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diff --git a/2020/10/2020-10-11.md b/2020/10/2020-10-11.md new file mode 100644 index 0000000..6f60ba1 --- /dev/null +++ b/2020/10/2020-10-11.md @@ -0,0 +1,59 @@ + +time to heat up domestic water: pasta pot, hot tub, etc + +function of starting temperature, environmental temperature, insulation, volume/surface area + +## Paper read: "The impact of mathematical modeling languages on model quality in systems biology" + + The impact of mathematical modeling languages on model quality in systems biology: A software engineering perspective + Christopher Sch¨olzel1, Valeria Blesius, Gernot Ernst, and Andreas Dominik + https://www.biorxiv.org/content/10.1101/2019.12.16.875260v3 + +Interesting refs: + +- [A long journey into reproducible computational neuroscience](https://www.frontiersin.org/articles/10.3389/fncom.2015.00030/full) +- Guidelines for Reproducibly Building and Simulating Systems Biology Models +- Is My Model Good Enough? Best Practices for Verification and Validation of Musculoskeletal Models and Simulations of Movement +- Antimony: A Modular Model Definition Language +- SimuPy: A Python Framework for Modeling and Simulating Dynamical Systems +- Systems Modeling and Programming in a Unified Environment Based on Julia +- Recent advances in biomedical simulations: a manifesto for model engineering + +> [...] Guyton model, which is probably among the most complicated monolithic models in systems biology [...] + +## Modia: Modelica-like in Julia + +Slides: https://modiasim.github.io/Modia.jl/slides/Systems-Modeling-and-Programming-Slides.pdf + +Code: https://github.com/ModiaSim/Modia.jl + +Expresses a strong interest in visual representation. + + +## Lean / mathlib + +<https://leanprover-community.github.io/> + +<https://www.quantamagazine.org/building-the-mathematical-library-of-the-future-20201001/> + + +## Other + +Had not heard of "SimScape", a component of MATLAB along side Simulink. + +There is a somewhat arbitrary list of "100 theorems" used to compare systems +like Lean and Coq: <https://www.cs.ru.nl/~freek/100/>. What would a model or +physical systems equivalent include? + +Interchange-like format for Modelica: <https://fmi-standard.org/> + +What features should next modelthing iteration have? + +- s-expr native syntax +- modularity/hierarchy +- "hybrid" (including discrete) +- input: mathml +- output: c, wasm, julia, modelica, mathml, latex, text +- some datastore, with ability to fetch code from website/API + +What are the type systems and data model of computer algebra systems? |