANSI webstore; bookseller listing
  • BAREN96 – Barenblatt, G. I. (1996). Scaling, Self-similarity, and Intermediate Asymptotics. Cambridge University Press. doi:10.1017/CBO9781107050242; ISBN 9780521435222. Checked: Cambridge Core chapter pages; DOI inferred from the Core front-matter identifier 9781107050242
  • BO78 – Bender, C. M., Orszag, S. A. (1999; first publ. McGraw-Hill 1978). Advanced Mathematical Methods for Scientists and Engineers I: Asymptotic Methods and Perturbation Theory. Springer. doi:10.1007/978-1-4757-3069-2. Checked: Springer book and chapter pages (Perturbation Series, WKB Theory). 1978 date not rechecked
  • BUCK14 – Buckingham, E. (1914). On physically similar systems; illustrations of the use of dimensional equations. Physical Review 4(4), 345–376. doi:10.1103/PhysRev.4.345. Checked: Crossref
  • CHAM1890 – Chamberlin, T. C. (1890). The method of multiple working hypotheses. Science ns-15(366), 92–96. doi:10.1126/science.ns-15.366.92. Checked: Crossref
  • DYSON04 – Dyson, F. (2004). A meeting with Enrico Fermi. Nature 427, 297. doi:10.1038/427297a. Checked: Nature URL; ADS bibcode 2004Natur.427..297D
  • ENGEL98 – Engel, A. (1998). Problem-Solving Strategies. Springer (Problem Books in Mathematics). doi:10.1007/b97682; ISBN 9780387982199. Checked: Springer page incl. chapter list (Invariance, Coloring, Extremal, Box, Induction Principle)
  • FEYN74 – Feynman, R. P. (1974). Cargo cult science. Engineering and Science 37(7), 10–13. URL calteches.library.caltech.edu/3043/1/CargoCult.pdf. Checked: Caltech library record; quotes read
  • FLP-II19 – Feynman, R. P., Leighton, R. B., Sands, M. (1964; online ed.). The Feynman Lectures on Physics, Vol. II, Ch. 19: The Principle of Least Action. Caltech. URL www.feynmanlectures.caltech.edu/II_19.html. Checked: page located
  • FUNS24 – Romera-Paredes, B., et al. (2024). Mathematical discoveries from program search with large language models. Nature 625, 468–475. doi:10.1038/s41586-023-06924-6. Checked: Nature page (citation, method, evaluator quote). Title from knowledge
  • GL14 – Gelman, A., Loken, E. (2014). The statistical crisis in science. American Scientist 102(6), 460. doi:10.1511/2014.111.460. Checked: American Scientist page
  • GN09 – Gowers, T., Nielsen, M. (2009). Massively collaborative mathematics. Nature 461, 879–881. doi:10.1038/461879a. Checked: Nature page (citation; body paywalled, not read)
  • GOLD91 – Goldberg, D. (1991). What every computer scientist should know about floating-point arithmetic. ACM Computing Surveys 23(1), 5–48. doi:10.1145/103162.103163. Checked: ACM DL page. Volume/pages not rechecked (Crossref rate-limited)
  • GOWERS00 – Gowers, W. T. (2000). The two cultures of mathematics. In Arnold, Atiyah, Lax, Mazur (eds.), Mathematics: Frontiers and Perspectives. American Mathematical Society. ISBN 0821826972; URL www.dpmms.cam.ac.uk/~wtg10/2cultures.pdf. Checked: author PDF located (fetch failed: TLS); book listing. Content summarized from knowledge
  • HADAM45 – Hadamard, J. (1945). The Psychology of Invention in the Mathematical Field. Princeton University Press. URL philpapers.org/rec/HADTPO-8. Checked: Mathematical Gazette review (Princeton UP 1945, xiii+143 pp.); PhilPapers record. Stage model stated from knowledge
  • HALMOS70 – Halmos, P. R. (1970). How to write mathematics. L'Enseignement Mathématique 16. doi:10.5169/seals-43857. Checked: verified 2026-10-06: DataCite record for the DOI (title, creator, publisher, 1970), volume 16 from the e-periodica link; pages 123-152 as cited elsewhere, UNVERIFIED
  • HAMIL34 – Hamilton, W. R. (1834). On a general method in dynamics. Phil. Trans. R. Soc. Lond. 124, 247–308. doi:10.1098/rstl.1834.0017. Checked: Royal Society article URL carrying the DOI; Trinity College Dublin transcription. Pages from a secondary listing
  • HIGHAM02 – Higham, N. J. (2002). Accuracy and Stability of Numerical Algorithms, 2nd ed. SIAM. doi:10.1137/1.9780898718027. Checked: SIAM ePubs page; Library of Congress record
  • IEEE754 – IEEE (2019). IEEE Std 754-2019, IEEE Standard for Floating-Point Arithmetic. IEEE. doi:10.1109/IEEESTD.2019.8766229. Checked: IEEE Xplore document 8766229
  • IOAN05 – Ioannidis, J. P. A. (2005). Why most published research findings are false. PLoS Medicine 2(8), e124. doi:10.1371/journal.pmed.0020124. Checked: Crossref
  • ISO24495-1 – ISO (2023). ISO 24495-1:2023, Plain language — Part 1: Governing principles and guidelines. ISO. URL www.iso.org/standard/78907.html. Checked: ISO page (June 2023, ed. 1). Definition and four principles via a secondary source (plainnumbers.org.uk). | June 2023; definition and four principles from iTeh sample
  • ISO24495-3 – ISO (2026). ISO 24495-3:2026, Plain language — Part 3: Science writing. ISO. URL www.iso.org/standard/86938.html. Checked: ISO page (published 2026-05-12, ed. 1). | ed. 1, May 2026, scope
  • JAYNES03 – Jaynes, E. T. (2003; ed. G. L. Bretthorst). Probability Theory: The Logic of Science. Cambridge University Press. doi:10.1017/CBO9780511790423. Checked: Cambridge Core contents page
  • KOSMANN11 – Kosmann-Schwarzbach, Y. (2011). The Noether Theorems: Invariance and Conservation Laws in the Twentieth Century. Springer. doi:10.1007/978-0-387-87868-3. Checked: Springer PDF link; ISBN 9780387878676 listing
  • KR05 – Klein, J. R., Roodman, A. (2005). Blind analysis in nuclear and particle physics. Annu. Rev. Nucl. Part. Sci. 55, 141–163. doi:10.1146/annurev.nucl.55.090704.151521. Checked: Annual Reviews URL; full text read (four methods, unblinding rules). | PDF copy; abstract and methods
  • KUHN62 – Kuhn, T. S. (1962; 50th anniv. ed. 2012). The Structure of Scientific Revolutions. University of Chicago Press. ISBN 9780226458120. Checked: UChicago Press / BiblioVault record
  • LAKA76 – Lakatos, I. (1976). Proofs and Refutations: The Logic of Mathematical Discovery (eds. J. Worrall, E. Zahar). Cambridge University Press. doi:10.1017/CBO9781139171472. Checked: Cambridge Core chapter page (chapter DOI …472.003, print 1976); terms cross-checked in Stanford Encyclopedia of Philosophy "Imre Lakatos" (rev. 2026-06-19)
  • LAKA78 – Lakatos, I. (1978). The Methodology of Scientific Research Programmes: Philosophical Papers Vol. 1 (eds. J. Worrall, G. Currie). Cambridge University Press. doi:10.1017/CBO9780511621123. Checked: Cambridge Core page showing book DOI; hard core, protective belt and progressive/degenerating checked in the same Stanford Encyclopedia entry
  • LANCZ86 – Lanczos, C. (1986; Dover reprint of 4th ed.). The Variational Principles of Mechanics. Dover. ISBN 9780486650678. Checked: bookseller ISBN listings (4th ed. noted). First-edition date not rechecked
  • MAH10 – Mahajan, S. (2010). Street-Fighting Mathematics: The Art of Educated Guessing and Opportunistic Problem Solving. MIT Press, open access, CC BY-NC-SA. ISBN 9780262265881 (OA); URL direct.mit.edu/books/oa-monograph/5339. Checked: Project MUSE record (OA, licence, six chapter titles)
  • MAH14 – Mahajan, S. (2014). The Art of Insight in Science and Engineering: Mastering Complexity. MIT Press, CC BY-NC-SA. ISBN 9780262526548; URL ocw.mit.edu/courses/res-6-011-the-art-of-insight-in-science-.... Checked: MIT OCW open-textbook page (licence, tool list)
  • MATHLIB20 – The mathlib Community (2020). The Lean mathematical library. Proc. CPP 2020 (ACM SIGPLAN), 367–381. doi:10.1145/3372885.3373824. Checked: Crossref. | Crossref record
  • MERMIN89 – Mermin, N. D. (1989). What's wrong with these equations? Physics Today 42(10), 9–11. doi:10.1063/1.2811173. Checked: Crossref
  • MKC09 – Moore, R. E., Kearfott, R. B., Cloud, M. J. (2009). Introduction to Interval Analysis. SIAM. doi:10.1137/1.9780898717716. Checked: SIAM ePubs book page
  • MP15 – MacCoun, R., Perlmutter, S. (2015). Blind analysis: Hide results to seek the truth. Nature 526, 187. doi:10.1038/526187a. Checked: Nature URL; ADS bibcode 2015Natur.526..187M
  • NASEM19 – National Academies of Sciences, Engineering, and Medicine (2019). Reproducibility and Replicability in Science. National Academies Press. doi:10.17226/25303. Checked: National Academies reading page (DOI; definitions quoted). | definitions and Recommendation 6-1 text
  • NICK98 – Nickerson, R. S. (1998). Confirmation bias: A ubiquitous phenomenon in many guises. Review of General Psychology 2(2), 175–220. doi:10.1037/1089-2680.2.2.175. Checked: SAGE record; PDF header (vol. 2 no. 2, 175–220). | citation and definition; DOI not printed
  • NOETH18 – Noether, E. (1918). Invariante Variationsprobleme. Nachr. Ges. Wiss. Göttingen, Math.-Phys. Kl. 1918, 235–257. Engl. transl. M. A. Tavel, Transport Theory Statist. Phys. 1, 186–207 (1971); arXiv:physics/0503066. Checked: EuDML record; arXiv abstract page (both journal references)
  • NOSEK18 – Nosek, B. A., Ebersole, C. R., DeHaven, A. C., Mellor, D. T. (2018). The preregistration revolution. PNAS 115(11), 2600–2606. doi:10.1073/pnas.1708274114. Checked: Crossref
  • OR10 – Oberkampf, W. L., Roy, C. J. (2010). Verification and Validation in Scientific Computing. Cambridge University Press. doi:10.1017/CBO9780511760396. Checked: Cambridge Core chapter pages; front-matter identifier
  • OT02 – Oberkampf, W. L., Trucano, T. G. (2002). Verification and validation in computational fluid dynamics. Progress in Aerospace Sciences 38, 209–272. doi:10.1016/S0376-0421(02)00005-2. Checked: ScienceDirect PII; ADS bibcode 2002PrAeS..38..209O. End page from a secondary listing
  • PDG24 – Navas, S., et al. (Particle Data Group) (2024; 2025 update). Review of Particle Physics. Phys. Rev. D 110, 030001. doi:10.1103/PhysRevD.110.030001. Checked: APS DOI link; 2025 Introduction PDF read (S = [χ²/(N−1)]^½; δ₀ = 3N^½δx̄)
  • PLATT64 – Platt, J. R. (1964). Strong inference. Science 146(3642), 347–353. doi:10.1126/science.146.3642.347. Checked: Crossref
  • POLYA45 – Pólya, G. (1945; Princeton Science Library ed. 2014). How to Solve It: A New Aspect of Mathematical Method. Princeton University Press. ISBN 9780691164076; doi:10.1515/9781400828678. Checked: bookseller ISBN listings (2014 ed., Conway foreword); De Gruyter DOI record with "Auxiliary problem" and "Test by dimension" entries
  • POLYA54A – Pólya, G. (1954). Mathematics and Plausible Reasoning, Vol. 1: Induction and Analogy in Mathematics. Princeton University Press. ISBN 9780691025094; doi:10.1515/9780691218304. Checked: Princeton UP page; De Gruyter DOI page; 1954 Philosophy of Science review
  • POLYA54B – Pólya, G. (1954). Mathematics and Plausible Reasoning, Vol. 2: Patterns of Plausible Inference. Princeton University Press. ISBN 9780691025100; doi:10.1515/9781400823727. Checked: Princeton UP page; De Gruyter DOI page
  • POP59 – Popper, K. R. (1959; Routledge Classics 2002). The Logic of Scientific Discovery. Routledge. ISBN 9780415278447; doi:10.4324/9780203994627. Checked: Routledge product page; Taylor & Francis eBook DOI
  • ROACHE02 – Roache, P. J. (2002). Code verification by the method of manufactured solutions. J. Fluids Eng. 124(1), 4–10. doi:10.1115/1.1436090. Checked: DOI resolver title; volume/pages from ASME URL path and a secondary listing
  • ROACHE94 – Roache, P. J. (1994). Perspective: A method for uniform reporting of grid refinement studies. J. Fluids Eng. 116(3), 405–413. doi:10.1115/1.2910291. Checked: Crossref
  • SCHOEN85 – Schoenfeld, A. H. (1985). Mathematical Problem Solving. Academic Press. ISBN 9780126288704. Checked: ScienceDirect book page; Science 1986 review listing (Academic Press, 1985). Four-part framework stated from knowledge, not re-read in the research pass
  • SCHOLZE21 – Scholze, P. (2021). Half a year of the Liquid Tensor Experiment: Amazing developments (5 Jun 2021). Xena Project blog. URL xenaproject.wordpress.com/2021/06/05/half-a-year-of-the-liqu.... Checked: fetched; quotes read
  • SINDY16 – Brunton, S. L., Proctor, J. L., Kutz, J. N. (2016). Discovering governing equations from data by sparse identification of nonlinear dynamical systems. PNAS 113, 3932–3937. doi:10.1073/pnas.1517384113. Checked: arXiv:1509.03580 page; ADS bibcode 2016PNAS..113.3932B. End page from a secondary listing. | Crossref record
  • SK00 – Salari, K., Knupp, P. (2000). Code Verification by the Method of Manufactured Solutions. Sandia National Laboratories (OSTI 759450). URL www.osti.gov/biblio/759450. Checked: OSTI record. Report number SAND2000-1444 not rechecked on the page
  • TAO06 – Tao, T. (2006). Solving Mathematical Problems: A Personal Perspective. Oxford University Press. ISBN 9780199205608. Checked: OUP product page (5 Oct 2006; ch. 1 "Strategies in Problem Solving")
  • TAO10 – Tao, T. (2010). 245A: Problem solving strategies (blog post, 21 Oct 2010). What's New. URL terrytao.wordpress.com/2010/10/21/245a-problem-solving-strat.... Checked: fetched; 21 named strategies read
  • THURS94 – Thurston, W. P. (1994). On proof and progress in mathematics. Bull. Amer. Math. Soc. 30(2), 161–177. doi:10.1090/S0273-0979-1994-00502-6; arXiv:math/9404236. Checked: Crossref (gives 161–178); arXiv journal reference (161–177); text read for quotes
  • WA08 – Weinstein, L., Adam, J. A. (2008). Guesstimation: Solving the World's Problems on the Back of a Cocktail Napkin. Princeton University Press. ISBN 9780691129495. Checked: bookseller ISBN listing; Old Dominion University (ODU) Digital Commons record
  • ZEITZ17 – Zeitz, P. (2017). The Art and Craft of Problem Solving, 3rd ed. Wiley. ISBN 9781119239901. Checked: Wiley product page. Chapter content not re-read

Cognitive and decision hygiene

  • KLEIN07 – Klein G. (2007). Performing a Project Premortem. Harvard Business Review, Sept 2007. www.researchgate.net/publication/3229642_Performing_a_Projec.... Checked: author, venue, month, 30% claim; volume and pages UNVERIFIED
  • MELLERS14 – Mellers B. et al. (2014). Psychological Strategies for Winning a Geopolitical Forecasting Tournament. Psychological Science 25(5), 1106–1115. doi:10.1177/0956797614524255. Checked: WashU profile and abstract
  • REDTEAM21 – UK Ministry of Defence, DCDC (2021). Red Teaming Handbook, 3rd ed. UK MoD. www.gov.uk/government/publications/a-guide-to-red-teaming. Checked: 3rd edition added 30 Jun 2021; contents not read
  • TK74 – Tversky A., Kahneman D. (1974). Judgment under Uncertainty: Heuristics and Biases. Science 185(4157), 1124–1131. doi:10.1126/science.185.4157.1124. Checked: citation and anchoring quote from a PDF copy; DOI not resolved (UNVERIFIED)

Communication

Metrology and units

  • CODATA22 – Mohr P.J., Newell D.B., Taylor B.N., Tiesinga E. (2025). CODATA recommended values of the fundamental physical constants: 2022. Rev. Mod. Phys. 97, 025002. doi:10.1103/RevModPhys.97.025002. Checked: NIST-hosted PDF; published 30 Apr 2025. | INSPIRE record
  • GUM08 – JCGM (2008). JCGM 100:2008, Evaluation of measurement data — Guide to the expression of uncertainty in measurement. BIPM. doi:10.59161/JCGM100-2008E. Checked: BIPM JCGM page (also lists Amendment 1:2026 on nonlinear models, doi:10.59161/PPDI3267). | DOI on BIPM JCGM page; clauses 7.1.4, 7.2.1, 7.2.2, 7.2.6, 7.2.7 read on the ISO-hosted HTML
  • GUMS1 – JCGM (2008). JCGM 101:2008, Supplement 1 to the GUM — Propagation of distributions using a Monte Carlo method. BIPM. doi:10.59161/JCGM101-2008. Checked: BIPM JCGM page. | BIPM DOI landing page
  • JCGMPUB – JCGM (2026). JCGM publications list (incl. JCGM 100:2008/Amd.1:2026 "Nonlinearity in measurement models"; JCGM GUM-5:2026; GUM-1:2023; GUM-6:2020). BIPM. www.bipm.org/en/committees/jc/jcgm/publications. Checked: titles listed; amendment text not read
  • NISTCUU – NIST (2024–2026). CODATA Fundamental Physical Constants. NIST PML. physics.nist.gov/cuu/Constants/index.html. Checked: 2022 values shown; 2026 adjustment data deadline 31 Dec 2026
  • SI19 – BIPM (2019, rev. June 2026, v4.01). The International System of Units (SI Brochure), 9th edition. BIPM. doi:10.59161/AUEZ1291. Checked: BIPM page version table (4.01 Jun 2026; 3.02 Aug 2025; 3.01 Aug 2024; 2.01 Dec 2022), DOI, CC BY 4.0. | BIPM SI Brochure page (recommended citation, 2026 update)
  • SP330 – Newell, D. B., Tiesinga, E. (eds.) (2019). The International System of Units (SI), 2019 ed. NIST SP 330. doi:10.6028/NIST.SP.330-2019. Checked: NIST publication page. | NIST publication page, date 2019-08-20
  • SP811 – Thompson, A., Taylor, B. N. (2008). Guide for the Use of the International System of Units (SI). NIST SP 811. doi:10.6028/NIST.SP.811e2008. Checked: NIST page (notes it predates the 2019 SI revision). | NIST version history (2008 ed., March 2008, no later edition); manuscript checklist items read; DOI not checked
  • TN1297 – Taylor, B. N., Kuyatt, C. E. (1994). Guidelines for Evaluating and Expressing the Uncertainty of NIST Measurement Results. NIST Technical Note 1297. doi:10.6028/NIST.TN.1297. Checked: NIST publication page. | NIST publication page
  • VIM12 – JCGM (2012). JCGM 200:2012, International Vocabulary of Metrology — Basic and general concepts and associated terms (VIM), 3rd ed. BIPM. doi:10.59161/JCGM200-2012. Checked: BIPM DOI landing page. | DOI; definitions 2.3 and 1.19 read in the PDF

Provenance of data, software and sources

  • CFF – Druskat S. et al. (n.d.; schema 1.2.0). Citation File Format. citation-file-format.github.io/. Checked: version 1.2.0; GitHub, Zenodo and Zotero support; full author list and release year UNVERIFIED
  • CRRW – Crossref (2023–2025). Retraction Watch (documentation), and Rittman M., "Retraction Watch retractions now in the Crossref API" (29 Jan 2025). Crossref. www.crossref.org/documentation/retrieve-metadata/retraction-.... Checked: acquired Sept 2023; `update-to` with source publisher|retraction-watch; daily CSV on GitLab
  • CSL – Zelle R.M., Wiernik B.M., Bennett F.G., D'Arcus B., Maier D. (2022). CSL 1.0.2 Specification. Citation Style Language. docs.citationstyles.org/en/stable/specification.html. Checked: spec page; release announced for 1 Jan 2022; schema repository says CSL-JSON is "not yet fully normative"
  • DOIURI – DOI Foundation (2024). DOI URI Scheme Specification. DOI Foundation. www.doi.org/resources/DOI_URI_Scheme.pdf. Checked: dated 13 Nov 2024; case-insensitive within Basic Latin; UTF-8 percent-encoding
  • FAIR – Wilkinson M.D. et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3, 160018. doi:10.1038/sdata.2016.18. Checked: Nature article page, principle list
  • FAIR4RS – Barker M., Chue Hong N.P., Katz D.S. et al. (2022). Introducing the FAIR Principles for research software. Scientific Data 9, 622. doi:10.1038/s41597-022-01710-x. Checked: article page; cites RDA output DOI 10.15497/RDA00068
  • ISO26324 – ISO (2025). ISO 26324:2025 Information and documentation — Digital object identifier system, ed. 3. ISO. www.iso.org/standard/88862.html. Checked: March 2025; replaces the withdrawn 2022 edition
  • ORCID – ORCID (n.d.). Structure of the ORCID Identifier. ORCID Support. support.orcid.org/hc/en-us/articles/360006897674. Checked: 16 characters, ISO/IEC 7064 MOD 11-2, https URI display
  • SWCIT – Smith A.M., Katz D.S., Niemeyer K.E., FORCE11 SCWG (2016). Software citation principles. PeerJ Computer Science 2, e86. doi:10.7717/peerj-cs.86. Checked: FORCE11 page, six principles
  • SWHID – SWHID.org / ISO/IEC (2025). ISO/IEC 18670:2025 (SWHID); SWHID Specification v1.2. www.swhid.org/specification/v1.2/5.Core_identifiers/. Checked: standardized 23 Apr 2025; swh:1:{cnt,dir,rev,rel,snp}; SHA-1, Git-compatible
  • ZENODO – Zenodo (n.d.). What is DOI versioning? Zenodo Support. support.zenodo.org/help/en-gb/1-upload-deposit/97-what-is-do.... Checked: concept DOI vs version DOI

Reproducibility

  • BOETTIGER15 – Boettiger C. (2015). An introduction to Docker for reproducible research. ACM SIGOPS Operating Systems Review 49(1), 71–79. doi:10.1145/2723872.2723882. Checked: arXiv:1410.0846 journal reference
  • CLAERBOUT92 – Claerbout J., Karrenbach M. (1992). Electronic documents give reproducible research a new meaning. SEG Technical Program Expanded Abstracts 1992, 601–604. doi:10.1190/1.1822162. Checked: via Barba (2018) arXiv:1802.03311; SEG page returned 403
  • PENG11 – Peng R.D. (2011). Reproducible research in computational science. Science 334(6060), 1226–1227. doi:10.1126/science.1213847. Checked: PMC copy
  • SANDVE13 – Sandve G.K., Nekrutenko A., Taylor J., Hovig E. (2013). Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10), e1003285. doi:10.1371/journal.pcbi.1003285. Checked: PLOS page, rule titles

Research integrity and AI use

Research tools

Cited on research tools. 105 entries.

The twelve tools of the original survey

  • AIF2-20 – Udrescu, S.-M., Tan, A., Feng, J., Neto, O., Wu, T., Tegmark, M. (2020). AI Feynman 2.0: Pareto-optimal symbolic regression exploiting graph modularity. Advances in Neural Information Processing Systems 33 (NeurIPS 2020), 4860–4871. arXiv:2006.10782. Checked: arXiv abstract page and the proceedings.neurips.cc abstract page
  • CADABRA07 – Peeters, K. (2007). A field-theory motivated approach to symbolic computer algebra. Computer Physics Communications 176, 550–558. doi:10.1016/j.cpc.2007.01.003, arXiv:cs/0608005. Checked: INSPIRE API. The issue number was not shown. The title was missing from your candidate
  • CADABRA18 – Peeters, K. (2018). Cadabra2: computer algebra for field theory revisited. Journal of Open Source Software 3(32), 1118. doi:10.21105/joss.01118. Checked: the JOSS paper page (Crossref was rate-limited)
  • CLAW16 – Mandli, K. T., Ahmadia, A. J., Berger, M., Calhoun, D., George, D. L., Hadjimichael, Y., Ketcheson, D. I., Lemoine, G. I., LeVeque, R. J. (2016). Clawpack: building an open source ecosystem for solving hyperbolic PDEs. PeerJ Computer Science 2, e68. doi:10.7717/peerj-cs.68. Checked: Crossref
  • DEEPXDE21 – Lu, L., Meng, X., Mao, Z., Karniadakis, G. E. (2021). DeepXDE: A Deep Learning Library for Solving Differential Equations. SIAM Review 63(1), 208–228. doi:10.1137/19M1274067. Checked: Crossref
  • DEVITO19 – Louboutin, M., Lange, M., Luporini, F., Kukreja, N., Witte, P. A., Herrmann, F. J., Velesko, P., Gorman, G. J. (2019). Devito (v3.1.0): an embedded domain-specific language for finite differences and geophysical exploration. Geoscientific Model Development 12(3), 1165–1187. doi:10.5194/gmd-12-1165-2019. Checked: Crossref
  • DEVITO20 – Luporini, F., Louboutin, M., Lange, M., Kukreja, N., Witte, P., Hückelheim, J., Yount, C., Kelly, P. H. J., Herrmann, F. J., Gorman, G. J. (2020). Architecture and Performance of Devito, a System for Automated Stencil Computation. ACM Transactions on Mathematical Software 46(1), 1–28. doi:10.1145/3374916. Checked: Crossref. It shows pages 1–28 and no ACM article number
  • DOLFINX23 – Baratta, I. A., Dean, J. P., Dokken, J. S., Habera, M., Hale, J. S., Richardson, C. N., Rognes, M. E., Scroggs, M. W., Sime, N., Wells, G. N. (2023). DOLFINx: The next generation FEniCS problem solving environment. Zenodo preprint v1, 31 Dec 2023. doi:10.5281/zenodo.10447666. Checked: Zenodo record page and fenicsproject.org/citing. The citing page currently asks for DOLFINx, two Basix papers and UFL. It no longer lists the 2012 book or FEniCS 1.5
  • ETK12 – Löffler, F., Faber, J., Bentivegna, E., Bode, T., Diener, P., Haas, R., Hinder, I., Mundim, B. C., Ott, C. D., Schnetter, E., Allen, G., Campanelli, M., Laguna, P. (2012). The Einstein Toolkit: A Community Computational Infrastructure for Relativistic Astrophysics. Classical and Quantum Gravity 29(11), 115001. doi:10.1088/0264-9381/29/11/115001. Checked: einsteintoolkit.org/citation.html and INSPIRE. The site now says to cite "the DOI assigned to the current release" first. Its download page shows the latest release as "Hypatia", ET_2026_05, released 10 July 2026; no release DOI was shown
  • FENICS12 – Logg, A., Mardal, K.-A., Wells, G. N. (eds.) (2012). Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book. Springer, Lecture Notes in Computational Science and Engineering (ISSN 1439-7358). doi:10.1007/978-3-642-23099-8. Checked: Crossref. Crossref does not show the volume number (84)
  • FENICS15 – Alnæs, M., Blechta, J., Hake, J., Johansson, A., Kehlet, B., Logg, A., Richardson, C., Ring, J., Rognes, M. E., Wells, G. N. (2015). The FEniCS Project Version 1.5. Archive of Numerical Software 3(100). doi:10.11588/ans.2015.100.20553. Checked: DataCite API. Crossref returns 404 because the DOI is registered with DataCite, not Crossref
  • FIPY09 – Guyer, J. E., Wheeler, D., Warren, J. A. (2009). FiPy: Partial Differential Equations with Python. Computing in Science & Engineering 11(3), 6–15. doi:10.1109/MCSE.2009.52. Checked: Crossref
  • FRITZSON14 – Fritzson, P. (2014). Principles of Object Oriented Modeling and Simulation with Modelica 3.3: A Cyber-Physical Approach. Wiley (print 12 Nov 2014; ISBN 9781118859124). doi:10.1002/9781118989166. Checked: Crossref, which names the publisher as "Wiley" (IEEE Press not shown). Wiley's own page returned 403
  • LEVEQUE02 – LeVeque, R. J. (2002). Finite Volume Methods for Hyperbolic Problems. Cambridge University Press (monograph; print 26 Aug 2002, online 2012). doi:10.1017/CBO9780511791253. Checked: Crossref
  • MODELICA-SPEC – Modelica Association (2026). Modelica Language Specification, Version 3.7 (May 2026). The previous release was 3.6 (2023), and 3.8-dev is in development. No DOI. Checked: modelica.org/language ("Modelica Specification 3.7 (May 2026, current)") and specification.modelica.org's version table
  • MTK21 – Ma, Y., Gowda, S., Anantharaman, R., Laughman, C., Shah, V., Rackauckas, C. (2021). ModelingToolkit: A Composable Graph Transformation System For Equation-Based Modeling. arXiv preprint, v1 9 Mar 2021, v3 9 Feb 2022, no journal-ref. arXiv:2103.05244. Checked: arXiv abstract page (v3)
  • PYSR23 – Cranmer, M. (2023). Interpretable Machine Learning for Science with PySR and SymbolicRegression.jl. arXiv preprint (astro-ph.IM), v1 2 May 2023, v3 5 May 2023, no journal-ref. arXiv:2305.01582, doi:10.48550/arXiv.2305.01582. Checked: arXiv abstract page; the PySR repo's CITATION.md gives the same BibTeX (@misc)
  • QUTIP12 – Johansson, J. R., Nation, P. D., Nori, F. (2012). QuTiP: An open-source Python framework for the dynamics of open quantum systems. Computer Physics Communications 183(8), 1760–1772. doi:10.1016/j.cpc.2012.02.021. Checked: Crossref
  • QUTIP13 – Johansson, J. R., Nation, P. D., Nori, F. (2013). QuTiP 2: A Python framework for the dynamics of open quantum systems. Computer Physics Communications 184(4), 1234–1240. doi:10.1016/j.cpc.2012.11.019. Checked: Crossref
  • QUTIP5 – Lambert, N., Giguère, E., Menczel, P., Li, B., Hopf, P., Suárez, G., Gali, M., Lishman, J., Gadhvi, R., Agarwal, R., Galicia, A., Shammah, N., Nation, P., Johansson, J. R., Ahmed, S., Cross, S., Pitchford, A., Nori, F. (2026). QuTiP 5: The Quantum Toolbox in Python. Physics Reports 1153, 1–62. doi:10.1016/j.physrep.2025.10.001, arXiv:2412.04705. Checked: arXiv page (journal-ref) and Crossref (18 authors, issued January 2026). It is now a journal paper dated 2026, not a 2024 preprint

The additions of 2026-10-06 and the general catalogue

  • AGDA – Agda developers. Agda documentation (2.9.0). agda.readthedocs.io. Checked: version shown; license UNVERIFIED
  • AIRFLOW3 – Apache Airflow (2025). Apache Airflow 3 is Generally Available! airflow.apache.org/blog/airflow-three-point-oh-is-here/. Checked: release date 22 Apr 2025
  • APPTAINER2021 – Linux Foundation (2021). New Linux Foundation Project Accelerates Collaboration on Container Systems Between Enterprise and HPC Environments. www.linuxfoundation.org/press/press-release/new-linux-founda.... Checked: date 30 Nov 2021, Singularity → Apptainer
  • ARB2017 – Johansson F. (2017). Arb: Efficient Arbitrary-Precision Midpoint-Radius Interval Arithmetic. IEEE Trans. Computers 66(8), 1281–1292. doi:10.1109/TC.2017.2690633. Checked: Crossref record
  • ARXIVTOU – arXiv (n.d.). Terms of Use for arXiv APIs. arXiv. info.arxiv.org/help/api/tou.html. Checked: one request per 3 s, single connection; metadata CC0; no e-print redistribution. | CC0 metadata, rate limit
  • AUTOGEN2023 – Wu Q., Bansal G., Zhang J., et al. (14 authors) (2023). AutoGen: Enabling Next-Gen LLM Applications via Multi-Agent Conversation. arXiv:2308.08155. Checked: arXiv abstract page (dates 16 Aug 2023 / 3 Oct 2023)
  • AUTOGENREPO – Microsoft. microsoft/autogen README. github.com/microsoft/autogen. Checked: maintenance-mode notice, MIT/CC-BY-4.0
  • CLAUDEAGENTSDK2025 – Anthropic (2025). Building agents with the Claude Agent SDK. claude.com/blog/building-agents-with-the-claude-agent-sdk. Checked: date 29 Sep 2025, rename statement
  • CLAUDEAGENTSDKMIG – Anthropic (n.d.). Migrate to Claude Agent SDK. code.claude.com/docs/en/agent-sdk/migration-guide. Checked: package renames, breaking changes
  • CREWAI – crewAIInc. crewAI. github.com/crewAIInc/crewAI. Checked: MIT, standalone
  • CROSSREF-API – Crossref (n.d.). REST API documentation. www.crossref.org/documentation/retrieve-metadata/rest-api/. Checked: free, no sign-up, polite pool
  • DEDALUS2020 – Burns K.J., Vasil G.M., Oishi J.S., Lecoanet D., Brown B.P. (2020). Dedalus: A flexible framework for numerical simulations with spectral methods. Phys. Rev. Research 2, 023068. doi:10.1103/PhysRevResearch.2.023068. Checked: Crossref record; PyPI 3.0.5 (31 Jan 2026), GPL3
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  • DLMF – Olver F.W.J., Olde Daalhuis A.B., Lozier D.W., Schneider B.I., Boisvert R.F., Clark C.W., Miller B.R., Saunders B.V., Cohl H.S., McClain M.A., eds. (2026). NIST Digital Library of Mathematical Functions, Release 1.2.8. dlmf.nist.gov. Checked: release number and date (15 Sep 2026), editors
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  • FEYNCALC10 – Shtabovenko V., Mertig R., Orellana F. (2025). FeynCalc 10: Do multiloop integrals dream of computer codes? Comput. Phys. Commun. 306, 109357. doi:10.1016/j.cpc.2024.109357. Checked: INSPIRE record
  • FEYNCALCREPO – FeynCalc developers. FeynCalc/feyncalc. github.com/FeynCalc/feyncalc. Checked: 10.2.1 (June 2026), GPLv3+, Mathematica 10–14
  • FIREDRAKE2016 – Rathgeber F., Ham D.A., Mitchell L., Lange M., Luporini F., McRae A.T.T., Bercea G.-T., Markall G.R., Kelly P.H.J. (2016). Firedrake: Automating the Finite Element Method by Composing Abstractions. ACM TOMS 43(3), 1–27. doi:10.1145/2998441. Checked: Crossref record; PyPI 2026.10.0 (2 Oct 2026), LGPL-3.0-or-later
  • FLINT – The FLINT team (2026). FLINT: Fast Library for Number Theory, history and changes. flintlib.org/doc/history.html. Checked: 3.0.0 (20 Oct 2023) merge statement; 3.6.0 (29 Jun 2026)
  • FORM5-2026 – Davies J., Kaneko T., Marinissen C., Ueda T., Vermaseren J.A.M. (2026). FORM Version 5.0. arXiv:2601.19982. Checked: INSPIRE (authors, preprint date 2026-01-27; no DOI listed); abstract features
  • FORMREPO – FORM developers. form-dev/form (releases, COPYING). github.com/form-dev/form. Checked: 5.0.1 (24 Jun 2024) latest tag; GPL v3 text
  • GAP – The GAP Group (2026). GAP – Groups, Algorithms, and Programming, Version 4.16.1. www.gap-system.org. Checked: version and date (23 Aug 2026)
  • 'GRCHOMBO2021 – Andrade, T., Areste Salo, L., Aurrekoetxea, J. C., et al. (32 authors) (2021). GRChombo: An adaptable numerical relativity code for fundamental physics. Journal of Open Source Software 6(68), 3703. doi:10.21105/joss.03703. Checked: verified 2026-10-06: the JOSS paper page (Crossref was rate-limited); GitHub README: BSD-3, 'predecessor to GRTeclyn
  • GUARDRAILSAI – Guardrails AI. guardrails. github.com/guardrails-ai/guardrails. Checked: Apache-2.0, validators/Hub
  • HEPLEAN2025 – Tooby-Smith J. (2025). HepLean: Digitalising high energy physics. Comput. Phys. Commun. 308, 109457. doi:10.1016/j.cpc.2024.109457. Checked: Crossref record and Physlib README
  • HNN2019 – Greydanus S., Dzamba M., Yosinski J. (2019). Hamiltonian Neural Networks. NeurIPS 2019, 15353–15363. arXiv:1906.01563. Checked: dblp record; repository (PyTorch, Apache-2.0)
  • INSPECT – UK AI Security Institute (n.d.). Inspect. inspect.aisi.org.uk ; github.com/UKGovernmentBEIS/inspect_ai. Checked: MIT, features, maintainers | site home page fetched
  • INSPIRE – INSPIRE (n.d.). Terms of use. help.inspirehep.net/knowledge-base/terms-of-use/. Checked: CC0 metadata; API used live in the research pass
  • ISABELLE – Isabelle developers (2026). Isabelle2025-2. isabelle.in.tum.de. Checked: release (Jan 2026), BSD-style license; Nipkow/Paulson/Wenzel 2002 book citation UNVERIFIED
  • JULIA2017 – Bezanson J., Edelman A., Karpinski S., Shah V.B. (2017). Julia: A Fresh Approach to Numerical Computing. SIAM Review 59(1), 65–98. doi:10.1137/141000671. Checked: Crossref record
  • JUPYTER2016 – Kluyver T., Ragan-Kelley B., Pérez F., et al. (15 authors) (2016). Jupyter Notebooks – a publishing format for reproducible computational workflows. In Positioning and Power in Academic Publishing, IOS Press, 87ff. doi:10.3233/978-1-61499-649-1-87. Checked: Crossref record
  • LANGGRAPH1 – LangChain (2025). LangChain and LangGraph Agent Frameworks Reach v1.0 Milestones. www.langchain.com/blog/langchain-langgraph-1dot0. Checked: date 22 Oct 2025; repository MIT
  • LEAN4-2021 – de Moura L., Ullrich S. (2021). The Lean 4 Theorem Prover and Programming Language. CADE-28, LNCS, Springer, 625–635. doi:10.1007/978-3-030-79876-5_37. Checked: Crossref record
  • LEAN4PHYS2025 – (authors UNVERIFIED) (2025). Lean4Physics: Comprehensive Reasoning Framework for College-level Physics in Lean4. arXiv:2510.26094. Checked: abstract introduces a separate "PhysLib" and LeanPhysBench
  • LEANDOJO2023 – Yang K., Swope A., Gu A., Chalamala R., Song P., Yu S., Godil S., Prenger R., Anandkumar A. (2023). LeanDojo: Theorem Proving with Retrieval-Augmented Language Models. NeurIPS 2023 Datasets and Benchmarks. arXiv:2306.15626. Checked: authors, venue and deprecation notice on leandojo.org; exact title wording UNVERIFIED
  • LEANDOJOV2 – Hsiang R., Adkisson W., George R.J., Anandkumar A. (2025). LeanDojo-v2. NeurIPS 2025 Mathematical Reasoning and AI workshop. github.com/lean-dojo/LeanDojo-v2. Checked: repository (MIT) and leandojo.org; paper title UNVERIFIED
  • LMFDB – The LMFDB Collaboration (n.d.). The L-functions and modular forms database. www.lmfdb.org. Checked: citation guidance, release 1.2.1; license page not readable
  • LNN2020 – Cranmer M., Greydanus S., Hoyer S., Battaglia P., Spergel D., Ho S. (2020). Lagrangian Neural Networks. arXiv:2003.04630. Checked: author list in reference repository README (JAX, Apache-2.0); arXiv ID; publication venue UNVERIFIED
  • M2 – Grayson D.R., Stillman M.E. Macaulay2, a software system for research in algebraic geometry. macaulay2.com. Checked: version 1.26.06 (10 Jun 2026); license UNVERIFIED
  • MAF-GA – Microsoft (2026). Microsoft Agent Framework Version 1.0. devblogs.microsoft.com/agent-framework/microsoft-agent-frame.... Checked: date 3 Apr 2026, GA, MIT
  • MAF-PREVIEW – Microsoft (2025). Introducing Microsoft Agent Framework. Azure Blog. azure.microsoft.com/en-us/blog/introducing-microsoft-agent-f.... Checked: date 1 Oct 2025, public preview, AutoGen + Semantic Kernel convergence
  • MATHLIB4REPO – leanprover-community. mathlib4. github.com/leanprover-community/mathlib4. Checked: Apache-2.0
  • MAXIMA – Maxima project. Maxima, a Computer Algebra System. maxima.sourceforge.io. Checked: GPL, Macsyma lineage; version UNVERIFIED
  • MCP-AAIF – Model Context Protocol (2025). MCP joins the Agentic AI Foundation. blog.modelcontextprotocol.io/posts/2025-12-09-mcp-joins-agen.... Checked: date, Linux Foundation directed fund, co-founders
  • MCP-SPEC – Model Context Protocol (2026). Specification, version 2026-07-28. modelcontextprotocol.io/specification/latest. Checked: version string, feature list
  • METAMATH2019 – Megill N.D., Wheeler D.A. (2019). Metamath: A Computer Language for Mathematical Proofs. Lulu Press. ISBN 978-0-3597-02237. Checked: BibTeX and ISBN on us.metamath.org
  • MPMATH – mpmath development team (2026). mpmath 1.4.1. mpmath.org. Checked: PyPI version, date (15 Mar 2026), BSD-3
  • NEMOGUARDRAILS2023 – Rebedea T., Dinu R., Sreedhar M.N., Parisien C., Cohen J. (2023). NeMo Guardrails: A Toolkit for Controllable and Safe LLM Applications with Programmable Rails. EMNLP 2023 System Demonstrations, 431–445. doi:10.18653/v1/2023.emnlp-demo.40. Checked: ACL Anthology; repository Apache-2.0
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  • PARI – The PARI Group (2026). PARI/GP version 2.19.0. Univ. Bordeaux. pari.math.u-bordeaux.fr. Checked: version, date (28 Sep 2026), GPLv2+
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  • PDG2026 – Takahashi F., et al. (Particle Data Group) (2026). Review of Particle Physics. Int. J. Mod. Phys. A 41, 2630011. doi:10.1142/S0217751X26300115. Checked: pdg.lbl.gov citation; Crossref record (published 5 Aug 2026)
  • PHYSLIB – The Physlib community (2024–). Physlib: The Lean Physics Library. GitHub. github.com/leanprover-community/physlib. Checked: README (merger of PhysLean and Lean-QuantumInfo, Apache-2.0, Lean v4.32.0, citation block)
  • PINT – Pint developers (2026). Pint 0.26.1. pypi.org/project/Pint/. Checked: version, date (10 Sep 2026), BSD
  • PREFECT – PrefectHQ. prefect. github.com/PrefectHQ/prefect. Checked: Apache-2.0, v3
  • PROMPTFOO – promptfoo; TechCrunch (2026). OpenAI acquires Promptfoo to secure its AI agents. techcrunch.com/2026/03/09/openai-acquires-promptfoo-to-secur... ; github.com/promptfoo/promptfoo. Checked: date 9 Mar 2026, MIT, "remains open source" README line
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  • PYSINDY2022 – Kaptanoglu A., de Silva B., Fasel U., Kaheman K., Goldschmidt A., Callaham J., Delahunt C., Nicolaou Z., Champion K., Loiseau J.-C., Kutz J., Brunton S. (2022). PySINDy: A comprehensive Python package for robust sparse system identification. JOSS 7(69), 3994. doi:10.21105/joss.03994. Checked: Crossref record; PyPI 2.1.0 (8 Jan 2026), MIT
  • QUARTO – Posit (2026). Quarto. quarto.org ; github.com/quarto-dev/quarto-cli. Checked: MIT license; version 1.11.5 from site metadata
  • ROCQ9 – The Rocq Development Team (2025). Rocq Prover 9.0.0 Release Notes. rocq-prover.org/releases/9.0.0. Checked: date 12 Mar 2025, rename statement; release list to 9.2.0 (27 Mar 2026)
  • S2-2023 – Kinney R., Anastasiades C., Authur R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140. Checked: arXiv abstract page; API page (free, key recommended)
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  • SAGEMANIFOLDSSITE – SageManifolds project. sagemanifolds.obspm.fr. Checked: feature list, integration in SageMath
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  • SCIPY2020 – Virtanen P., Gommers R., Oliphant T.E., et al. (2020). SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods 17, 261–272. doi:10.1038/s41592-019-0686-2. Checked: Crossref record
  • SCIX – ADS/SciX team (2026). ADS to SciX Transition Office Hours. adsabs.github.io/blog/transition. Checked: transition date 16 Nov 2026, redirect statement
  • SINGULAR – Decker W., Greuel G.-M., Pfister G., Schönemann H. Singular — a computer algebra system for polynomial computations. www.singular.uni-kl.de. Checked: GPL, recommended authors; current version UNVERIFIED
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  • SYMPY2017 – Meurer A., Smith C.P., Paprocki M., Čertík O., Kirpichev S.B., et al. (29 authors) (2017). SymPy: symbolic computing in Python. PeerJ Computer Science 3:e103. doi:10.7717/peerj-cs.103. Checked: Crossref record (title, authors, venue, year)
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Further reading

Located and checked during the research pass of 2026-10-05, not cited on the toolkit's pages.

Method

Four research passes ran on 2026-10-05 and 2026-10-06 (agent flow control; research methods; research tools; further dimensions), each reading its sources live and recording what it fetched; a fifth pass checked the original physics tools' citations. Where two passes cited one work, the entries were merged under one key and both check notes kept. Rate limits (HTTP 429 from Crossref and Semantic Scholar) and blocked pages are named in the notes; an entry checked from a secondary page says so. The passes' reports are kept whole in the project's records.

Back to the Research Toolkit.