Organizing Dissertation Research

Hello to dear researchers, students, professors, associates and working professionals!

It is always an amazing experience to research and produce something of help for our fellow scholars out there. Though, we are not a direct part of any of your scholastic and pedagogical labors yet it always feels great to be some sort of indirect aid.

Ok, so today we will be organizing research notes with you.Research notes typically include research materials, reference resources and bibliography examples as you sift through the web, collecting and recording content for your research.

How to Take Research Notes the Smart Way?

Either you are working on a dissertation or writing a research paper, somewhere along the way you will be juggling your  thesis statement, introduction writing or formatting the conclusion for your thesis. The back and forth process of checking and analyzing research information can be a tedious task unless you follow an organized and self-disciplined approach which would help you in getting done with your research, faster.

Working in the offline mode, students normally opt for research note cards or research paper notes. The process involves a lot of writing and then editing and re-editing. In summing up the scenario, a lot of time is taking in organizing your research rather than writing your research.

Working With Research Notes

Working with research notes, on the internet can save you a lot of time spent otherwise in organizing materials. You can simply use one or a couple of research tools to store and record your data.

As you work in narrowing down your focus you will find yourself in need of more and more facts to back up your opinion. We always advise  to first have a bird’s eye view of all types of available opinions and speculations and then handle your angle of choice by evaluating materials available by your side.

The method of your research notes, hence vastly depends on your research methodology and the type of your research design:

  1. Quantitative (Fixed) Research Design
  2. Qualitative (Flexible) Research Design
  3. Mixed Research Methods

Collaboration and Organizing of Your Research Notes from Multiple Formats (PDF, Word, Excel and Text Files)

The premier responsibility of a research note organizer should be the ability to collect, record and organize your research notes in multiple formats. Next requisite is the ability to retrieve and use your data with ease and speed.

As per your need and requirement, you can choose between web based applications or simple browser add-ons to help you in your in handling and taking your research notes.

Helpful  Browsers Add-Ons to Organize Your Research Notes

Blue Organizer

Blue Organizer is available as a Firefox add-on and helps you to collect and record all types of content including, mp3s, documents, images, videos and podcasts etc. The tool also personalizes your research experience by looking into your browsing history and offers you valuable suggestions and resources.


EverNote is an application which comes with browser a add-on. It would help you to organize and save your research material notes by either adding clippings of web pages or saving entire URLs.


Zotero is an amazing add-on for Firefox which is very helpful for managing and organizing your bibliographies and reference materials The tool has the option to take and save your notes and analyze your research.

Web Based Applications for Managing Research Notes

Noodle Tools

NoodleTools is an excellent web based application for note-taking, outlining, citation, document management, archiving/annotation and collaborative research and writing.

Research Gate

Research Gate is a great web based organizing tools for scientific research with  collaboration and available research publications at your end for quick referencing and note taking.


Docear is is an academic literature suite. It integrates everything you need to search, organize and create academic literature into a single application: digital library with support for PDF documents, reference manager, note taking and with mind maps taking a central role. What’s more, Docear works seamlessly with many existing tools like Mendeley, Microsoft Word, and Foxit Reader

Personal Brain

Personal Brain helps you to organize your notes in multiple formats and is more of a mind mapping tool. It helps to project your ideas, notes and snippets in front of you to evaluate and synthesize from all materials, while not missing anything in your research.

Mac Based Research Note Organizers


Devoonthink is a commercial research organizing tool for Macintosh. It aims in enabling you to work in a paperless office by collecting and storing all of your data in easily accessible style.


Papers help you in downloading organizing and citing research materials and references, all from one source. The app also offers the option to collaborate with fellow colleagues and researchers for peer review and information sharing with your research notes.

How do I choose a dissertation topic?
Ah...the long and often frustrating process of finding a topic. Here are some general tips from the PhinisheD archives.

An interesting thread on starting the process of finding a topic: How do I select a dissertation topic? by Gary Brian.

Another interesting thread on starting the process of finding a topic: Need thesis ideas by Jennifer.

How long should a dissertation be?
In some disciplines, a dissertation under 200 pages is frowned upon. In others, 50 page dissertations are the norm. Probably the best way to determine "how big should mine be?" is to go weigh the dissertations in your department library.

Jason talks about the expectation of different lengths for the dissertation in different disciplines: Diss length in humanities vs science by Jason R.

How should my dissertation look?
Not a silly question, but an entire class of questions, including "How long should my dissertation be?," "How should my dissertation be structured?," "How many graphs or tables should I use?," "What goes in the appendix?," and a host of other related questions. Long-time PhinisheD pillar David always has the same response: Go to the library and look at the last three dissertations to come out of your advisor's lab. That is David's Rule, and you would be wise to heed it. Familiarizing yourself with work your advisor has already approved will benefit you in countless ways.

How do you manage references?/What bibliographic software do you use?
Many people at PhinisheD have asked about experiences with various bibliographic software.
  • Many PhinisheD users recommend EndNote to search online bibliographic databases, organize references, and create instant bibliographies. EndNote integrates well with Microsoft Word and Word Perfect (Windows and Mac, student $110, free trial version).
  • From the same company that makes Endnote, ProCite is another popular bibliographic program (Windows and Mac, student $110, free trial version).
  • Ibidem is part of an integrated academic package from Nota Bene (Windows, student pricing for Nota Bene Scholar's Workstation $249, free trial version).
  • Citation combines a bibliography and notecard program (Windows, academic $199, free trial version).
  • A free bibliographic option for Mac users is the limited version of Papyrus. This has all the features of the full version of Papyrus ($90), except each bibliography database is limited to 200 entries. Program is no longer being updated.
  • A free bibliographic program for Windows users is BiblioExpress. BiblioExpress can be run off of a single floppy disk, and is the freeware edition of the more extensive program BiblioScape (academic lite $50, academic standard (integrates with MS Word, $100, free trial version).
  • Another free Windows option is Scholar's Aid Lite. Main differences are lack of a spellchecker, and limitation to five files (tip from Claire: this can be circumvented using the "save as" feature). The full version is Scholar's Aid (student $75, free trial version).
The first post on a general discussion of bibliographic software: query about bibliographical software packages by David Mackinder.

Should I write my dissertation chapters consecutively?
Many dissertation writers find the task of organizing their dissertation work to be an unexpected challenge.

PhDyke's question on what to start writing her dissertation sparked some interesting responses: How to get from Zero Draft to Chapters? by PhDyke.

Tom describes why it is often best to do the first chapter last: Doing the lit review last by Tom.

Todd asks about writing chapters concurrently.

Chapter 1 is a special case: some say it should be written first, some say it should be written last. Lilac Wine and Marsha Kobre Anderson discuss Chapter 1 and when you should write it.

What should I know about last-minute dissertation formatting issues?
Most dissertation writers are surprised to find that to graduate, it is not important that their dissertation be good, but only that it be formatted correctly. And formatting to the university's satisfaction is no easy task....

Kharyssa deals with the format nazis: Dag nabbit! by kharyssa.

CarolC reiterates advice about formatting margins.

What can I expect at a dissertation proposal defense?
Jade gets some good advice about what to expect at the defense: Proposal defense by Jade.

What can I expect at a dissertation defense?
Anne gets great advice about preparing for her dissertation defense.

How do you take notes? / What notetaking software do you use?
Different notetaking styles work for different people. Some people produce written notes, some start out with written notes and then transfer to the computer, and some enter notes directly into the computer.

Notetaking Strategies

One favorite notetaking strategy is to use index cards and file in a rolodex or shoebox. Some people use a two-column ledger, with one column used for the source citation and the other used for the comments or quotations. One strategy for transferring information to the computer is to do focused freewriting on the notes, which are then transfered to a thesis binder. Claire describes the advantages and limitations of using a pen scanner to input text. Jade uses voice recognition software to input her notes. Another strategy is to use software designed for notetaking. Junebug's question on notetaking sparked a thread where PhinisheD Pholk shared their notetaking strategies. So did Rosamunde's question about note-taking and quotes.

Notetaking Software

Many bibliographic programs, such as EndNote, provide a searchable keyword and notes section. See the Bibliography FAQ for more suggestions on bibliographic software. See also the Software section of the Links for more ideas.

How do you manage your research materials?
The first rule of thumb is to always copy or back up original research material. Field data, transcript tapes, and other hard-won data should be reproduced, with one copy kept off-site, preferably in a fire-proof box. The cost of copying materials is small relative to the cost of redoing all of the original research!

There are two main systems for filing photocopied book chapters and journal papers. One is to organize by topic, which has the advantage of being able to quickly refresh your memory on a topic and good portability; the downside is that papers often fit into more than one topic, and it is easier to misfile and lose papers than with an alphabetical system. Another is to organize by alphabetical order (either first author or PI/group), which has the advantage of more robust organization but makes gathering together related papers more of a chore. GeoGal sets off a discussion on filing systems. Whichever filing system you choose, keywords in bibliographic software should help.

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