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# academia
g
In parrallel of my research activities I manage an metabolomics analytics service platform and we use it to share report with the client. For each of them we have a git for the codes and scripts used and also to serve static pages with plotly plots fro example. And then a web hosted Dendron to generate the report. This is nice because it allows us to make links with previous projects and results of a group.
  • g
    Maybe a first hint is that the new note are note created under a bib.* format but as follows
  • g
    I gues they should be bib.rutz-2022.md ?
  • m
    I like having all of them grouped under the 
    bib
    node, so that's why I set it up this way for me. You can still have it your way, you need to change the 
    dendron.yml
    a bit from what I posted:
    Copy code
    yaml
    hooks:
        onCreate:
            -
                id: newbib
                pattern: bib*
                type: js
    now it will match any note starting with "bib", but keep in mind that if you create a note like 
    bibtex.md
    it will also run the hook for it
  • m
    But to answer the question more directly, if you make the note name 
    bib.rutz-2022.md
    the hook I posted will ask Zotero about data for citation key 
    rutz-2022
  • m
    I originally thought that you can make it work with your style of titles, but it would require changes in multiple places so I don't recommend that anymore (deleted that message for clarity)
  • g
    Aha .. Its indeed doing something
  • g
    Now the note is no longer empty
  • g
    But this is the message I get
  • g
    `Importing data from Zotero failed with error:
    Copy code
    TypeError: Cannot read properties of undefined (reading '2')
`
    m
    • 2
    • 6
  • d
    hey i don’t usually come in this channel but curious, do u research folks like using dendron? i’m gonna assume yes, im just curious what’s the usual tooling around here
  • d
    i’m pushing dendron on my team in general , but we actually have a whole subset team of researchers. so maybe i can provide some insights on a journaling flow that is synergistic w research
  • g
    Hi @d1onys1us in my group we use it in several ways. We have started the Digital Botanical Gardens Initiative a few monthes ago. This is expected to last for several years but we decided to have an Open Notebook Science approach on this one (https://en.wikipedia.org/wiki/Open-notebook_science) We use a common Dendron for this its here http://www.dbgi.org/dendron-dbgi/ Expect to find a mess here ! We still need to develop more systematic logging approaches. But for now we are happy with this.
  • g
    We have are using it also in the frame of DBGI to display a taxonomy of a botanical garden with automatically generated pages see http://www.dbgi.org/dendron-jbuf/
  • g
    In parrallel of my research activities I manage an metabolomics analytics service platform and we use it to share report with the client. For each of them we have a git for the codes and scripts used and also to serve static pages with plotly plots fro example. And then a web hosted Dendron to generate the report. This is nice because it allows us to make links with previous projects and results of a group.
  • g
    However one of the issues we have here is that some groups, despite being happy with the searchable interface of a Dendron website, would like to have a more classical pdf report. I have looked a little bit into export to pdf from Dendron but didn't find a convenient solution.
  • g
    Happy to explore possibilities if anyone as a clue here !
  • g
    Finally I have a multivault Dendron workspace collecting all the clients vaults, project specific Dendrons (eg. DBGI) and two generic vaults one for research activities one for platform activities. Each as a public and a private version. The tough thing is to force myself to write by default in the public ones ! But heading there !
  • g
    Happy to read how other researchers use Dendron 🙂
  • r
  • g
    This looks great @Raphaël ! I am afraid my German level is not enough though to fully appreciate but I like your Digital Philosophie Garden !
  • g
    That's super cool! I should move to open notebook science now that I have more control over my projects
  • m
    `Importing data from Zotero failed with
  • r
    Thanks!
  • d
    Markdown researchers — do you find markdown + pan doc enough for you to publish academic style papers? Or do you need to reach for more with something like overleaf/latex
  • d
    If so - do you use any tooling to see markdown pandoc converted live? Almost like a pandoc hot reload for a preview page? Really curious about these
  • g
    I have to use latex since journal formatting is usually a tex file in my field
  • a
    I saw that some authors published their works via quarto. Does it fit better than Dendron, as a wiki/book publishing method? https://quarto.org/
  • b
    curious as to the field of academia whether there are clusters. Did you get any more than straw man responses?
  • b
    was initially wary of the imperial measuring quart fiascos as well as the 4-up and to the right graph but this looks like actual source not sores; after my first pass I am somewhat concerned about "built for scientific jupyter publications" discounting a nice ux or accessible design principles
  • b
    like when I see, "light or dark" I get chills like Lucas is writing the script about a rigid cult on the light side vs the equally problematic cult of the dark side