Integrate with a reference manager?

[young24]

I just searched the market of the reference managers. I don't like EndNote. There are 3 plausible options: Zotero, ReadCube, and Mendeley.

Zotero

Pros

• Free
• Open Source
• link with NutStore with WebDev

Cons

• only 300 MB storage
• Chrome Extension works poorly with some journals. (e.g., cell)
• only support PDFs

ReadCube

Pros

• good web interface

Cons

• Not free

Mendeley

Pros

• Large Free Storage (2 GB)
• good Chrome plug-in
• good web-interface
• support multiple file types

Cons

• not sure whether it can link with cloud services

[young24]

integrate the Reference folder with reference managers

[xutq]

Mendeley's build-in search engine is weird.

[young24]

It is perfect on my computer, however, I believe you can adjust it manually. @xutq

[young24]

I'm just aware that we can just add a link to the web library in a markdown to achieve the goal. So that,

1. click the link
2. jump to the web library
3. Done.

Then if you want to download any files from the library, just click on the download button of that paper in the web library. (This can be achieved easily by Mendeley.) @xutq

[xutq]

Should this library be set to a shared library?

[young24]

Yes, you have to invite other team members to share this library. Moreover, Mendeley provides links for each file in the library, which allows us to manipulate files separately.
So that, actually, we can build a hyperlink-style library on GitHub with the help of Mendeley. It is approximately my ideal storage model. Put real files in the Mendeley library and put their links on GitHub. @xutq

[young24]

Sadly, there's no reference manager works with Markdown. Ideally, there should be a reference list noted with Markdown. So that when you add a file to the library (stored outside GitHub), an item would be automatically added to the Markdown list. In this way, GitHub can still track every manipulation but be free of the storage burden.

[xutq]

What is the situation of tracking the changes of references?

[young24]

When you add/remove/edit an item to/from/in the library @xutq

[xutq]

What is the reason/necessity to track them?

[young24]

Put all in one place. In the ideal storage model, you can access to every detail of the project from GitHub.

[young24]

It's better to rephrase the idea in Git terms. Get version control on catalog items. Therefore, there are actually three procedures for an ideal reference manager:

1. Generate the catalog automatically for each item in the folder. (e.g., Author-title-year)
2. Record the catalog in Markdown style in an organized way. / Silent record just in the library.
3. Git version control on the markdown file in step 2.

Mendeley provides APIs which enable the possibility of generating such a catalog in Markdown file. However, is that okay to update this catalog markdown file directly on GitHub? This would cause some unnecessary pull-down, which might not good for the collaboration.