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The problem with this (and Mendeley, Papers, Bibtex, etc.) is that each paper/thought is isolated. Roam Research (http://roamresearch.com/ http://roamresearch.c

The problem with this (and Mendeley, Papers, Bibtex, etc.) is that each paper/thought is isolated. Roam Research (http://roamresearch.com/ http://roamresearch.com/) is my new jam.

perchard 7y ago
Roam is awesome but this and other reference management software serves a different purpose (for me, at least). I use BibDesk (like Zotero and other examples mentioned here) in conjunction with a plaintext (markdown) Zettelkasten[0]. BibDesk to save references (papers etc.) and copy formatted citations; which are then pasted into Zettels (c.f. a page in Roam). [0] https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1 https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettel...
- gpanders 7y ago
  I do this exact same thing! If I write a new Zettel that references something I read in a book (for example), all I do is get the ISBN of the book (usually off of Amazon), use Zotero's auto-import feature, copy the reference and paste it into my note. The whole thing takes all of ~20 seconds, it's very efficient. I know Zotero has a lot of other features, but 99% of my workflow with it is what I described above.
bloopernova 7y ago
I'm gently easing myself into the Roam knowledgebase management style by using Emacs+org-mode+org-roam. It's definitely one of those topics where you could spend a huge amount of energy organizing but not much actually doing :) Regarding roamresearch.com: How do you find yourself writing/organizing pages? Daily journal with a log of what you did first, then linking out from there? (don't feel pressured to write a novel in response, I don't want to steal time from your day!)
- rollinDyno 7y ago
  What I do is just annotate absolutely everything. I try not to think much about structure. What matters is that my thoughts are put down into text. Structure and organization comes later. Once your second brain is searchable, you can quickly find those keywords and the context thanks to Roam bidirectional links. This is one way to approach your notes, when you know what you're looking for. Another way to approach your notes is by browsing. You can create a page with the structure or outline that you come up with, and then fill them with links to blocks in other notes. In here, you can practice a step of progressive summarization and rephrase your notes.
  - bloopernova 7y ago
    Thank you, I appreciate you taking the time to respond! :)
- bigbossman 7y ago
  I'm actually trying to free myself from the habit of organizing/structuring/planning. It gets in the way. Still obviously experimenting. I'll usually just start putting things into Daily Notes, but if a connected set of notes gets too long, I'll make a separate page and add a [[]] link in the Daily Note.
Chris2048 7y ago
How does Roam differ from a wiki app like Zim/Tomboy?
- bloopernova 7y ago
  Roam is way of using a wiki. i.e. you could quite easily set up a wiki to act in much the same way as Roam. The journal part of Roam, the page-per-day part, is very useful. You write down what you're doing each day, use tags and links to build up a second brain, so to speak. Let's say, today I'm working on kubernetes. I add a tag for k8s, which is a link to the k8s page, where I have all sorts of interesting links and notes dumped. When I'm on the k8s page, I also get a list of pages that link to the k8s page, which helps me to remember some other subject that might be relevant. It uses the Zettelkasten Method: https://zettelkasten.de/posts/overview/ https://zettelkasten.de/posts/overview/ and you can also get a lot of value from reading "How to Take Smart Notes" by Sönke Ahrens. The value also comes from it mirroring your thoughts and experiences, as I said, the second brain thing. (I'm terrible at explaining stuff, sorry :( I hope I didn't bore you to bits)
- bigbossman 7y ago
  Automatic backlinks + all blocks can be referenced or embedded. It allows you to remix your thoughts effortlessly. It's like an idea blender.
asdff 7y ago
What exactly is roam? The website tells me nothing. Zotero has folders and tags for organizing your thoughts how you like.
- bloopernova 7y ago
  See my comment reply to Chris2048 below your comment. It's a wiki like system that helps you to create a second brain of sorts. You write down what you do, and link between lots of different pages, such as "aws" to "ec2" to "vm" to "vmware" to "vmotion". Roam (and org-roam, an Emacs module that I use) shows you what links back to a page, which is incredibly helpful for remembering knowledge and how things fit together.
  - _theory_ 7y ago
    Seems to me this is like tagging, but instead of making the tags at the end of your thought, you're annotating words within your writing, which become the tags. I grant you that it is more intuitive to do it this way.
mooneater 7y ago
How do you export? Seems like a wiki but proprietary?
getpolarized 7y ago
We're shipping a new version of Polar (https://getpolarized.io/ https://getpolarized.io/) this weekend that is sort of closer to the roam/zettelkasten idea of managing notes. Here's a video explaining the new functionality: https://www.youtube.com/watch?v=6M6jNlairGc https://www.youtube.com/watch?v=6M6jNlairGc Basically all the documents you read can have tags. So you can manage all your documents via whatever tag you want. You can then read those documents in Polar directly and highlight parts of text that are interesting. These highlights, notes, comments, and flashcards that you create can also have tags. We call these annotations. We then have an annotation manager which you can manage by tag so you can pivot everything around the tags you're working with. This version is pushed to the web version of Polar now and the new desktop version will make it out this weekend. We're also working on a new Polar 2.0 which will support Android and tablets and have better pen support too so you can work directly in a tablet rather than a desktop/laptop. We're also working on a dark mode but first need to get 2.0 out the door.
- michael_fine 7y ago
  Does the new version handle citations/bibtex export? I really want to use polar but that’s the main value of zotero for me atm.
  - getpolarized 7y ago
    We're getting there.. The backend supports it now. If you send me a list of your requirements (just create a github issue here https://github.com/burtonator/polar-bookshelf/issues https://github.com/burtonator/polar-bookshelf/issues) I will look at adding the functionality you need. We're adding support for DOI lookup and APIs like Arxiv so you could just add a DOI to polar and it will fetch the PDF and keep the metadata. Will also support export to bibtex too. Our big focus right now is shipping 2.0 so that we have a more modern platform that can scale us moving forward.
    - michael_fine 7y ago
      Great to hear! I'm actually a week away from finishing my undergrad thesis (ironically procrastinating on that now), so kinda stuck with Zotero for now. Once that's complete I'll take a good look at polar.
michael_fine 7y ago
Does roam support automatic importation of bibliographical info and export to bibtex? That’s the main value of zotero for me. Also latex math embedding notes would be great
pergadad 7y ago
What is Roam's financing/business model? So far the beta seems free but investing much time in a tool which then might significantly change is a risk...?
- luismmolina 7y ago
  They are planning to charge $12-15 USD with an annual plan.
cycomanic 7y ago
The best application that I ever used for this was docear. Unfortunately it's not being developed anymore and some other things make it a bit painful to use. I'm still waiting for someone to integrate mindmaps with reference management in a better way.
agambrahma 7y ago
Have to say that with its latest release, Tinderbox (https://www.eastgate.com/Tinderbox https://www.eastgate.com/Tinderbox) have most of this in a _non-cloud, local-storage_ form.

The problem with this (and Mendeley, Papers, Bibtex, etc.) is that each paper/thought is isolated. Roam Research (http://roamresearch.com/ http://roamresearch.com/) is my new jam.

perchard 7y ago

Roam is awesome but this and other reference management software serves a different purpose (for me, at least). I use BibDesk (like Zotero and other examples mentioned here) in conjunction with a plaintext (markdown) Zettelkasten[0]. BibDesk to save references (papers etc.) and copy formatted citations; which are then pasted into Zettels (c.f. a page in Roam). [0] https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1 https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettel...

gpanders 7y ago
I do this exact same thing! If I write a new Zettel that references something I read in a book (for example), all I do is get the ISBN of the book (usually off of Amazon), use Zotero's auto-import feature, copy the reference and paste it into my note. The whole thing takes all of ~20 seconds, it's very efficient. I know Zotero has a lot of other features, but 99% of my workflow with it is what I described above.

bloopernova 7y ago

I'm gently easing myself into the Roam knowledgebase management style by using Emacs+org-mode+org-roam. It's definitely one of those topics where you could spend a huge amount of energy organizing but not much actually doing :) Regarding roamresearch.com: How do you find yourself writing/organizing pages? Daily journal with a log of what you did first, then linking out from there? (don't feel pressured to write a novel in response, I don't want to steal time from your day!)

rollinDyno 7y ago
What I do is just annotate absolutely everything. I try not to think much about structure. What matters is that my thoughts are put down into text. Structure and organization comes later. Once your second brain is searchable, you can quickly find those keywords and the context thanks to Roam bidirectional links. This is one way to approach your notes, when you know what you're looking for. Another way to approach your notes is by browsing. You can create a page with the structure or outline that you come up with, and then fill them with links to blocks in other notes. In here, you can practice a step of progressive summarization and rephrase your notes.
- bloopernova 7y ago
  Thank you, I appreciate you taking the time to respond! :)
bigbossman 7y ago
I'm actually trying to free myself from the habit of organizing/structuring/planning. It gets in the way. Still obviously experimenting. I'll usually just start putting things into Daily Notes, but if a connected set of notes gets too long, I'll make a separate page and add a [[]] link in the Daily Note.

Chris2048 7y ago

How does Roam differ from a wiki app like Zim/Tomboy?

bloopernova 7y ago
Roam is way of using a wiki. i.e. you could quite easily set up a wiki to act in much the same way as Roam. The journal part of Roam, the page-per-day part, is very useful. You write down what you're doing each day, use tags and links to build up a second brain, so to speak. Let's say, today I'm working on kubernetes. I add a tag for k8s, which is a link to the k8s page, where I have all sorts of interesting links and notes dumped. When I'm on the k8s page, I also get a list of pages that link to the k8s page, which helps me to remember some other subject that might be relevant. It uses the Zettelkasten Method: https://zettelkasten.de/posts/overview/ https://zettelkasten.de/posts/overview/ and you can also get a lot of value from reading "How to Take Smart Notes" by Sönke Ahrens. The value also comes from it mirroring your thoughts and experiences, as I said, the second brain thing. (I'm terrible at explaining stuff, sorry :( I hope I didn't bore you to bits)
bigbossman 7y ago
Automatic backlinks + all blocks can be referenced or embedded. It allows you to remix your thoughts effortlessly. It's like an idea blender.

asdff 7y ago

What exactly is roam? The website tells me nothing. Zotero has folders and tags for organizing your thoughts how you like.

bloopernova 7y ago
See my comment reply to Chris2048 below your comment. It's a wiki like system that helps you to create a second brain of sorts. You write down what you do, and link between lots of different pages, such as "aws" to "ec2" to "vm" to "vmware" to "vmotion". Roam (and org-roam, an Emacs module that I use) shows you what links back to a page, which is incredibly helpful for remembering knowledge and how things fit together.
- _theory_ 7y ago
  Seems to me this is like tagging, but instead of making the tags at the end of your thought, you're annotating words within your writing, which become the tags. I grant you that it is more intuitive to do it this way.

mooneater 7y ago

How do you export? Seems like a wiki but proprietary?

getpolarized 7y ago

We're shipping a new version of Polar (https://getpolarized.io/ https://getpolarized.io/) this weekend that is sort of closer to the roam/zettelkasten idea of managing notes. Here's a video explaining the new functionality: https://www.youtube.com/watch?v=6M6jNlairGc https://www.youtube.com/watch?v=6M6jNlairGc Basically all the documents you read can have tags. So you can manage all your documents via whatever tag you want. You can then read those documents in Polar directly and highlight parts of text that are interesting. These highlights, notes, comments, and flashcards that you create can also have tags. We call these annotations. We then have an annotation manager which you can manage by tag so you can pivot everything around the tags you're working with. This version is pushed to the web version of Polar now and the new desktop version will make it out this weekend. We're also working on a new Polar 2.0 which will support Android and tablets and have better pen support too so you can work directly in a tablet rather than a desktop/laptop. We're also working on a dark mode but first need to get 2.0 out the door.

michael_fine 7y ago
Does the new version handle citations/bibtex export? I really want to use polar but that’s the main value of zotero for me atm.
- getpolarized 7y ago
  We're getting there.. The backend supports it now. If you send me a list of your requirements (just create a github issue here https://github.com/burtonator/polar-bookshelf/issues https://github.com/burtonator/polar-bookshelf/issues) I will look at adding the functionality you need. We're adding support for DOI lookup and APIs like Arxiv so you could just add a DOI to polar and it will fetch the PDF and keep the metadata. Will also support export to bibtex too. Our big focus right now is shipping 2.0 so that we have a more modern platform that can scale us moving forward.
  - michael_fine 7y ago
    Great to hear! I'm actually a week away from finishing my undergrad thesis (ironically procrastinating on that now), so kinda stuck with Zotero for now. Once that's complete I'll take a good look at polar.

michael_fine 7y ago

Does roam support automatic importation of bibliographical info and export to bibtex? That’s the main value of zotero for me. Also latex math embedding notes would be great

pergadad 7y ago

What is Roam's financing/business model? So far the beta seems free but investing much time in a tool which then might significantly change is a risk...?

luismmolina 7y ago
They are planning to charge $12-15 USD with an annual plan.

cycomanic 7y ago

The best application that I ever used for this was docear. Unfortunately it's not being developed anymore and some other things make it a bit painful to use. I'm still waiting for someone to integrate mindmaps with reference management in a better way.

agambrahma 7y ago

Have to say that with its latest release, Tinderbox (https://www.eastgate.com/Tinderbox https://www.eastgate.com/Tinderbox) have most of this in a _non-cloud, local-storage_ form.