Research Papers (Citations)

[JazzLion]

Hi,

What applications do you use to for your citation management?

I will be studying JD(Law) in Sydney and I will need some applications geared for students/university students/law students needs.

For keeping a manageable database of citations and notes, I have been thinking of using 'Papers 2'. (http://www.mekentosj.com/papers/) The only problem for me with Papers 2, is that it does not support 'Australian Guide to Legal Citation'

What other applications do you use for;
Scheduling of Classes
Scheduling of Tasks/Assignments
Citation Management
Notation Management
Brainstorming

Cheers

 

[miles01110]

What other applications do you use for;
Scheduling of Classes - Google Calendar / memorization
Scheduling of Tasks/Assignments - Google Calendar / memorization
Citation Management - LaTeX
Notation Management - LaTeX
Brainstorming - my brain

See above.

 

[swedefish]

Scheduling of Classes - iCal
Scheduling of Tasks/Assignments - OmniFocus and iCal
Citation Management - EndNote (but intend to switch to Bookends)
Notation Management - ibid
Brainstorming - my plain old paper notebook

 

[Rusty33]

Hi,

What applications do you use to for your citation management?

I will be studying JD(Law) in Sydney and I will need some applications geared for students/university students/law students needs.

For keeping a manageable database of citations and notes, I have been thinking of using 'Papers 2'. (http://www.mekentosj.com/papers/) The only problem for me with Papers 2, is that it does not support 'Australian Guide to Legal Citation'

Hi Jazz Lion,

I am a PhD student in law at ANU and can empathise with you your dilemma.

My first piece of advice would be to choose your reference manager based on the word processor you plan to use. If you plan to use MS Word (don't), Scrivener or latex, your options will be quite different. I have written my thesis using scrivener, and can offer some insight based on my experience.

I too tried using Papers 2 for a while, but found its citation manager to be completely unsatisfactory (e.g. no capacity to edit citations, enter prefix or suffix information etc). In fact, I have tried numerous citation managers over the course of my candidature, including Zotero, Papers, Mendelay, Sente, and Endnote. However, for one reason or another, I always ended up going back to endnote.

Endnote is certainly not the flashiest, nor the most feature rich of any of the others mentioned....but I have found it to be the most consistent and stable of the lot - a must when writing lengthy documents. You peers will all use endnote so you will have interoperability, your IT person will know endnote backwards & forwards for when your database screws up, it allows you to create/modify your own citation styles without having to learn a programming language, and most importantly...it plays nicely with my word processor.

If you like the functionality/tagging/organisational elements of papers2 then I would suggest that you use it in conjunction with endnote. I should note that Sente also meets many of these needs, but is quite pricey (endnote is provided free of charge from your institution). If you are not a fan of endnote, download Sente and give it a crack.

Cheers

 

[swiftaw]

BibDesk

 

[JazzLion]

Hi Jazz Lion,

I am a PhD student in law at ANU and can empathise with you your dilemma.

My first piece of advice would be to choose your reference manager based on the word processor you plan to use. If you plan to use MS Word (don't), Scrivener or latex, your options will be quite different. I have written my thesis using scrivener, and can offer some insight based on my experience.

I too tried using Papers 2 for a while, but found its citation manager to be completely unsatisfactory (e.g. no capacity to edit citations, enter prefix or suffix information etc). In fact, I have tried numerous citation managers over the course of my candidature, including Zotero, Papers, Mendelay, Sente, and Endnote. However, for one reason or another, I always ended up going back to endnote.

Endnote is certainly not the flashiest, nor the most feature rich of any of the others mentioned....but I have found it to be the most consistent and stable of the lot - a must when writing lengthy documents. You peers will all use endnote so you will have interoperability, your IT person will know endnote backwards & forwards for when your database screws up, it allows you to create/modify your own citation styles without having to learn a programming language, and most importantly...it plays nicely with my word processor.

If you like the functionality/tagging/organisational elements of papers2 then I would suggest that you use it in conjunction with endnote. I should note that Sente also meets many of these needs, but is quite pricey (endnote is provided free of charge from your institution). If you are not a fan of endnote, download Sente and give it a crack.

Cheers

Thank you for sharing your insight. I think I will just switch to endnote and use papers2 just for organizational tasks.

It would be a nightmare if endnote's database got corrupted, I believe I will do frequent backups of it.

What made you choose Scrivener over MS Word?

 

[ryNze]

EndNote for me =)
University requires us to use it.

 

[Rusty33]

Thank you for sharing your insight. I think I will just switch to endnote and use papers2 just for organizational tasks.

It would be a nightmare if endnote's database got corrupted, I believe I will do frequent backups of it.

What made you choose Scrivener over MS Word?

No worries.

Make sure that you do NOT back up your endnote database using dropbox...dropbox WILL corrupt your database as it does know how to properly lock all of the random files that endnote uses. I have lost a weeks worth of work because of my dropbox/endnote combo. At the very least, make sure dropbox is switched OFF whilst your endnote database is open...

This is not a problem unique to endnote either...A colleague of mine also lost her zotero database doing the same thing.

Also, I neglected to mention that another good option for you might be bookends...again, probably not supported by your IT department, but its organisational features and integration into scrivener seem to pretty much be on par with endnote X4....although endnote X5 is tipped to be a substantial improvement when it is released for OSX.

As for scrivener, I have found to be an absolute dream in terms of having every single piece document, transcript, PDF, notes, chapters, etc all in the same easily accessible project. Not to mention the ease at which it handles long, documents! have a look at some of the video tutorials on youtube...you will not be disappointed!

 

[FloatingBones]

Make sure that you do NOT back up your endnote database using dropbox...dropbox WILL corrupt your database as it does know how to properly lock all of the random files that endnote uses. I have lost a weeks worth of work because of my dropbox/endnote combo. At the very least, make sure dropbox is switched OFF whilst your endnote database is open...

If dropbox is the only backup you are using for your writing, you need to add a second mechanism of backup. There shouldn't be a use case where you can lose weeks' worth of work because of a single data corruption.

This is not a problem unique to endnote either...A colleague of mine also lost her zotero database doing the same thing.

Absolutely. This is a general rule for all of computerdom: databases must be quiesced before they are backed up.

As for scrivener, I have found to be an absolute dream in terms of having every single piece document, transcript, PDF, notes, chapters, etc all in the same easily accessible project. Not to mention the ease at which it handles long, documents! have a look at some of the video tutorials on youtube...you will not be disappointed!

Scrivener is a winner. Here is the list of video tutorials and here is a list of the support documents, wikis, and faqs. The support forums on the L&L webpage are particularly good, and the community there is very supportive. One resource not listed above is the Tidbits Publishing book Take Control of Scrivener 2.

 

[shwc]

Scheduling: ical
Citation and PDF management: Bookends
Writing needs: Mellel or Pages

 

[munkery]

Scheduling of Classes

iCal

Scheduling of Tasks/Assignments

iCal

Citation Management

BibDesk
- made to work with LaTeX (LyX & MacTeX)
- allows for user generated citation templates that work with office suites and text editors (Pages & LibreOffice)
- fairly efficient to use with office suites even without integration
- integrates with Skim

Mendeley
- plugins for MS Word and Open/LibreOffice
- citation styles for +1000 journals
- create bibliographies instantly
- and more

Notation Management

Is this referring to mathematical formulae?

LyX & MacTeX

LibreOffice - Math = an application designed for creating and editing mathematical formulae.

Brainstorming

Growly Notes

Or, classic pencil/pen and paper approach.

 

[Rusty33]

If dropbox is the only backup you are using for your writing, you need to add a second mechanism of backup. There shouldn't be a use case where you can lose weeks' worth of work because of a single data corruption.

Sometimes data loss happens to even the best of us!

That said, I could not agree with your statement more. A time capsule was the best $300 I have ever spent, and has saved my bacon on more than one occasion.

 

[Zeiss]

I'm a senior academic in Australia and I use Scrivener for compiling papers, lectures, chapters and my Phd. It is by far the most suitable task for any academic writing need. I got so sick of trying to track changes in documents, breaking long papers into chapters and manually keeping track of it all, etc ,etc. It is for me the most crucial piece of software for writing that I know of (of course personal preference comes in here). Be sure to spend some time with it outside of a deadline period to make sure you are using it well, and that you understand the compile function.

I also am a big fan of Papers2 for storing, reading and taking notes of any thesis papers I find. Endnote is great, but you end up using it, plus something for notation of notes, plus something to store all your Pdf articles converted from ebooks etc, so I spent some time with Papers2 and am happy with it for my needs - I like the everything in one solution.

Scheduling and task management - iCal and OmniFocus, which I have on my laptop, desktop in my home studio, iphone and iPad - it does a nice job of syncing all (through Mobile Me - not sure what will happen with iCloud).

Lastly I use Evernote cause it also syncs between everything, so I have thoughts, research ideas, conference notes etc all in one place as well - and if they relate to a specific book chapter or article I have in Pages2, then I transfer them over.

Be mindful that there is no application (wouldn't a great iResearch app from Apple be wonderful) that will do everything, and it all takes a bit of discipline and care to keep on top of it all - but if you do, it will make your study life much easier.

 

[ozaz]

Citation Management - Mendeley
Notation Management - ??????
Brainstorming - Pen and paper, but have been intending to try SciPlore, http://www.sciplore.org/software/sciplore_mindmapping/

For keeping a manageable database of citations and notes, I have been thinking of using 'Papers 2'. (http://www.mekentosj.com/papers/) The only problem for me with Papers 2, is that it does not support 'Australian Guide to Legal Citation'

I think I'm right in saying that Papers uses the open citation style language (CSL) also used by Zotero and Mendeley. If you're willing to learn CSL you can create whatever style you want from scratch or by tweaking existing CSL styles
http://blogs.plos.org/mfenner/2010/...-interview-with-rintze-zelle-and-ian-mulvany/
http://citationstyles.org/downloads/primer.html

Admittedly it requires time investment to learn CSL whereas Endnote's graphical tool for creating proprietary endnote styles does not. However, my point is just that the absence of your required style in Papers is a removable obstacle.

Endnote is certainly not the flashiest, nor the most feature rich of any of the others mentioned....but I have found it to be the most consistent and stable of the lot - a must when writing lengthy documents.....

..........it allows you to create/modify your own citation styles without having to learn a programming language, and most importantly...it plays nicely with my word processor.

Agreed. EndNote is easily the best for writing. It incorporates the easiest tool for editing/creating styles, the cite-while-you-write word plugin is stable and mature, and the RTF scan feature is something a lot of the newer apps don't have or don't do well. RTF scan is required to be able to use niche writing apps like Scrivener that don't have cite-while-you-write plugins.

I use Mendeley because I like the organization, reading, annotation/notes, and syncing features, and becuase it's cross-platform, and I think their decision to release open APIs (http://dev.mendeley.com/) gives it great potential as a platform. However, I really do miss the relative ease of writing you get when using Endnote.

Make sure that you do NOT back up your endnote database using dropbox...dropbox WILL corrupt your database as it does know how to properly lock all of the random files that endnote uses. I have lost a weeks worth of work because of my dropbox/endnote combo. At the very least, make sure dropbox is switched OFF whilst your endnote database is open...

This is not a problem unique to endnote either...A colleague of mine also lost her zotero database doing the same thing.

One of the big benefits of Zotero & Mendeley is that they have built-in sync that will avoid such problems. Your colleague was probably trying to avoid paying the measly the $20/year Zotero charge for this service!

I'm a senior academic in Australia and I use Scrivener for compiling papers, lectures, chapters and my Phd. It is by far the most suitable task for any academic writing need. I got so sick of trying to track changes in documents, breaking long papers into chapters and manually keeping track of it all, etc ,etc. It is for me the most crucial piece of software for writing that I know of (of course personal preference comes in here). Be sure to spend some time with it outside of a deadline period to make sure you are using it well, and that you understand the compile function.

Scrivener does seem great for academic writing because, amongst other things, the way it is designed seems to encourage keeping the 'big picture' in mind, and fosters non-linear writing and writing in small chunks. However it seems to me that it is mainly useful for solo writing (i.e. thesis writing, or what is was designed for - writing a novel). When writing papers for journals, don't you get to a stage very early in your drafting where you have to export to word in order to write collaboratively with co-authors?

Be mindful that there is no application (wouldn't a great iResearch app from Apple be wonderful) that will do everything, and it all takes a bit of discipline and care to keep on top of it all - but if you do, it will make your study life much easier.

This seems like something colwiz is trying to achieve, http://www.colwiz.com/features

 

[Rusty33]

This seems like something colwiz is trying to achieve, http://www.colwiz.com/features

This is intriguing....thank you for sharing!!!
Have you had any experience using it? Thoughts?

 

[ozaz]

This is intriguing....thank you for sharing!!!
Have you had any experience using it? Thoughts?

I haven't really tried it and probably won't do so any time soon because I'm generally happy with Mendeley for reference management and don't know if I need the other features. It doesn't seem to be any better than Mendeley for writing features. However, I have signed up to their free 3GB offer (just in case it emerges that it is very good): http://blog.colwiz.com/2011/10/11/3gb-free-storage-–-your-research-backed-up-in-the-cloud/

Given their aim seems to be a (researchers) cover-all-needs app I don't think they have quite gone far enough because there doesn't seem to be a notebook feature.

 

[Rusty33]

I haven't really tried it and probably won't do so any time soon because I'm generally happy with Mendeley for reference management and don't know if I need the other features. It doesn't seem to be any better than Mendeley for writing features. However, I have signed up to their free 3GB offer (just in case it emerges that it is very good): http://blog.colwiz.com/2011/10/11/3gb-free-storage-–-your-research-backed-up-in-the-cloud/

Given their aim seems to be a (researchers) cover-all-needs app I don't think they have quite gone far enough because there doesn't seem to be a notebook feature.

Thanks for your input. I gave it a whirl and you are spot on with your assessment - lots of potential, but just not there yet. Perhaps one day...

 

[erad2010]

Mindnode is great for brainstorming. Free on the Mac app store

 

[JKColo22]

I am also a JD student. I suggest you try CircusPonies Notebook for taking notes. Keeping all your notes in a single document that actually looks like a Physical notebook with dividers/tabs/highliting/etc. works well for me (just ensure you backup regularly!). I suggest you stick with Word 2008 for other docs. Yes it's a MSSucks product but you wont have to worry about losing formatting upon conversion to .doc when you turn in your lengthy assignments or collaborate with others.

Please excuse the typos- sent from my iPhone.

 

[Rusty33]

I think all bonafide researchers could really benefit from using a service like this - paying someone else to write my PhD for me would have certainly saved me a lot of hassle! Who needs a reference manager?

In other news - I notice that Papers 2.1 has been released. Has anyone here had any experience using it? I tried using v2.0, but found 'Magic Manuscript' to be utterly useless. I understand that this feature has received considerable attention in this update....can anyone comment?