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I have recently started with research. Within a few weeks, I have piled up atleast 15 papers in "to be read" list. Since I am working as well, and access the papers on laptop, desktop, tablet or university computers. What is the best way to manage which files I have read. Percentage of pages read, would be a plus. Is there a cloud based or cross platform software (a pdf reader is enough for me), where I can mark files after I have read and associate todos with them ?Also, usually a few papers are related and having a visual indication of such would be nice as well.

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Mendeley is a free alternative to Evernote (but they also have a Pro plan for more features). You can install its client application and use it independently of a Mendeley online account (I did so about a year ago - Things might have changed now). It has fairly good PDF management features.

I noticed Mendeley website is becoming like a social media where members can create groups, share readings etc.

From Wikipedia: Mendeley is a desktop and web program for managing and sharing research papers, discovering research data and collaborating online. It combines Mendeley Desktop, a PDF and reference management application (available for Windows, Mac and Linux) with Mendeley Web, an online social network for researchers.

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I would suggest using Zotero, I created a Zotero folder "to-read" to pile up the pending papers. You can assign existing properties or make new ones to each individual paper like "PagesRead", "Related Paper", "Tags", "Notes" etc. I have tried Mendeley and many other tools but Zotero stands out to be the best for managing research papers.

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I put research materials into Evernote. The Windows, iOS and Android apps have an integrated PDF reader, so I can read documents wherever I am. I pay for a pro account, so I can have access on handheld devices when I'm offline.

Depending on what project the material is for I use different notebooks or tagging to track what has and hasn't been read. For some materials it goes into a Reading notebook until I've read it, then is deleted or moved elsewhere. Other materials I tag #toRead and #beenRead ("read" as different tenses doesn't come through in tagging...)

Additional tags could be applied to documents that are related to track that relationship. Evernote also lets you link between notes, which would be another way to track relationships.

I don't think there is a native way to track pages read, although you could put a reminder in the same note as a pdf file what the last page was.

As a bonus, Evernote just recently added reminders, so you could put an alarm on a paper to remind you to read it.

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I use citeulike, a free alternative of Mendeley. It's web based, and you can upload your personal PDF's. It manages your papers, priority for reading, notes, tags, BibTeX export, etc. Their bookmarklet allows you to export information from journal websites directly (or if you have access to DOI, it accesses databases for you).

Personally, I put papers that I will read immediately in my todo list, which is just a text file synchronized via Dropbox. Citeulike allows me to search papers I have read so far or I should read quickly.

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I am not a fan to rely on software for this job. I have a folder in my PC desktop where I collect the pdf files that need to be read. Then, when I read each one, I archive it in another folders.

In your case, you may have similar folder (to read list) but synchronized via Dropbox or so. You may also need another one for the files you finish reading which will be archived later.

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I'm using to manage my books. This offers everything you might wish (reading progress, ratings, comments, reviews ... ) and gives you also recommendations based on your lists - really nice feature that allowed me to find more great books.

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Goodreads is good for books, but the OP was looking for something to keep track of research papers read, which goodreads doesn't keep a thorough list of. – Amanda R. Jun 3 at 15:58
@AmandaR. You're right I didn't notice the true purpose... – Hexodus Jun 13 at 10:40

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