This kind of falls between Help and Use (help on use, I suppose), so I'm posting here.

So I was reading a cognitive neuroscience paper the other day, and looking for something to help me learn the material. I happened to run across The Brain in my applications folder and gave it a try. What I wound up with was a huge, horizontal mess.

With something like James Burke's Connections, there seems to be a natural hierarchy of information. Someone came before someone else, or was influenced by them, etc. Whereas, for instance, when I'm mapping out the ventral stream (that processes the "what" information for what we see), I wind up with a lot of Jumps. The ventral stream is associated with these concepts, but most of them do not fall into a nice hierarchy. The pic attached shows what it looks like. The scroll bar on the left isn't visible in the pic, but there are more jumps than shown in the pic.

It seems that perhaps The Brain is more suited to help one remember the members of, say, a sales team and who is supposed to perform what function, than to help one learn information. I really wanted a tool to help me make connections between topics, but even after reading and transcribing one paper, it seems to be an unnavigable wilderness.

Am I just using the tool incorrectly?

Is there a way The Brain can help me process and retain this information, or is it merely a repository for information?


Screenshot 2016-01-26 11.27.29.png 


Scientific publications are, by their very nature, complex and very dense.  The reasons for the complexity are obvious.  The reasons for the dense-ness is that authors are limited to a certain number of words or space in a publication.  So they are forced to cram a lot of concepts into a limited space.

Mapping all of the concepts in any given paper will produce the unwieldy mindmap you posted above.  It is likely better to map out the major theoretical themes, as well as the specific hypotheses tested in the paper, rather than ALL of the concepts.  Then go back and see if you can link those major themes and hypotheses to more basic concepts. 

Those basic concepts (e.g., the role of the ventral and dorsal streams in sensation and perception) should probably be mapped separately, since they are themselves complex.
John, a few reactions:

1.  Not intuitively clear what the difference is between a repository and a tool for learning.  A book is both, but is hard to visualize for complicated things.  A mindmap can be very useful, but isn't great for "3-D linking."  A Brain let's your organize information, no matter how complex, in a visual way that makes sense to you.  Why wouldn't that help you learn?   Even just building the visualization would assist the learning process. 
2.  The "expanded view" you're working in gets pretty overwhelming pretty fast for almost any complex materials.  Alternative views keep the information and links much more manageable.  Using the tagging and reports feature can let you see just certain parts of the Brain at any given time.  I suspect that would be very useful for the learning you're envisioning, particularly when information isn't necessarily hierarchical in toto.  With alternative reports you can look at parts of the picture, each part organized in a way that makes a lot of sense.   
3.  The key thing with Braining a complex topic is to have an organizational framework that makes sense.  It's hard for me to tell for sure, but some of the ways information is organized in your Brain looks like you simply filled it out based on the materials you were reading, but you haven't gone back in afterwards to ask yourself "is this really the right way to organize the information." I do that repeatedly with a complex topic, and each time it gets more intuitive and lasts longer before I realize there's "a better way."

I guess a key question is: what other tools are you looking at for what you're trying to accomplish?  Is there something out there that gives you more power/flexibility?  


There is quite a difference between a textbook and a paper. What you did here is extract everything there was in the paper. This is a huge task and you will not be able to do that for many papers because it takes too much time... You should concentrate on the new stuff in the paper and this will give you only a couple of thoughts per paper. At a later point, when you put in a different paper with a similar concept, the thoughts of the first paper will automatically pop up and you will be able to connect the two papers. And this is the unique power of TB.

But yes, this is beyond the learning stage. It helps if you already have a sound knowledge in the field and you can connect things. I would not use TB for learning. There I would go for a hand-drawn mind map on a large sheet of paper. As much as I like technology, learning is still about you, a book and a lot of time in a quiet library. 
Thanks for the helpful comments everyone!

I'm sure this will get easier as I progress through my PhD studies.

I appreciate any more comments related to distilling information like this.



A few thoughts for you, John. 

1) TheBrain is really useful for connecting related ideas in free form (e.g., all the software on my hard drive that can do stuff with graphics -- but I sometimes forget I own them and what they can do even though they are in my Applications folder! I can list, typify, categorize, attach notes, and connect in any way I see fit these different apps, and connect them to different projects I'm working on, too.)

TheBrain also can connect and show relationships between disparate and not obviously related pieces of information (e.g., all the people who worked for the same company, or attended the same university, or held the same political beliefs over time).  What it is not terribly great at is drawing a linear, static diagram of relationships between concepts. And I think this is what you were trying to do. See next item.

2) The relationship between concepts can be presented by a Concept Map. This visual representation of information shows the relationships between each key idea.

A good explanation can be found here:

The challenge with such maps is they can become quite complex in short order. And some say they quickly become all but unintelligible to everyone but the mapmaker himself. (See for example the attached. I made this concept map to illustrate a communication theory that I thought was long on mushy verbal statements but short on clarity. I presented the map to the author of the theory himself in an attempt to disambiguate the confusion. He was only stymied.)

See also this link to Xmind's blog on using that software to create concept maps:

A challenge with concept maps: They don't grow very well organically as you add new information, which I sense is what you want to do as you learn more and new concepts along your learning journey.

3) I don't know what platform you are on, but if you are on Windows, you might look at Idea Shuffler as an alternative way of organizing information. (I can't use this as I am on a Mac.)

4. If you are on a Mac, I suggest using DevonTHINK and TheBrain in concert. That's what I do. DevonThink is the big storage vault database for containing the raw data in multiple databases -- organized by topic. Then key concepts are pulled out for connecting free-form relationships in TheBrain. 

I really do wish one program could do it all: Take all my notes, organize my information, search my data every which way, connect information in any way I chose, then display that information in amazingly beautiful ways ready for presentations.  What's that I hear? Oh, it's Aerosmith: Dream On!

As it stands now, I collect my developmental psychology info on my iPhone and Mac using plain text notes (nothing beats the ultimate transportability of plain text!), move those and my PDFs and other documents into DevonThink Pro, and then select information to put into TheBrain.

I truly wish it were otherwise. Yet, at this time, I cannot do it any other way.

Best wishes with your studies!

Don B., PhD

Thanks for reminding me about Cmap. I've successfully used it in the past, and I think I was hoping TheBrain would be a kind of 3D version of that. I think for my purposes, Cmap is probably the way to go. Perhaps I can find a use for TheBrain , but at the moment, $200+ with student discount (and on a grad student stipend) is too rich for what it can do for me.

The Cmap documentation that you linked to is excellent!

Thanks also for the recommendation of DEVONthink. I'm still trying to wrap my head around its paradigm, if that paradigm is useful to me now, etc. It could include the functionality that I wish EndNote has, so I'll give it some consideration. I can foresee EndNote with 150+ references as being a burden when it comes time to write my dissertation. Then again, it will at least export a BibTeX file. I'll have to see how well DEVONthink plays with LaTeX.

On the upside, OmniFocus is keeping track of all my verbs pretty well. Just need to get a handle on these nouns.

Finally, as andreas alluded to, nothing beats pen and paper. Need a dashed line? A pen does that. Want a wavy line? A pen does that. Vertical text in the margin? Pen. Big ellipse? Pen. Love my Waterman rollerball and Clairefontaine/Rhodia paper.

Thanks again to all who have replied.
Still open to suggestions!




I wanted to share another quick link for you.  While it might not deliver the answer of "how to manage you jump thoughts"... I thought the specific topic may be of interest to you.

It's a nice case example of TheBrain being used for Thoracic Surgery Education.

And as for feedback from seeing your original screenshot - have you started using Thought Types in your Brain?  It's a great way to add further classification with out the need for additional (and sometimes unneeded) connections/links within your Brain.  For example: You may have DOZENS of topics in your Brain that are related to bioengineering, psychiatry or physics - but they don't all need to be connected as a JUMP.  Try creating a Thought Type for BIOENGINEERING and apply this to specific sub or related topics such as Doug Lauffenburger and Heinz Wolff which are located in seperate areas of the same Brain.

Please note - I utilized Wikipedia to help me with that example [wink]


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