Keeping stuff organized

[beanbagchairs]

I am prepping myself for graduate school. I am thinking to get a new laptop and possibly an ipad. My problem is that I have notes everywhere (this notebook, that notebook, on the side of printed papers, etc). I cant bring 'em all to my new place;besides I just ruined some after spilling water on them. I am wondering how are you guys keeping your things organized. I am thinking something along this way:

Laptop - primary workstation

Ipad - reading papers, taking notes, synchronized to Laptop via Mendeley (papers) and Dropbox (everything else)

Ditch my organizer (book) and use my ipad instead, such that I can synch that to my laptop.

I am not sure if ipad is a better way of taking notes though (ease of use of a stylus?)

Do you have a better system of organizing things, namely?

1. Keeping notes and papers in digital format, such that they are always accessible

2. Have these notes organized by topics or dates?

3. Have a lab journal?

4. References (JabRef?? Mendeley works too?)

5. Weekly backup?

Any ideas?

Yes, I have this constant need of organizing every aspect of my life

Edited March 19, 2011 by shashakoe

[eklavya]

1. Keeping notes and papers in digital format, such that they are always accessible

2. Have these notes organized by topics or dates?

3. Have a lab journal?

4. References (JabRef?? Mendeley works too?)

5. Weekly backup?

1. i never take notes, but all my papers, powerpoints, assignments are stored in my laptop - which btw is also the main workstation from scripting to playing games. and every week or so, i backup my data in an external HD

2. usually, semester\class\<paper folder><assignment folder><lecture slides folder><and so on>\<arrange documents by date>

3. yes, but electronic - saves paper, easy to access later, and works great if you need to send a slice of your lab work to your advisor and collaborators

4. endnote

5. yep

your idea of getting a reader (like ipad) is great, and i respect you for making this move. i HATE people when they print numerous papers just because they find a section of that paper somewhat useful. most likely, you are never going to use the papers that you printed last week, because you will be brainstorming on another direction a week later. in case you do need to go back, searching on your machine is lot faster and convenient than going through the stack of useless papers you printed. so, electronic note-keeping is a very noble move.

[ogopo]

You must MUST check out Papers2 for mac. I gather that since you are planning to get an iPad, that you are a mac person? Seriously, get papers. It's much easier if you go to the website and just check it out but it will basically do everything you need. It organizes all of your papers, book chapters, your own manuscripts, notes, etc. in one convenient place. You can find any paper in your library based on title, journal, author, date and you can even do full-text searches. Papers2 (the first edition did not have this) also has a citation function, which is marvelous.

I think this is the third time I have talked about Papers in these forums, they really should start paying me.

I have a binder for each of my classes. I try to organize them with those binder tab divider things with sections like assignments, course notes, assigned reading, project, etc. Each of my binders is a different bright colour. It makes me happy to look at them.

I definitely have to agree that paper articles are hard to keep track of. Try to get everything in electronic format, even if it means scanning them yourself.

I have a paper lab journal but I would consider using an ipad if I had one. Then again, I would be worried about spilling things on it.

And ALWAYS back up. In fact, I'm going to go back up right now

[Kathiza]

Any suggestions on how to keep PDFs (Articles, Papers, different stuff...) organized for Windows-users?

I'm going crazy, I can't find anything anymore...

I'm using EndNote and started to import the files and attach the full text to the references. But that does not really help because they are still all over the place...

I've heard good things about Mendeley. But what does it do exactly?

[eklavya]

Any suggestions on how to keep PDFs (Articles, Papers, different stuff...) organized for Windows-users?

the best way to organize things is by making folders, sub-folders, sub-sub-folders and so on to segregate everything (pdfs, powerpoints, research papers, etc) so that you can easily keep track of where things are. if your pdfs are all over, you can use iFilter (free to download on adobe's site) to search for the pdfs. after this is installed, you can search for the pdfs using windows search, using some keywords that are used in the pdf anywhere.

mendeley does things similarly to endnote, but for some reason, i like endnote better.

[neuropsych76]

. i HATE people when they print numerous papers just because they find a section of that paper somewhat useful. most likely, you are never going to use the papers that you printed last week, because you will be brainstorming on another direction a week later. in case you do need to go back, searching on your machine is lot faster and convenient than going through the stack of useless papers you printed. so, electronic note-keeping is a very noble move.

i'm guilty of this, sorry! my honors thesis binder was huge and had tons of unorganized articles flowing out of it.

i'm hoping to increase my organization for grad school as well. i think going digital will certainly help. is investing in an ipad/kindle type device worth it? or is just a laptop sufficient? (though i'll probably need a new laptop as well)

[natsteel]

You must MUST check out Papers2 for mac.

+1 I've been using Papers for over a year now and just upgraded to Papers2. I don't know what I'd do without it. I also use an app called Notebook for Mac which I use to take class notes. I generally record my classes with my iPod while taking notes with Notebook and then afterwards I drop the audio file right onto the Notebook page for that class session. I use Things for Mac as my task manager and to help me plan and keep track of what's due and when for each class and paper. That's been indispensable as well.

I also use Scrivener when writing a long research or historiographic essay. If you haven't seen this application, google it. It's incredible.

I use Evernote for random or on-the-spot notetaking and Curio for mind-mapping/paper conception. Of course, I use EndNote for citation management and DevonThink Pro for having one searchable database of all my files.

I backup most of this stuff to my Dropbox account, i.e., email archives, calendars, contacts, tasks, EndNote libraries, Notebooks, etc.... I also keep my main semester folder with subfolders for each class in my Dropbox folder so it's always backed up along with all my "project" (essay) folders. I also just got a Kindle which has been really good for reading journal article pdfs since I spend a lot of time traveling during the day. And, almost everything above is also synced to my iPod.

I have been considering getting an e-pen as well... the Livescribe looks really interesting.

[qbtacoma]

Has anyone used Zotero? I played with it briefly but I didn't find it all that helpful. However, I didn't use it for any heavy-duty projects either.

[Kathiza]

and DevonThink Pro for having one searchable database of all my files.

Oh my god, this is fantastic. At least it looks like it. But I just discovered there is no Windows-Version :-(

I would have even spent the money, because this program does exactly what I want a program to do...

[ogopo]

Holy cow natsteel! If I used as many programs as you I think I would need a program just to keep track of all my programs! You sound unbelievably organized

Kathiza, I have not heard anything about Mendelay but have you considered Zotero? A girl in my group doing her PhD swears by it. I'm pretty sure she will abandon it for Papers2 now that it's out but with Zotero you can organize and cite with it. Also, it's FREE! And it's built into your browser. I could be wrong but I think you can only use it with Firefox. The good thing is that I'm pretty sure it's also available for Windows.

Ok.. my statements are becoming wishy-washy. I need sleep.

And if all else fails, just get a mac. You know you wanna...

[truckbasket]

I also use an app called Notebook for Mac which I use to take class notes. I generally record my classes with my iPod while taking notes with Notebook and then afterwards I drop the audio file right onto the Notebook page for that class session.

There are several apps for the iPad that not only record, but also sync typed notes to the recording for you. Notability is good for that as if you want to hear a part of a lecture again, you just touch the note (or keyword) that you typed and the audio goes right to it.

Although I do love the iPad, and use it for reading an annotating PDF's, browsing the web, searching through texts, reference, planning etc., I still find myself relying on handwritten post-its and scraps of paper that live in my pockets for weeks. Also, if I need to scrutinize a document, the physical copy with margin notes method still works best for me.

[Amalia222]

All this sounds highly technical. But I do want to add the importance of having a backup of your work. These days, they make 16GB flash drives that will hold basically everything you've ever written (not photos or big files, but you can save a million essays!). Every week or so, I save my "My Documents" folder into a memory key, so if anything ever happens to my computer my work is safe. Over the years, I replace flash drives, and store the old flashdrives, labeling them by year so I know where to look for older stuff. Paper is absolutely going the way of the Dodo. When profs don't allow laptops in class, these days I usually transcribe my notes later to my computer, which is an excellent way to review the material. I organize my files as the person above noted, using sub-folders. I have different sub-folders for different kinds of documents, and I always re-name my documents when I save them so I know what it is (scanners can be pesky, because they will save stuff as "file 001" "file 002" if you let them!). Good luck.

[natsteel]

Holy cow natsteel! If I used as many programs as you I think I would need a program just to keep track of all my programs! You sound unbelievably organized

Kathiza, I have not heard anything about Mendelay but have you considered Zotero? A girl in my group doing her PhD swears by it. I'm pretty sure she will abandon it for Papers2 now that it's out but with Zotero you can organize and cite with it. Also, it's FREE! And it's built into your browser. I could be wrong but I think you can only use it with Firefox. The good thing is that I'm pretty sure it's also available for Windows.

Ok.. my statements are becoming wishy-washy. I need sleep.

And if all else fails, just get a mac. You know you wanna...

HA! I guess it does sound like a lot of programs, but I think I've developed a pretty efficient workflow, so it all seems pretty seamless to me. Being well-organized basically means that my bad habit of procrastination costs me less than it might otherwise.

About the Mac... many (though not all) of the programs I use are only for Mac and that is why I bit the bullet and bought a MacBook Pro. I got the cheapest one available at the time and even though it was more than I should have spent on a new computer, I haven't regretted it for a moment. I would never willingly go back to Windows now. That said, Scrivener is coming out with a Windows version soon (if you haven't seen this program, check it out). And there is Mendeley instead of Papers. Evernote is available for PC, there is OneNote instead of Notebook, and Things also has PC equivalents.

About a year ago, I set out to really nail down my workflow before I started graduate school. I began doing it when I was writing my junior honors essay. Now, I'm doing my senior honors essay and I have the flow down pat. I can honestly say that my efficiency and productivity have improved significantly from getting organized and designing my own workflow.

[Eigen]

My organizational system is in a constant state of re-working, but here's the gist:

I try to keep computer-based files in folders with more depth than length- use more subfolders, it's easier to find what you're looking for.

I keep all my PDFs organized with Endnote- when you attach a PDF to a citation, it makes a file in your Endnote library with that PDF- makes it easy to find with or without the program, if you follow a good naming convention for your files.

Name your files clearly- I use import #, Author (Year) and then a note... So 0356, Keskin (2009) Complex DNA Folding for example. Makes finding them in the folder quite easy- the number reference lets me know how long ago I imported the file, and the other information lets me remember what the paper was about.

You can also attach other documents through Endnote- so if I redraw the figures from a paper I attach those, if I write up a summary of the paper, I attach that- etc.

Papers that I'm working with a lot, I print and store in 3-ring binders that are project specific. I have 4 main projects going at the moment, each has a binder with the most salient and oft-referred to papers in it, as well as notes, data, etc.

I use MS Office OneNote to keep screen clippings (order forms, etc) as well as notes, and a collection of figures/images that I've worked up to use in papers, presentations, etc. I also use it for short typed procedures, or for annotations/notes I take during literature searches. The notes go into "notebooks" that mimic the physical ones I have, one for each major project.

I just got an iPad, so it's taking over more of the function of the physical notebooks, but they will stick around for data storage- it's easier to get instrument data from them rather than to have to dig through my file cabinet.

When I just had 50-100 papers early on, it was much easier... Now that I'm around 500 papers that I need to keep track of and be able to find quite easily, my organizational system has changed quite a bit. Especially the naming systems I use for the files.

[CitizenHobbes]

+1 I've been using Papers for over a year now and just upgraded to Papers2. I don't know what I'd do without it. I also use an app called Notebook for Mac which I use to take class notes. I generally record my classes with my iPod while taking notes with Notebook and then afterwards I drop the audio file right onto the Notebook page for that class session. I use Things for Mac as my task manager and to help me plan and keep track of what's due and when for each class and paper. That's been indispensable as well.

I also use Scrivener when writing a long research or historiographic essay. If you haven't seen this application, google it. It's incredible.

I use Evernote for random or on-the-spot notetaking and Curio for mind-mapping/paper conception. Of course, I use EndNote for citation management and DevonThink Pro for having one searchable database of all my files.

I backup most of this stuff to my Dropbox account, i.e., email archives, calendars, contacts, tasks, EndNote libraries, Notebooks, etc.... I also keep my main semester folder with subfolders for each class in my Dropbox folder so it's always backed up along with all my "project" (essay) folders. I also just got a Kindle which has been really good for reading journal article pdfs since I spend a lot of time traveling during the day. And, almost everything above is also synced to my iPod.

I have been considering getting an e-pen as well... the Livescribe looks really interesting.

Hey Natsteel, I use a lot of these programs too, in almost the exact same way! I have two questions for you, though. 1: So am I right in understanding that you differentiate your use between Notebook and EverNote as you use Notebook for taking class notes, but EndNote for random note taking? (I'm assuming web clippings and the like.) What stops you from using EverNote to take class notes? Preference? Or is there a practical reason I'm missing?

Also, you say that you back up your data to DropBox. Do you do this with EverNote too? If so, how? I've been wanting to do this but I haven't figured out how to manage it

Thanks!

[LAAnthro11]

+1 I've been using Papers for over a year now and just upgraded to Papers2. I don't know what I'd do without it. I also use an app called Notebook for Mac which I use to take class notes. I generally record my classes with my iPod while taking notes with Notebook and then afterwards I drop the audio file right onto the Notebook page for that class session. I use Things for Mac as my task manager and to help me plan and keep track of what's due and when for each class and paper. That's been indispensable as well.

I also use Scrivener when writing a long research or historiographic essay. If you haven't seen this application, google it. It's incredible.

I use Evernote for random or on-the-spot notetaking and Curio for mind-mapping/paper conception. Of course, I use EndNote for citation management and DevonThink Pro for having one searchable database of all my files.

I backup most of this stuff to my Dropbox account, i.e., email archives, calendars, contacts, tasks, EndNote libraries, Notebooks, etc.... I also keep my main semester folder with subfolders for each class in my Dropbox folder so it's always backed up along with all my "project" (essay) folders. I also just got a Kindle which has been really good for reading journal article pdfs since I spend a lot of time traveling during the day. And, almost everything above is also synced to my iPod.

I have been considering getting an e-pen as well... the Livescribe looks really interesting.

Natsteel, your workflow looks pretty amazing. I am using DevonThink Pro Office, Mendeley, Scrivener, and my boss (I'm a research assistant) uses LiveScribe and loves it. Pair that with ExpressScribe and you're good to go! The question I have for you is: how do you manage the DEVONThink - EndNote flow? I want to use EndNote for the CiteWhileYouWrite but it feels tedious/repetitive to manually put things into EndNote, since I can't find an easy metadata export function from DEVONThink. Do you have any particular reason for using Papers2 over Mendeley?

Also, re: the Windows question, Quiqqa looks pretty amazing and is only available for Windows, so I would use that if I were on a PC. I think it's comparable to Mendeley, and maybe Papers2? Plus seems to have a good annotation component.

Does anyone have a good annotation program? DEVONThink is okay, but not entirely intuitive. Ditto for Mendeley, Adobe, Scim, etc. I want to be able to highlight passages and add notes, and then hit a button and have the highlighted passages and the notes exported to a word document.iAnnotate appears to do it, but I don't have an IPad. Thoughts?

Edited October 14, 2011 by LAAnthro11

[Eigen]

I can't think offhand of a windows program that annotates like you want, but it's not hard to do manually. Just open a word document next to your article, and type notes as you go.

I keep a folder in Dropbox of PDFs an one of annotation files, and then link both to the article citation in endnote.

[LAAnthro11]

@Eigen: Good point about the manual annotations. That's basically what I do within Devonthink, and it works pretty well. Honestly, sometimes pen-on-paper feels the best for reading and annotating endless articles!

I'm on a Mac, and Endnote just recently came out with X5 for the Mac. I think I'll use it more now, because the upgrade added much more functionality. That combined with Dropbox (wonderful dropbox!) sounds like a good tip.

[natsteel]

Hey Natsteel, I use a lot of these programs too, in almost the exact same way! I have two questions for you, though. 1: So am I right in understanding that you differentiate your use between Notebook and EverNote as you use Notebook for taking class notes, but EndNote for random note taking? (I'm assuming web clippings and the like.) What stops you from using EverNote to take class notes? Preference? Or is there a practical reason I'm missing?

Also, you say that you back up your data to DropBox. Do you do this with EverNote too? If so, how? I've been wanting to do this but I haven't figured out how to manage it

Thanks!

I know this is a little late, but... Yes, I use Notebook for class notes and EverNote for random notes (paper ideas, book lists, and my own reading notes and book reviews). There is a way to back up your Evernote by going to FILE -> EXPORT NOTES TO ARCHIVE. I then put the archive file in Dropbox as it's quite small. Also, I suppose I could just as easily use EverNote for class notes but because I used to record my undergrad classes, Notebook allowed me to drop the audio file (and other multimedia stuff) right onto the note page. I think that by now EverNote has much of the same functionality.

Natsteel, your workflow looks pretty amazing. I am using DevonThink Pro Office, Mendeley, Scrivener, and my boss (I'm a research assistant) uses LiveScribe and loves it. Pair that with ExpressScribe and you're good to go! The question I have for you is: how do you manage the DEVONThink - EndNote flow? I want to use EndNote for the CiteWhileYouWrite but it feels tedious/repetitive to manually put things into EndNote, since I can't find an easy metadata export function from DEVONThink. Do you have any particular reason for using Papers2 over Mendeley?

Also, re: the Windows question, Quiqqa looks pretty amazing and is only available for Windows, so I would use that if I were on a PC. I think it's comparable to Mendeley, and maybe Papers2? Plus seems to have a good annotation component.

Does anyone have a good annotation program? DEVONThink is okay, but not entirely intuitive. Ditto for Mendeley, Adobe, Scim, etc. I want to be able to highlight passages and add notes, and then hit a button and have the highlighted passages and the notes exported to a word document.iAnnotate appears to do it, but I don't have an IPad. Thoughts?

At this point, I have (almost) completely dropped EndNote. At first, Papers did not have citation management (in the sense of CWYW). It has added that to v2 and it is so much more intuitive than CWYW ever was (which was why I never used it). I share some of your frustration with DevonThink. I basically use it as index of my document folders on my HD (for its search capabilities). I do most of my annotations in Papers and if I have a highlighted passage I want the text of, I just hit CMD-C as soon as I've highlighted it and then CMD-V it into the notes section.

One last thing, if you're working on large projects or large research papers, I have found Scrivener to be indispensable. It's incredible for note-taking, outlining, writing, and organizing your research/sources. It used to be Mac only but a Windows version is out now, I think. It was originally made for screenwriters and novelists but with a bit of tweaking it's fantastic for writing and organizing 30+ page history research papers (and even historiography papers). Plus it even comes with an export feature that will automatically format your paper and footnotes to whatever style you pick. I'm an obsessive when it comes to following style guidelines and I was surprised at how good the formatting was. DISCLAIMER: I'm not shilling for the company, but just trying to share an application which not only increased my productivity but changed the way I do research and write for the better.

[Safferz]

You guys are all so organized! I don't use software, but I'd like to look into it... I don't think my current ways will cut it in grad school.

[LispectorBrownVieira]

For bibliographical purposes, I've found RefWorks to be SO much simpler than endnote...maybe it's just how my library works? But virtually everything in academic journals/worldcat is directly exportable to RW...where within the program you can organize articles and sources by folders.

Ill look into papers2...but I thought scrivener actually was way too complicated! OneNote is amazing -- but cant use it on my MacBook air sadly...Happy researches!

[Eigen]

I'll add that I've yet to find any journal or database that wasn't directly exportable to Endnote... I've done nearly a thousand papers that way.

[mandarin.orange]

I'm late to this topic, but hope to revive with a few questions...

I have an ever-growing collections of journal .pdfs to organize and eventually use in my dissertation. I've been using Zotero to index them into folders/groups - it's great for that, but I'm ready to take it to the next level and am trying to figure out its more advanced features. E.g., syncing with Word 2008 as I type. One thing I've noticed is it doesn't seem "smart enough" to extract author(s), article name, journal title, etc. from .pdfs.

Has anyone found software that can do this, rather than me having to manually enter the info into fields?

I have found Scrivener to be indispensable. It's incredible for note-taking, outlining, writing, and organizing your research/sources....Plus it even comes with an export feature that will automatically format your paper and footnotes to whatever style you pick.

Thanks for turning me onto this product - I'm pretty excited about the demos and tutorials I've seen, but pause to download it because very little is mentioned in the tutorials about creating bibliographies in different styles. It seems adept at doing the footnotes, but what about MLA refs in parentheses? Also, can it handle the issue I mentioned above?

[natsteel]

I'm late to this topic, but hope to revive with a few questions...

I have an ever-growing collections of journal .pdfs to organize and eventually use in my dissertation. I've been using Zotero to index them into folders/groups - it's great for that, but I'm ready to take it to the next level and am trying to figure out its more advanced features. E.g., syncing with Word 2008 as I type. One thing I've noticed is it doesn't seem "smart enough" to extract author(s), article name, journal title, etc. from .pdfs.

Has anyone found software that can do this, rather than me having to manually enter the info into fields?

Papers2 will do this, among many other things. You can even search and import from JSTOR, Project MUSE, Amazon, Google Scholar, etc... right from within the application.

My workflow can basically be boiled down to Papers2-Scrivener-Word. I use Papers2 to manage my PDFs (about 2500 and counting), Scrivener for research and writing, and Word basically just for final page layout details.

Thanks for turning me onto this product - I'm pretty excited about the demos and tutorials I've seen, but pause to download it because very little is mentioned in the tutorials about creating bibliographies in different styles. It seems adept at doing the footnotes, but what about MLA refs in parentheses? Also, can it handle the issue I mentioned above?

Scrivener itself will not "create" a bibliography. Papers2 will, however. It allows you to select your citation style and then you can simply go to your library and highlight the works you want included in your bibliography, right-click and choose "Copy as Reference" and then just paste it into Scrivener or Word.

However, right now Papers2 only has the option to copy as a "reference," i.e., a bibliography entry. I use it for footnotes and just change the periods into commas and reverse the author's first and last name. But the developers say they are working on allowing the copy-and-pasting of footnote/endnote citations as well as bibliography entries.

I hate to sound like a shill, but the combination of Papers and Scrivener literally changed the way I do research and write papers. Scrivener was originally designed for screenwriters and novelists, but its latest version has become far more accommodating to academics to the point of including MLA and Chicago style paper formatting. I'm a stickler for formatting and I was impressed by how completely the Chicago template nailed it. I'm in History and if anyone is looking at Scrivener and wondering how it might be used for long research papers, I'd be happy to show you screenshots of how I've used it effectively for large research projects.

Edited December 28, 2011 by natsteel

[mandarin.orange]

Thanks so much for your reply!

It looks like Zotero may have a way after all to retrieve metadata - I found this but haven't had a chance to experiment with it yet.

Scrivener looks amazing. The split screen alone may be worth the price, and I just wrote a term paper for a seminar class that was heavily dependent on historical research with many primary sources. Even at only 15 pp of text, it was getting cumbersome in Word; I couldn't imagine handling something longer in your discipline with just a word processing program.

I also have lots of ideas for shorter articles and pieces on current events in science, or teaching pedagogy...Scrivener looks like a great way to "archive" and organize these thoughts (and, quotes or refs I'll come across that are related) while the idea is still in its infancy stages.

Thanks again!

Edited December 28, 2011 by mandarin.orange