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I am doing research in computer Science as a PhD student. I have some research ideas and for months I've been continuously thinking about them, developing them and make them more specific. I mean, these ideas continually change until one day they are finalized. Over time they are more specific and complex.

I use Evernote to write down my ideas, and sometimes maybe also brainstorm mapping tools like Mindmeister. But I found these tools are not good enough, e.g. not easy to structurize my ideas, or modify, elaborate them, in a word, manage my ideas.

Do u have any good methods or tools for the organization/management of your developing research ideas? How do those professors and professional scholars and researchers deal with this issue?

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migrated from cstheory.stackexchange.com Oct 17 '12 at 17:10

This question came from our site for theoretical computer scientists and researchers in related fields.

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@DanielE.Shub would the question be more acceptable as a slightly more general variant, like: “Are there specific organizational processes or tools (not necessarily software) that can help in developing and structuring research ideas?” –  F'x Oct 17 '12 at 18:32
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@Daniel - It seems like the community voted against closing such questions in the meta discussion you linked to. –  eykanal Oct 17 '12 at 19:00
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One piece of advice: don't allow the search for the right tool to delay actually working. Nothing wrong with scraps of paper, as long as you can keep track of them :) –  Suresh Oct 17 '12 at 20:28
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Strong +1 JeffE’s mention of Moleskine! Using them made me take note-taking more seriously that I did before. –  F'x Oct 18 '12 at 9:27

5 Answers 5

up vote 8 down vote accepted

Aibase has the option to put formulas, mind-maps, bullet points lists, diagrams, sketches, to-do list in ONE document, basically a hybrid software (Evernote + MindMapping) for creative project managment. Best software I ever bought for knowledge and project management

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I explained the software here more in detail

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I'd have really appreciated the answer if you'd have come up with an open source or free software solution. –  M. G. Rashed Oct 18 '12 at 19:36
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@Md.GolamRashed ??? Sorry, but very good software sometimes costs money, 50$ for a software I now use for several years isn't that much. Even the popular Evernote costs at some points money. The best opensource software similar to aibase is probably freemind, but it lacks a lot of its functions –  Hauser Oct 18 '12 at 20:19
    
I was feeling quite tempted by this until I realised it was Windows only :( –  Nathaniel Dec 28 '12 at 15:58

Anytime I get a chance, I try to use the productivity applications. These may be associated with time management or structuring ideas etc. I found out that there is no best way to do this. Every application has some heuristics behind, and these are mostly decided by the developers. Sometimes an app may seem to solve your problem, but later you may realize that it is not what you want or need. In my opinion, you need to come up with your own way to do it. However, let me list some ways/advices I encounter:

  • Open a google document. Write down your ideas as a list. If you need to structure them, nest the list items. Go over the document periodically.
  • Take a look at wunderlist. They have done a good job task/note management. wunderlist 2 has just released with new features.
  • Trello is another example. It may seem to be an project management tool, but you can use for managing your ideas on a whiteboard-style.
  • Springpad is another way to save/organize things online.
  • Your example Evernote, and others like do.com, todoist can be listed also. If you really need to find the right application you need to search hard. Take a look at here as well.
  • Mindmup is a online mind mapping tool.
  • Hiro is another newly released tool. Try it here.

For me, the best way is to keep a small notebook and write down what I have done in terms of research day by day. I also note the ideas for my thesis. After some point, when you go back and check your progress, you would be amazed how much things changed and become more mature. But the most important thing is that I realized what is best for me is to grep a pen and write down it on a paper rather than some website.

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Why evernote and not onenote? –  Jase Dec 19 '12 at 3:52
    
I just listed the ones I know for that time. Of course, you can add onenote to the list above and others you happen to know. For example, wunderlist 2 has just released with new design and lots of new features. –  mert Dec 22 '12 at 11:48
    
+1 for Trello. Great especially for working with others. –  Amory Aug 16 '13 at 23:01

May I recommend Org mode? It's free software, and it was created by Carsten Dominik, an academic himself. Its focus is to help you maintain hierarchical notes and to-do lists, but it has a lot of other features that are useful for juggling large amounts of information, such as tags, links, many kinds of summary reports, and capture (a way to quickly add a note in the right place before you forget it), as well as many features useful for scientists in particular, like tables, spreadsheets, mathematical notation, export (as papers, slideshows, or websites), and support for source code and reproducible research. Perhaps best of all, Org documents are text files, so you can munge them with standard Unix tools at whim. I've moved more and more of my workflow to Org since I started using it in 2010, and I regret nothing.

Org has a steep learning curve, which gets steeper if you aren't already a disciple of the Church of Emacs. But as I see it, getting used to Emacs is worth it even without Org mode, especially if you do a lot of programming. I was an Emacs zealot for years before I took up Org.

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Whiteboards & (electronic) notebooks.

My notes start in one of two places:

  1. On a whiteboard
  2. Being jotted down to my to-do list to be thought of more in depth later, usually because I'm away from work. These will then later be thought through on the whiteboard.

The primary benefit of the whiteboard is the freeform mapping. There are many mind-mapping software packages out there; I don't think any are as good as an actual whiteboard. On a physical board, you can write easily, sketch ideas, connect concepts, erase stupid stuff, and leave it there while you type easily. You can do this with a program, but you need to use a mouse and keyboard, which I find overly constrictive.

I typically sketch the idea out there, and then just write it down either to paper or to an electronic notes program. I use Simplenotes, but there are many very similar programs... Evernote is very popular. Unless you're very savvy with the command line, I recommend against just using text files, as there's a huge benefit to having the features that come with these programs: quick searching, tagging, and attachments.

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Why not Microsoft OneNote? Is there a benefit to Simplenotes or Evernote over OneNote? –  Jase Dec 25 '12 at 2:56
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@Jase - The benefits for me were: (1) price; Evernote and Simplenotes are free, (2) famliarity; Simplenotes is brain-dead simple to use. That being said, if you own and are already familiar with OneNote, this workflow should fit perfectly well with it (or with the dozens of other notetaking options) as well. –  eykanal Dec 25 '12 at 14:34

I like to use DevonThink for managing developing research projects. It's a Mac-based software which offers a data and knowledge management system. The relevant steps in my workflow for refining research ideas to concepts and then projects are as follows:

  • Collect literature on a relevant topic and put it into a dedicated DevonThink group.
  • When I see important points for the project in a particular paper, I create an annotation text document in the same group to write down these points.
  • I import email related to the project (for example discussions with colleagues) into the database, so that I can link to them when making use of ideas obtained from there.
  • When starting to synthesize ideas, I do it in a text document where I can insert links to or even image snapshots from the source documents in the DevonThink database.
  • When working on a project, I create journal files in the DevonThink database, writing down what I did, what results I got, and maybe pasting screenshots or relevant result diagrams into the journal file.
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