Ipsa scientia potestas est.
(Knowledge itself is power.)
I am actually looking for a program to organize and to code my papers for my thesis. I would like to code my paper regarding different topics, so afterward I can see which paper I can use for each topic. Would this program be able to do this?
The answer to this question warrants its own posting. The term “code” is a bit ambiguous, but if I understand the question as it was meant, the question is whether you can use CPN to collect notes and mark or tag papers where the information should end up (e.g., theory, results, discussion; or chapter 1, chapter 2, etc.).
The short answer to the question is: “Yes, but …”, so let’s have a look at the “but”s.
First off, there are different ways to deal with papers, depending on what you actually want to do.
Classifying whole papers
If you are just interested in classifying or tagging whole papers, you might do this far more easily by just taking the PDFs and add tags to them. Mavericks (OS 10.9) supports tags, so does DEVONthink, and almost any reference manager. However, I would not recommend such a solution — it is far too unspecific. So, paper X with 3-50 pages belongs to the introduction, or to chapter 4. But where exactly does it belong there? And which part of the paper belongs where? It’s a rather superficial sorting that does facilitate a little bit of writing, but not that much.
If you want to do this with CPN, take a page for each paper, and add a keyword or sticker (the graphics attached to an outlining cell). You can also use a single page, create the structure outline of your thesis (introduction, theory, results, etc./chapter 1, 2, 3) and just write the name of the paper beneath the respective header. I would not recommend it, but it is easily possible.
Classifying parts of papers
More interesting is to tag parts of a paper as useful for your thesis — and where these parts should end up. After all, writing a scientific text is just building with LEGO bricks. You need to correctly cite the bricks for your argumentation from different articles and add your own bricks from your own thoughts, arguments, data, and interpretation. Looking at a paper this way … screening it for parts you can use … I found it really helpful. Of course, there are limits. You can’t just cherry-pick the results and arguments that speak for your thesis, and ignore the rest. Likewise, you always have to make sure you preserve the spirit of the article when you home in for the details: If author X strongly argues for position A overall, but mentions an argument for B (because you have to address counter-arguments and rebuttals), you can’t cite author X’s argument for B as if author X was for B.
But taking a “LEGO brick” view is really helpful when dealing with papers — and using them (correctly cited and correctly interpreted) for your work.
Here, CPN can help. No matter what you do, you need to copy-paste the text that is useful (the LEGO brick) into your own notes. Make sure you tag the cell with the source information. CPN supports keywords for cells, and using the citation information (authorname_year) as tag/keyword is really helpful here. Take care how you copy it — some copy & paste methods of CPN remove the keyword. So make sure you have the keywords always visible (ensure that “View” => “Keywords” is checked). If you cannot copy & paste the information from the article, you have to either use OCR (optical character recognition) software or manually transcribe it. Acrobat (the full version) does have OCR (“Document” => “OCR text recognition”), so do other programs. Have a look at this posting if the PDF file does not cooperate. I also strongly recommend taking a look at digital reading — either in this book on page 349 (“Reading Digitally”), or in this posting.
Then, there are multiple ways to deal with the selected parts of the paper. I focus on three I still use.
CPN with one page per article
You can create a CPN page per article and just copy and paste your notes about this specific article there. Then you have the information available. From an article of 3 to 50 pages, you only have to deal with the notes that are relevant for you. You can also add some needed context information. For example, what does the article argue for overall, how good were the studies done? Where do the arguments break down? What are confounding variables?
If you put the article in focus, this might be useful. You can still add stickers for the information in cells to “code” where this particular piece of information should end up. In writing my dissertation thesis, I used tiny graphics like “Th” assigned as stickers to cells to “code” information I needed in the theory part of my dissertation. Later, you can either scroll down each page, looking for this sticker, or use the “Multidex” “Stickers” page to see all the information beneath each sticker. It worked, but I would not do this again for writing a thesis. But I do still have CPNs for the information I copy-pasted out of the articles I have read. As a backup.
Simply use a CPN (or multiple ones) to collect the interesting parts of the papers you have read. It’s a kind of backup repository. It’s got one page per paper you have read, using the author’s names and the year as title. Add a, b, c, etc. when these people wrote multiple papers. Ensure that you tag each cell on the page with the source — easily done by adding the authorname_year as keyword and then expanding all outline cells and adding it to all of them.
I think the much smarter solution is to start a thesis notebook. Create an outline how your finished dissertation thesis should be ordered. Usually, there is a structure that you have to use (e.g., Introduction, Theory, Methods, Results, Discussion, sometimes with multiple studies in an empirical part). Then copy-paste the relevant information (with the keyword) from your read papers CPNs into your thesis outline. Ensure that you remember that you have copied this information and that the information you copy is understandable on its own. This might mean you have to add some context information, e.g., in […] what the position of the author was, or that this was one of many arguments, or that this information is speculative. You are removing the information you use later — when you likely do not remember all of the paper, so provide some context information (trust me on this).
This has a number of advantages: You have all the information still available in the papers CPNs. Useful if you want to create Topic Notebooks. You can handle the information from the papers individually. Place it where-ever you need it. It’s not just that information x belongs in theory, you can place it below w and above y. You are also developing a “content outline” — not just a mere “structure outline” of your dissertation thesis. You can play with the LEGO bricks, yet always know a) where they came from (author_year information tagged/keyword to the cell), b) the context of that information (in […]), and c) flexible in its positioning in your outline.
And once you have created that content outline, added your own thoughts and data, you can make sure you have a coherent “narrative” and put it next to a good writing program (like Scrivener) and start typing.
If you work with the information beyond your thesis, think about creating topic notebooks. They are similar to a thesis notebook, but instead of focusing on a single work, you create a structure to handle the information regarding a whole topic. You find more information on topic notebooks here.
So, yup, you can code your papers with CPN.
One caveat though. CPN is very powerful, but it still got a rare “page not found” bug. So do backups. And for Science’s sake, do keep the old versions of your backups. If you ever try to create a page and CPN acts strange, e.g., you do not see the “Untitled” or just two overlapping circles, press Undo (cmd + z or cmd + y), quit the program and reopen your files. Otherwise you might lose some or all of your data.
Other than that … yeah, I think CPN is extremely powerful and extremely useful for writing a thesis.