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nLab > Latest Changes: biology

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  1.  

  1. Added work on Ologs and started restructuring the page

    rTuyeras

    diff, v5, current

  2. Added work on segments.

    rTuyeras

    diff, v5, current

  3. Added works on stock-flow diagrams

    rTuyeras

    diff, v5, current

  4. Added work on pedigrads

    rTuyeras

    diff, v5, current

  5. Added work on adjunctions and immune response. Reorganized sections at the end regarding higher structures.

    rTuyeras

    diff, v5, current

  6. Added works using operads, algebraic geometry and algebraic topology

    rTuyeras

    diff, v5, current

  7. Added more references

    rTuyeras

    diff, v5, current

    • CommentRowNumber8.
    • CommentAuthorUrs
    • CommentTimeDec 20th 2022
    • (edited Dec 20th 2022)

    Hi rTuyeras,

    thanks, these edits look like they could be interesting. Please allow me to provide some hints on formatting:

    Instead of verbatim dropping a url like

      http://www.few.vu.nl/~rplanque/Onderwijs/MathBio/PapersForProject/Rosen.pdf

    type

      [pdf](http://www.few.vu.nl/~rplanque/Onderwijs/MathBio/PapersForProject/Rosen.pdf)

    to obtain a decent hyperlink (pdf).

    For many authors we have pages on the nLab, which one can conveniently hyperlink to by enclosing the (full, usually) author name in square brackets.

    For example

      * [[Charles Ehresmann]]

    gives

    and

      * [[David Spivak]]

    gives

    etc.

    Generally, double square brackets around technical terms hyperlink them to their nLab page. The wiki is meant to make it easy to thoroughly hyperlink text, and this is in large parts the point of a wiki over a printed text.

    For instance

      * [[category theory|category-theoretic]]

    gives

    etc.

    Incidentally, all this markup works also here on the nForum. You can check out the “Source”-link at the top right of this comment to see how I coded this comment.

  9. Thanks for the feedback Urs.

    Changed links and references accordingly (page will need more work).

    rTuyeras

    diff, v5, current

  10. Added the UMAP algorithm and mentioned its relation to fuzzy simplicial sets

    rTuyeras

    diff, v7, current

  11. Reorganized the section about hyperstructures. Thism section needs more discussion, or in fact some formal content with an example of how it applies to organization levels in biology.

    rTuyeras

    diff, v7, current

  12. Moved the reference about n-categories to “other references”. Also moved the section about bigraphs in the “higher structures” section. We discuss the 2-categorical nature of bigraphs.

    rTuyeras

    diff, v9, current

    • CommentRowNumber13.
    • CommentAuthorUrs
    • CommentTimeDec 21st 2022
    • (edited Dec 21st 2022)

    Re #11:

    Yes, the paragraphs about hyperstructures don’t seem useful in their present form.

    Notice that this material originates from revision 1, written by David Corfield way back in 2009, and does not seem to have been touched since.

    My impression is that the only justification for mentioning hyperstructures as a tool in biology at this point is that Nils Baas has been hoping such an application does exist.

    I haven’t followed what evidence for this hope may have been provided since, but I suggest unless and until we see such evidence, that all mentioning of hyperstructures be deleted from the entry on biology.

  14. Resolved the discussion on hyperstructures.

    Added the following reference, which contains a brief example of hierarchical biological organizations in living organisms:

    NA Baas, On the Philosophy of Higher Structures, arXiv:1805.11943

    rTuyeras

    diff, v12, current

    • CommentRowNumber15.
    • CommentAuthorDavid_Corfield
    • CommentTimeDec 22nd 2022
    • (edited Dec 22nd 2022)

    Thanks for the work on this article since Rev 4, Rémy. The page is looking much better now.

    • CommentRowNumber16.
    • CommentAuthorrTuyeras
    • CommentTimeDec 22nd 2022
    Thanks!
    • CommentRowNumber17.
    • CommentAuthorDavid_Corfield
    • CommentTimeApr 15th 2024

    Added a couple of references

    • Jan-Hendrik S. Hofmeyr, A biochemically-realisable relational model of the self-manufacturing cell, Biosystems Volume 207, September 2021, doi: 10.1016/j.biosystems.2021.104463

    • Federico Vega, The cell as a realization of the (M, R) system, Biosystems Volume 225, March 2023, [doi:10.1016/j.biosystems.2023.104846](https://doi.org/10.1016/j.biosystems.2023.104846

    diff, v16, current

    • CommentRowNumber18.
    • CommentAuthorCorbin
    • CommentTimeSep 18th 2024

    Ologs: Rewrite the example olog to go in roughly the correct direction, to use standard biology jargon, and to follow the “good practices” from Spivak & Kent 2012; merge explanatory paragraph and Spivak & Kent 2012 ref with ontology log.

    diff, v17, current

    • CommentRowNumber19.
    • CommentAuthorUrs
    • CommentTimeSep 19th 2024

    The claims in the section on “Ologs” seem surprising. If you could add a reference substantiating this?

1 to 19 of 19

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