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grndstt

11/03/2022, 4:43 PM

Maybe a first hint is that the new note are note created under a bib.* format but as follows

grndstt

11/03/2022, 4:43 PM

I gues they should be bib.rutz-2022.md ?

Maarrk

11/03/2022, 6:07 PM

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

Maarrk

11/03/2022, 6:08 PM

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

Maarrk

11/03/2022, 7:00 PM

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)

grndstt

11/03/2022, 7:25 PM

Aha .. Its indeed doing something

grndstt

11/03/2022, 7:25 PM

Now the note is no longer empty

grndstt

11/03/2022, 7:25 PM

But this is the message I get

grndstt

11/03/2022, 7:26 PM

`Importing data from Zotero failed with error:

Copy code

TypeError: Cannot read properties of undefined (reading '2')
`

d1onys1us

11/03/2022, 9:43 PM

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

d1onys1us

11/03/2022, 9:44 PM

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

grndstt

11/04/2022, 7:08 AM

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.

grndstt

11/04/2022, 7:10 AM

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/

grndstt

11/04/2022, 7:12 AM

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.

grndstt

11/04/2022, 7:13 AM

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.

grndstt

11/04/2022, 7:14 AM

Happy to explore possibilities if anyone as a clue here !

grndstt

11/04/2022, 7:16 AM

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 !

grndstt

11/04/2022, 7:16 AM

Happy to read how other researchers use Dendron 🙂

Raphaël

11/04/2022, 3:56 PM

@grndstt https://wiki.aemaet.de/

grndstt

11/04/2022, 4:48 PM

This looks great @Raphaël ! I am afraid my German level is not enough though to fully appreciate but I like your Digital Philosophie Garden !

gizmo

11/05/2022, 2:11 PM

That's super cool! I should move to open notebook science now that I have more control over my projects

Maarrk

11/05/2022, 5:51 PM

`Importing data from Zotero failed with

Raphaël

11/07/2022, 11:18 AM

Thanks!

d1onys1us

11/09/2022, 8:47 PM

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

d1onys1us

11/09/2022, 8:48 PM

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

gizmo

11/10/2022, 12:52 AM

I have to use latex since journal formatting is usually a tex file in my field

andrey-jef

11/18/2022, 1:56 PM

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/

bitNomad

12/30/2022, 12:54 PM

curious as to the field of academia whether there are clusters. Did you get any more than straw man responses?

bitNomad

12/30/2022, 1:32 PM

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

bitNomad

12/30/2022, 1:33 PM

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