Does anyone know any good, effective tool that people use to synthesize large amount of information from research?

By "tool" I am referring to softwares or practices that effective researchers use to:

1. retain/recall large amount of research information,

2. progress quickly into a completely new field,

3. find parallels between different concepts and fields

At the moment, I am basically going through papers one page at a time at a time, jogging down the keywords, trying my best to understand their derivation and result before proceeding to the next.

There are several flaws with my current methodology.

  • I write everything on paper, and paper pile up plus it is exhausting to write things down by hand
  • I tend to lose track of prior results as I progress deeper into a subject, I would like some sort of review.
  • I keep coming back to the same concept but only defined in slightly different contexts
  • I keep all the papers I find in one spot but have no way to reference them using any other tools, this means in a few month I will have to trace back to the authors who wrote this or that

I would like something to help me become more effective at quickly gather new information but at the moment I am hesitant to compile everything under the sun in a Microsoft Word or type everything in Latex but if that is the state of the art in the research community then I will begin my research compilation today!

Don't hesitate to share your ideas :) I will place a bounty on this question

  • Are you a Ph.D. student? If so, I feel your pain. Have you tried Evernote? It can do many different things --
    – ewormuth
    Commented Aug 7, 2015 at 1:43
  • I have heard of Evernote but I am not sure of how common this tool is used in higher learning. I think this is relevant for anyone of all level who is interested in an area that is not so well established/cohesive i.e. no standard textbook, or fields of application, a field connected by a dozen of papers (or even ppts) under different authors
    – Fraïssé
    Commented Aug 7, 2015 at 1:54
  • 1
    I think many people in higher ed use Evernote. I'm not sure what you're asking for.
    – ewormuth
    Commented Aug 7, 2015 at 2:05
  • 2
    There are certainly tools to compile large amounts of information. That is, record things together in some form. Notebooks, databases, etc. However, I believe that the synthesis of the information can not be delegated to any instrument other than the human brain. I'm sure there are people that do research as to how the brain does it. Personally, my process is to dive into details, pull back and generalize, and see where the loose ends go. Later something will look familiar, and it may take a while for your brain to figure out what connects to what, but it usually gets there.
    – Jon Custer
    Commented Aug 7, 2015 at 13:05

5 Answers 5


I've become a great fan of Mendeley and tend to advocate it a lot - its a reference manager, but it also has a far more valuable property: manageable full text search in your entire library. Yes, Adobe Reader can search through multiple documents but the output is horrendous with multiple windows and Adobe freezing (unless they fixed whatever caused it in their security settings...)

Mendeley: Search -> get a list, open documents in tabs.

Effectively what it boils down to:

  • reference management

  • library management

(I've not found something easier or more convenient than Mendeley - though I would really like an independent library free open source library management system on my Linux Home Server... - just haven't found anything that fits my taste yet - e.g. no Webserver needed, no database storage...)

As to managing the output you produce:

  • Structure your information

If you have data files, use meaningful folders, use something organised and systematic, write up important information. I tend to scribble a lot, later scan and dispose of the scribbles as they seldom are looked at again, but everybody works differently. Some people prefer to type up all information immediately, the advantage of that is that the document becomes searchable.

But most importantly: Anything that is important, write it up and BACKUP.

Ideally have a backup of everything, but most definitely have at least one or better multiple backups of your important data.


For Qualitative coding and synthesizing of information, there are number of tools you can use (specifically addressing your concerns 1 & 3):


NVivo is a powerful workspace for your qualitative analysis and mixed methods research offering tools so you can deeply analyze your unstructured data.


Leximancer automatically analyses your text documents to identify the high level concepts in your text documents, delivering the key ideas and actionable insights you need with powerful interactive visualisations and data exports.

There are many other tools, but the above two are fairly standard practice among PhD/Researchers. Also, needless to say, they will require significant investment of time (if not financial - given most universities will have institutional subscription) and quite a lot of practice in order to use them appropriately.


You might look at Docear, which is a suite of tools centered on mind maps (tree-structured topic relationship charts). It doesn't completely address all your needs in an automated fashion. You would still need to establish a work flow and certain habits of organizing and reviewing your notes in order to build and maintain coherent "big picture". For example, you might create one mind map per academic article, and then create other mind maps centered on specific themes that link to the paper-centered maps.

For me, tree-structured mind maps were too restrictive. I tend to think in terms of concept graphs and/or argumentation graphs. Alas, there are no general purpose academic research tools featuring those types of structures and visualizations.


You mention not wanting to "compile everything under the sun in a Microsoft Word or type everything in Latex", but I think doing something similar to this may be helpful.

Here's what I have started doing and it's been very helpful for me over the past year or so as I've been learning a new field:

I am a PhD student in biology and am an aspiring teuthologist (the study of octopuses, squids, cuttlefishes, etc.). I have started to jot down everything I want to remember from the papers I've read. Not every detail, but just the things I want to have in my working memory and be able to recall in the future.

The key for me is organization so that I don't just have endless bullet points, or paragraphs. I use LyX and break up my thoughts into Parts, Chapters, Sections, Subsections, Subsubsections, etc.

Everything I want to remember in my field has to have a place. If I learn something completely novel, I just create a new heading and file that thought in place. I'm writing it akin to a book or journal article, so every fact or idea has a reference where I got it from. I also screenshot good figures and add them.

Here's my table of contents as it currently stands to give you an idea of where I am about a year in:

Table of Contents

It sounds like you may be in mathematics so it may take some creativity to see a parallel.

What I find so helpful about this approach is:

  • Each new bit of information I learn and want to remember fits into an organized framework.
  • When I learn something new, I'm forced to think through how it fits into my existing knowledge framework when I decide where to write about it.
  • Because it's broken down so finely, I can easily find information I want to brush up on and only read a paragraph or two to recollect all my past knowledge that has gotten fuzzy.
  • Because it's written by me, my brain often slides back into the clarity I had when writing a particular section. Especially helpful when I'm looking back at a topic I haven't examined in awhile and everything is foggy.
  • I've chosen what I want to remember so I am never filtering through irrelevant details.
  • Everything has a reference attached, so if I want those details I know which paper to find them in.
  • As I'm adding new information in a section, I'm forced to interact with relevant past knowledge, which helps integrate ideas and synthesize main concepts.
  • If a colleague or future student wants to learn something quickly, I can give them this "Reader's Digest" version.
  • I can create a section and leave it empty to remind myself I want to learn about that topic in the future

For full disclosure: the downsides

  • Organization is required. You can't get too lazy and just throw info anywhere.
  • Sometimes I have to put the same information in multiple places from different perspectives. e.g. if I learn about octopus brain physiology, then that info could go under the octopus biology heading with a subsection on brain physiology or under the brain physiology heading with a subsection on octopuses. Sometimes this is helpful though, because I see how the same info tells me something different from different perspectives.

Since this post is getting too long for anybody to bother reading, I think I'll stop it here. I hope someone else finds this method as helpful as I do! Plus maybe one day you will have a whole book written and you can publish it!

  • Thanks for your help. It has been a year since I asked this question and I am just starting to compile things in Latex. It is a chore, as it delays moving on to new fields as fast as possible, but I think it would be worth it as it finally dawned on me that my research field is not as organized as it had existed in my head when I first started
    – Fraïssé
    Commented Sep 7, 2016 at 17:45

Interesting question.

While no software trumps the human brain at this this type of synthesis (so take your fish oil and keep your brain healthy!), I think that you may find that Evernote greatly aids in the task (and there are similar advanced note apps like Nevernote and OneNote which provide similar functionality). This is probably not a silver bullet and is best used within a larger ecosystem of research/study aids, such as a good citation manager like Zotero and a good information search portal like Google Scholar, Pub Med, DeepDyve, etc.

I recommend Evernote because it allows me to:

  1. quickly compile information into notes (this goes with your #1)
  2. see it's automatically generated suggestions of which prior notes are related to the one I'm creating or reading (this goes with your #3)
  3. easily integrate information from other sources like webpages, documents, emails, etc (this goes with your #1)
  4. save my notes locally and/or synchronize them across devices via "the cloud" (this goes with your #1)
  5. encrypt sensitive information but optionally leave it unencrypted for the period of time that I'm logged in (this is nice, but not directly related to your 3 criteria, I suppose)
  6. easily organize notes, notebooks and stacks of notebooks on the fly ((this goes with your #2, I think)
  7. easily search all notes, any given notebook or stack of notes, or easily create/search based on tags

Note also that Endnote's free version is fully functional in every way that's relevant. They have a paid version that allows you to have more that 1 account on the machine, but no research-related tools are disabled in the free version.

  • I'd always be weary of relying on a third party service that in theory could go under at a moments notice - ideally whatever system you use should be as self reliant as possible.
    – DetlevCM
    Commented Aug 9, 2015 at 17:16
  • They are completely self-reliant. Hence local storage (#4) and Nevernote (main paragraph)
    – y0gapants
    Commented Aug 9, 2015 at 22:33
  • Evernote relies on its web access though.
    – DetlevCM
    Commented Aug 10, 2015 at 8:41
  • No, that's not accurate. Evernote does not need web access. Evernote gives an option for cloud storage (i.e. web accesses needed) and/or offline local storage (i.e. no web access needed).
    – y0gapants
    Commented Aug 10, 2015 at 13:41

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