Ah yes but my point was that Mendeley offers superior pdf file management to Zotero for example. If you look into the preferences in Mendeley it offers quite specific management of files locations, file renaming and so on. That I can tell, the other reference managers do not offer this - which is a major draw back in my estimation. Because Mendeley offers this - I don't actually need to use Mendely to find specific files by an author for example. I have it set up to store files by authors in specific folders and I can easily navigate to them through Finder. Zotero at least does not seem to allow this using a filing system aI cannot understand and thus have to use Zotero to find files.
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Ah yes but my point was that Mendeley offers superior pdf file management to Zotero for example. If you look into the preferences in Mendeley it offers quite specific management of files locations, file renaming and so on. That I can tell, the other reference managers do not offer this - which is a major draw back in my estimation. Because Mendeley offers this - I don't actually need to use Mendely to find specific files by an author for example. I have it set up to store files by authors in specific folders and I can easily navigate to them through Finder. Zotero at least does not seem to allow this using a filing system aI cannot understand and thus have to use Zotero to find files.
Sente will absolutely do this. I have it set to store PDFs in folders by author, then year. It renames the PDFs as [author] - [year] - [first 100 characters of title]. Zotero can be made to have similar capabilities with zotfile: http://zotfile.com
Papers (v2) For reading papers. Works quite well and has a nice interface. The best part is the ability to search multiple repositories at once to find what you are looking for. The iPad app is ok for reading papers, but a bit of a pain for sorting or annotating and there are better PDF readers available. It also doesn't have the "Match to repository" that the desktop app has for finding metadata.
There is the ability to export your library, or a specific collection to a .bib file for use with...
TexShop and more broadly mactex. I used LaTeX to write my undergrad dissertation. It was easier than Word, looks orders of magnitude better and great for organising things.
My raw files were stored on dropbox, and I used a free student GitHub account and often pushed my work to this as another backup and an edit history. You can also create releases and attach the PDFs so you know what copy you handed to a supervisor for them to comment on.
TimeMachine for another backup!
R for graphs/data analysis. And LibreOffice Calc for csv manipulation - opens much faster than Excel and does everything needed.
NvAlt for notes - stores everything as text files on dropbox and really easy to find android/ios editors.
There is the ability to export your library, or a specific collection to a .bib file for use with...
TexShop and more broadly mactex. I used LaTeX to write my undergrad dissertation. It was easier than Word, looks orders of magnitude better and great for organising things.
My raw files were stored on dropbox, and I used a free student GitHub account and often pushed my work to this as another backup and an edit history. You can also create releases and attach the PDFs so you know what copy you handed to a supervisor for them to comment on.
TimeMachine for another backup!
R for graphs/data analysis. And LibreOffice Calc for csv manipulation - opens much faster than Excel and does everything needed.
NvAlt for notes - stores everything as text files on dropbox and really easy to find android/ios editors.
Oh well I am learning here did not know Sente would do that. But again not paying for Sente - the free version would not be enough for me. Had not heard of zotfile, will look into it.
In Canada, and it's raining, so have more time inside!
Alas, I didn't count with many custom officers' obtuseness. They clearly haven't heard about second-hand purchases, where no receipt is handed.
Would a foreigner be taxed bringing his own machine to Brazil? I don't tend to keep useless papers on a trip.
Sure you do stick to Shuttleworth's word: every piece of software or configuration that requires command-line or manual work is a bug to be eradicated
I don't agree with the first part. Office doesn't run seamlessly on Windows, as transferring a file back and forth between various Windows/Office combinations would always yield unexpected results. Maybe the issue isn't as bad as it once was, but surely the installation process isn't smooth. It may have something to do with the myriad of settings a user can make, usually unbeknown to him.
On the other hand, as Microsoft has so many millions to develop Office and the fact it's their actual business, I don't feel Google is any serious competition (yet) in the office suite market, but given the amount of sensitive information they would lay their hands upon should they develop a suite, this is only a matter of time. They would have to make a real, user-installable software, not some cloud-based slow application. Neither is LibreOffice, since Oracle abandoned it. Still, one has to give credit to this alternative for being of high quality while relying mostly on volunteers.
Well Macs aren't as widespread as Windows, because Microsoft forces PC makers to bundle Windows (that's illegal) or face dire financial consequences. Another hypotheses points that MS Office being rather un-Mac-like in its presentation, Mac users may look for simpler, more integrated and more predictable software for a few usage cases, rather than the jack-of-all-trades MS Office attempts to be.
On OCR
I think it was in 2008, with a software called Iris something with a blue icon. Currently I use Acrobat on the Mac. Imperfect, but default results are good enough.
If you negate the actual causes of this popularity, then yes.
Using MS Office in corporations
Mine doesn't actually direct students to LibreOffice. In fact, models and workshops are always directed to MS Office. LibreOffice appeared a few years ago on these machines, though it's unclear why.
Efficiency through habit. Where is that magic link where you found a way to contact Microsoft for support on their software? Because all their knowledge base entries redirect users to the computer manufacturer, while the manufacturer always blames Microsoft.
I made the transition to OpenOffice from MS Office 2003, and haven't found it so hard. After an adaptation period, enough to undo MS Office habits, I found it easier and better organized, much like people transitioning from Windows to Mac, and I wasn't anywhere near an MS Office geek. This transition was successfully made by many EU governments, so it's not impossible, but as you rightly point, they don't have such a strong incentive to immediate productivity.
In the short term, costs are surely lower with MS Office because of sunk costs. In the long term, investing in training would allow for enormous savings on license prices.
Wow, you sound quite fatalist here. Remember users learning to use FOSS add a skill to their CV. I don't adhere to the view that FOSS are an inferior, ghetto-building piece of software, although they may appear so for various reasons. Being rather optimistic, once a sufficient mass of users is reached or a government makes it an official policy, or choose to actually enforce anti-bundle-sales laws, corporations would have no choice but to be aware of FOSS' existence, which can never be bad for its development. If just a few universities chose LibreOffice over MS Office, dedicating full-time developers to correct problems and fit the software for their own use, the whole community would benefit from these improvements, and perhaps it would be enough to bridge the 20% more that MS Office currently has over LibreOffice. Apple had done it with CUPS. Being volunteer-led is a problem when issues with seldom-used features need to be corrected. Note that proprietary software isn't free of these problems. It took Adobe many years-versions to tackle the inability to deselect one file in its Acrobat software when merging multiple files. Plus, it still doesn't sort file names following the Mac convention.
Or, you could ask the question as such: is it better that lower-classes people pirate expensive, proprietary software in hope of developing skills on them without any help, since free and extensive help isn't available for MS Office, or just use FOSS to gain a thorough understanding of the mechanisms, before making the jump to MS Office if so they want? In my view, social apartheid occurs when one is forced to place himself in a technical state of illegality. Once I had computer parts to give away, and found the only social-reinsertion computer-rebuilding business built machines that were obligatorily sold with Windows. Other countries had similar businesses, but selling them either naked, with a legal Windows, or with a Linux distro, price being adjusted. As I felt deeply wrong to force an unwanted OS on salvaged machines, I chose to trash these parts at a local dangerous goods disposal facility. They wouldn't use my free parts to make money for Microsoft, or at least advertise its use as mandatory when buying a PC.
Since going Mac, I felt that only uneducated script-kiddies would boast from pirating Windows and every software on it, or modify it. Not to say I haven't tried it: I once made a slipstreamed version of Windows, but because it was made with proprietary tools (not from Microsoft) from closed and undocumented software, displayed some weird bugs I was never able to solve.
Problem with boxed versions? Will never know, but surely it's easier for a student to go to its local campus store and buy a small box, often with frequent specials, than to wait for a key to come in an unreliable mailbox, not counting those who don't even have a credit card. As no support is available from Microsoft and that IT support department is not authorized to support software without the university seal on them, students are left in the cold.
SpiderOak is widely used. But despite their willingness to solve the problem, they haven't succeeded, and seem limited by technical design decisions.
Indeed one has to properly configure Firefox to avoid the memory-hogging behavior. Chrome doesn't need it because it is much less flexible. When adding similar extensions to them, Chrome isn't any faster, but lose big time on privacy. But since it's backed by heavy-handed Google branding, people are still getting it. My IT support friend always advises Firefox because it relies on its own proxy settings, rather than system-wide ones Chrome and IExplore use.
Would be pretty damn near impossible with MS Office to map them all. There are too many different functions, designed to cater to everyone but actually serving no one properly. I bet even Office developers aren't aware of all functions. Commercial software is mainly done using automated processes.
Haven't tried the draft display in Word since leaving it, and wouldn't have a way to since it doesn't nicely open ODT files. But agreed the split window is the single most lacking feature of Writer. You could always subscribe to LibreOffice's digest and send a message once in a while about features you'd like to see on LibreOffice. There aren't too many MS Office heavy users on this list because many are part of associations or companies using LibreOffice as their only office suite, or promoting its use, or providing training on it.
Just try to contact Microsoft on a bug you found in Office. Just for fun.
Being fair, as many other FOSS projects, LibreOffice suffers from too much democracy. While this is good in the real world, it never works in the software world. MS Office wants to please everyone, but end up being "meh" to most users, who still use it because their company have it installed. LibreOffice most daring suggestions always end up binned because it's not a "priority" according to lead developers. Same applies for pre-Windows 8 versions: long-standing problems, inconsistencies, despite numerous feedback left around the web. There was seemingly no strong direction, teams responsible for one aspect of the software never talked to one another. Windows 8, while considered an utter failure, was made under a strong direction, as developers said they wish it failed on the market and they were ashamed of the work they were forced to produce. Apple is widely considered as the most successful tech company in history because it went from near-bankruptcy in the mid-90s to the most valued one in a few years, under the direction of one strong man who assumed full responsibility for failures and successes alike. Their products are loved, and while they haven't been always clean (namely, tied sales of iPhones, grossly overpriced compared to very similarly-spec'd iPod Touch), nobody is forcing customers to buy, yet they do. The Linux kernel is one very fine piece of software because only one man has the final word on it.
I advocated for Ubuntu to officially support a reduced set of hardware combination, like OS X, favoring stability and reliability, while keeping the source open for community-based support.
No, I haven't. When OOXML was implemented (partly), I already moved long ago to LibreOffice, and it would have too costly to move back.
Indeed I have much distaste of them, and reading on their trade tactics made me dislike them even more, although most of it first came from the lack of enforcement of their own standards. There's a movement in French FOSS circles to ban bundled sales (well, they already are), with forum topics detailing how one buying a non-Mac machine can have its Windows license refunded according to law. Most of the time the amount refunded is minute compared to the lengths they go, but a majority succeed. I respect people who stick to their principles, no matter the cost.
On my part, I searched extensively years ago for a laptop that wouldn't be sold with Windows inside, eventually finding one US-based company.
Pleasing customers is not a word in Microsoft's vocabulary, at least not with Windows. What do they care if people didn't like Millenium, Vista, or Windows 8? It would still be bundled with a machine sale. Some manufacturers actually shipped some of their computers with XP installed and a free upgrade option to Vista, and current Win 8 machines sometimes have a Windows 7 disc included, so even if people don't give money to MS through Win 8, they do through Win 7. What's the difference? Somehow I doubt many people are actually buying boxed Windows versions as they're so expensive.
Perhaps they care a bit more about Office as it's not tied, but would not loose too much if they were to ignore users' requests since most profitable customers are corporations tied with a long-term contract. Even if they don't want to upgrade, Microsoft will always have the last word by dropping support, as it did with XP. Support has been dropped about a month ago, but corporate customers will still receive updates because they pay millions. Banks have paid for maintenance of XP-based ATMs, and the extra cost will sooner or later be passed on to customers. Microsoft follows the money, and there's no much money in the individual users' market, except in computer sales, where there is virtually no competition in the sub $1k segment. There's always an extra cost involved for buying an antivirus and an antispyware, that Microsoft doesn't provide. On more expensive markets, they launched the "Microsoft Premium" machines, but their availability is confidential, and Microsoft stores are unheard of this side of the border. I still do credit them for finally showing they heard criticisms of their products.
Part 2 of 2
I don't say FOSS is inherently superior to proprietary software. Rather, I consider Windows inferior because it doesn't natively support many standards, tries to impose its own, and needs all sort of heavy and cumbersome protection before even setting a byte out. In short, it isn't ready to use out of the box. Of course that didn't prevent me from selling a PC laptop I won at a contest. I never took it out of its box, and didn't even knew what color it was. Note this isn't specific to Microsoft: Flash is a de facto standard that needs to die. Same can be said of mandatory antivirus software: a field comparison between Symantec Security and McAfee / MalwareBytes pair showed the former, while more well-known, is extremely heavy on system resources while being inefficient: uninstalling it after a clean scan and installing the other pair commonly leads to discovery of previously-undetected threats.
I don't say FOSS is inherently superior to proprietary software. Rather, I consider Windows inferior because it doesn't natively support many standards, tries to impose its own, and needs all sort of heavy and cumbersome protection before even setting a byte out. In short, it isn't ready to use out of the box. Of course that didn't prevent me from selling a PC laptop I won at a contest. I never took it out of its box, and didn't even knew what color it was. Note this isn't specific to Microsoft: Flash is a de facto standard that needs to die. Same can be said of mandatory antivirus software: a field comparison between Symantec Security and McAfee / MalwareBytes pair showed the former, while more well-known, is extremely heavy on system resources while being inefficient: uninstalling it after a clean scan and installing the other pair commonly leads to discovery of previously-undetected threats.
Given it's probably, along with a browser, the single most used application, even more so than word processing, one has to choose a very ergonomic manager. You can't cut round corners on such software. On the other hand, I found Zotero's CSL quite, though not very, easy to edit. Sure there's no GUI to do so, but the syntax is clear enough even an untrained user can do it.
Are you sure it makes sense? I mean, paying less on a software you want but still paying for unneeded software doesn't make for a real saving, is it?
Hm, that wouldn't do it except on rather small papers. We usually read far more than we include as references. My problem with references was not so much as organizing them, but actually finding them. I have yet to find an reference search engine that would provide precise results while excluding unrelated articles, without me having to do the manual work
Did you have many formulas in your dissertation? I've heard that LaTeX was only useful in such cases.
I thought GitHub was only used for software development. Would you care to explain how you used it to share papers?
Does it support anything else than Dropbox? The latter is far from being the best online storage, not mentioning privacy concerns.
Just an addendum on MS Office supposedly behaving fine in Windows:
Just tried to install the 2013 version on a non-C: drive since it's close to full. I manually select another drive, but installer still stalls reporting that C: has insufficient space.
Just tried to install the 2013 version on a non-C: drive since it's close to full. I manually select another drive, but installer still stalls reporting that C: has insufficient space.
Well, I decided to unbury this thread after a while...
Well, LibreOffice is of some high quality mainly because it had its origins on proprietary software (StarOffice), not because of volunteers. In addition, some companies helped developing OpenOffice/LibreOffice.
No. Macs are not widespread because only expensive computers made by Apple can run OS X. Windows is widespread because it is easy to use and has good software available. Nearly nobody wants Linux installed on their computers, even though it is free.
And some European governments are going back to MS Office...
You can ask for features in LibreOffice. You know how long it will take for these features to be implemented? Forever and perhaps even longer.
Well, LibreOffice is of some high quality mainly because it had its origins on proprietary software (StarOffice), not because of volunteers. In addition, some companies helped developing OpenOffice/LibreOffice.
No. Macs are not widespread because only expensive computers made by Apple can run OS X. Windows is widespread because it is easy to use and has good software available. Nearly nobody wants Linux installed on their computers, even though it is free.
And some European governments are going back to MS Office...
You can ask for features in LibreOffice. You know how long it will take for these features to be implemented? Forever and perhaps even longer.
Keep the software simple and standard. Everybody finds their own workflow that varies with personal tastes and institutional software. After many years I have landed on Office 365. MS Word is standard among colleagues internationally, works great on my Mac, and I can work on drafts here on the Mac or on my Windows machine in my other office. Excel is a fine spreadsheet. OneNote is great on Macs now for random notes and is cross platform. PowerPoint is standard and cross platform. Office works on both major OS platforms and syncs with iOS via OneDrive. I manage PDFs with the OS folder system (Win or Mac) and built-in OSx Preview on my Mac. Reference management remains a pain, but everybody finds their own workflow for dealing with citations.
Originating, true, but it wouldn't have become what it is without an army of volunteer programmers.
Granted, price and now-new lack of upgradeability is a concern with Macs. But they require far less maintenance in the long run, making them very interesting for companies and institutions to own. TCO is similarly less with Linux. It's not that nobody wants it installed, it's because it has no public exposure. I have yet to hear about an experiment where non-Mac PCs would be sold without OS, and put in a showroom with both Linux and Windows. Windows isn't easy to use. People are just used to its lack of consistency, habits that are hard to undo when switching to another platform.
Can't tell otherwise on that one. LibreOffice development has become a huge bureaucratic mess. At least they're answering requests, unlike MS.
MS Office isn't simple nor standard. I never had a single occurrence of perfect file compatibility from LibreOffice to MS Office, not even on the same MS Office generation on different machines. The issue is less pronounced on Excel than it is on Word, though. PowerPoint is still a nightmare of compatibility, especially as you try to integrate multimedia files. All because Microsoft obstinately refuses to follow standards and prove through quality alone its software is better.
Window's 8 PDF viewer is a buggy piece of software, to the point our very pro-Windows IT department dropped the ball and started recommend Acrobat Reader (!).
As far as I am concerned, some of them are volunteers but others are paid by large companies.
And, as a matter of fact, I do not see well-written and complex open source software which was created and developed by employees. LibreOffice was largely developed as a proprietary product; and Linux itself was developed thanks to large amounts of money invested by large companies IBM put one billion dollars on it.
As for Macs being very interesting for companies to own, I do not believe it happens. Windows machines are much cheaper. The cheapest Mac, the Mac Mini, costs US$ 599. A cheap Dell Inspiron desktop costs US$ 219. The Dell is Celeron-based, while the Mac Mini has a much more powerful processor inside, but that does not really matter to a company that just wants its workers working. Suppose the company has to buy 2,000 computers. If it choses the Mac, it will spend US$ 1,198,000. If it chooses the PC, it will spend US$ 438,000. It is a huge difference. You could say that the Dells will last for a year, and the Mac can last 5 years. The Mac may have a longer lifespan, but not by that much. In addition, the difference (US$ 760,000) can be used as working capital by the company. And having access to working capital makes a lot of difference, believe me. In addition to all of this, support for the Mac tends to be more expensive than for Windows. Given this scenario, I fail to see how a Mac can be more interesting to companies and institutions. Of course the Mac can be more interesting to a local library that buys only 5 computers. But, if you think of large scale, then Macs are just not worth it.
And Windows is easier to use. Linux is a nightmare to use, no matter which desktop environment you choose. Linux developers fail to see how ergonomics can change the software experience. There are some things that are more intuitive than others, and that is because of the way people are and the way people were created. It is not just a matter of being accostumed to. There is science behind it. But, as it is not math or engineering or another hard science, Linux people fail to understand its existence. Put it this way: there are engineers and architects. The Linux world is full of engineers who cannot understand why somebody would ever hire an architect.
Microsoft is answering requests as well, and it implements them far faster than LibreOffice. Besides, it does not really matter that LibreOffice answers requests if it takes 10 years to do so.
Yes, Microsoft Office is standard. It is not a technical standard, nor an official standard. However, the vast majority of people use Microsoft Office for Windows. You can say ODF is a standard, but it does not matter because only a small fraction of people actually use it. So, it is worth nothing being a standard nobody adopts.
You can say that there may be incompatibilities between Office for Windows and Office for Mac. It does not matter as well because Office for Windows is the standard and only a fraction of people use Office for Mac. As a matter of fact, Office for Windows has become a de facto standard because nearly everybody uses it and everybody is supposed to use it or to have access to it.
No FOSS project would be where it is now without its volunteers. I recall having discussed with an HPLIP developper who never got access to all the necessary resources to test HP's Linux driver for all HP printers.
That is probably the reason. While TCO (of which purchase price is comparatively a low part) is higher with non-Mac PCs as they require more maintenance, upfront expense is also higher w/ Macs.
In a corporate setting, you'd be surprised to see how many PCs are used far more than their 2-years estimated useful life.
Have to agree on that. I can't recall the number of times I tried to seed the idea of better ergonomics on Ubuntu's now-defunct Brainstorm website, only to be dismissed as not knowing how to properly use a command line. Seems engineers don't know the difference between induction (where you have to think about an action then pass the corresponding flag as you recall it) and deduction (where a smartly-designed UI will present its option and the user would choose).
But MS could afford more of these designers in their flagship software that are MS Office and Windows. 7 was as convoluted as previous versions, 8 was a failure, even according to MS' own reports.
Please, post here how you managed to get help from MS for their pricey products where they didn't dismissed obvious blocking bugs as "talk to your manufacturer". I am curious. Even the IT guy in here gave up on trying to make a successful install of Office 365 on student's machines, arguably a very large user base with different Windows versions.
Get your words straight. My grammar may be incorrect at times, but a standard is norm made guaranteed by a normalising body. Otherwise, MS Office is common, in companies, that is.
Is it people's fault or the International Standardisation Organisation's if MS obstinately refuses to add support for Open Document in their suite? What are they afraid of?
Much like the imperial system is not standard in the proper sense. It's just common in the US.
You have to realise, as MS only recently did, that there's a world outside of Windows, and a large one at that. In many large settings, Macs are ~40% of the machines. You can't dismiss them as "non standard". In fact, no user in his right mind would intentionally make a document that wouldn't be compatible with MS Office for Mac. There's still much work to do to have them make Open Document files, though, or at least universal formats (such as PDF) when edition isn't required.
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Nice thread, although I haven't gotten through all the long posts yet!
Responding to the original post, my workflow is very similar to yours. Some people commented that you have a lot going on, I think I have even more going on... but it works for me.
Initial brainstorming or outlining for writing: Curio or Circus Ponies Notebooks (I also own OmniOutliner and NovaMind, which I use now and then).
Drafting/writing papers: Scrivener - no competition whatsoever. Final formatting and reference conversion in Word. I would have preferred Pages, but don't use it for the reasons you mention.
Referencing: EndNote. Have stuck to it, in spite of all it's inadequacies, because it's produced the most accurate results for me and because I've used it for fifteen years or so I just know my way around it. My objective is to test Bookends properly with my next paper, though, and I'd be very happy if I could just ditch EN.
Literature management: Bookends for organising all my literature. I've moved from Papers to Sente to Bookends. I left Papers because it wasn't very conducive to tagging, and left Sente because I found it unstable. Bookends has the best stability and customer support, IME.
GoodReader or PDF Expert on my iPad to mark up pdfs (occasionally Skim on the mac). All single source literature notes in DevonThink, with a duplicate in Evernote so I can access them from my iPad. All thematic reviews in Circus Ponies Notebooks, with hyperlinks to relevant refs in Bookends or DT.
I used to have a blog where I wrote about academic work flows. Some of the posts are getting a bit out of date now, but it might still be of use for people considering different apps for research.
Responding to the original post, my workflow is very similar to yours. Some people commented that you have a lot going on, I think I have even more going on...
but it works for me. Initial brainstorming or outlining for writing: Curio or Circus Ponies Notebooks (I also own OmniOutliner and NovaMind, which I use now and then).
Drafting/writing papers: Scrivener - no competition whatsoever. Final formatting and reference conversion in Word. I would have preferred Pages, but don't use it for the reasons you mention.
Referencing: EndNote. Have stuck to it, in spite of all it's inadequacies, because it's produced the most accurate results for me and because I've used it for fifteen years or so I just know my way around it. My objective is to test Bookends properly with my next paper, though, and I'd be very happy if I could just ditch EN.
Literature management: Bookends for organising all my literature. I've moved from Papers to Sente to Bookends. I left Papers because it wasn't very conducive to tagging, and left Sente because I found it unstable. Bookends has the best stability and customer support, IME.
GoodReader or PDF Expert on my iPad to mark up pdfs (occasionally Skim on the mac). All single source literature notes in DevonThink, with a duplicate in Evernote so I can access them from my iPad. All thematic reviews in Circus Ponies Notebooks, with hyperlinks to relevant refs in Bookends or DT.
I used to have a blog where I wrote about academic work flows. Some of the posts are getting a bit out of date now, but it might still be of use for people considering different apps for research.
Nice thread, although I haven't gotten through all the long posts yet!
Responding to the original post, my workflow is very similar to yours. Some people commented that you have a lot going on, I think I have even more going on...
Initial brainstorming or outlining for writing: Curio or Circus Ponies Notebooks (I also own OmniOutliner and NovaMind, which I use now and then).
Drafting/writing papers: Scrivener - no competition whatsoever. Final formatting and reference conversion in Word. I would have preferred Pages, but don't use it for the reasons you mention.
Referencing: EndNote. Have stuck to it, in spite of all it's inadequacies, because it's produced the most accurate results for me and because I've used it for fifteen years or so I just know my way around it. My objective is to test Bookends properly with my next paper, though, and I'd be very happy if I could just ditch EN.
Literature management: Bookends for organising all my literature. I've moved from Papers to Sente to Bookends. I left Papers because it wasn't very conducive to tagging, and left Sente because I found it unstable. Bookends has the best stability and customer support, IME.
GoodReader or PDF Expert on my iPad to mark up pdfs (occasionally Skim on the mac). All single source literature notes in DevonThink, with a duplicate in Evernote so I can access them from my iPad. All thematic reviews in Circus Ponies Notebooks, with hyperlinks to relevant refs in Bookends or DT.
I used to have a blog where I wrote about academic work flows. Some of the posts are getting a bit out of date now, but it might still be of use for people considering different apps for research.
It is great to know that Macademise was your blog. It was a great blog and it is a pity it was discontinued. But I guess life has to move on.
Indeed this thread has very long posts. These scholars do write a lot.
You seem to have a long list of software in your workflow. Is it worth it? My main concern is that, when you convert the final document to Word format, you have to re-format a lot of it. Doesn't it take too long? I am reconsidering my workflow and I often come to the conclusion that the best piece of software for writing is indeed Microsoft Word. Do not get me wrong: when I say Microsoft Word I mean Microsoft Word 2013 for Windows, and not Microsoft Word 2011 for Mac, which does not even come close to the Windows version.
I have to admit that I'm a bit envious of how people have managed to organize their digital academic lives!
My workflow tends to include the following:
# Desk Research
I usually download articles into a common folder ('unread articles/chapters') and then either read them on the screen (shorter than 15-20 pages) and digitally annotate as I go after sucking them into Papers, or print and annotate on paper. Regardless, I then transfer notes from the digital or analogue medium into a set of Moleskine notebooks that I've been building up for years and that contain notes on everything of importance that I've read over the past 8 years or so.
# Fieldwork Research
A key component of my work involves interviews, usually in a semi-structured format. I try and bring a pair of recording devices to each interview; my mobile phone at the time and, typically, my tablet of the day as well. It clutters things up a bit but ensures that if one of the devices dies I'm unlikely to lose the interview. Given that, for many of my subjects, I'm likely unable to get ahold of them face-to-face again sometimes for years, this redundancy is critical. Moreover, devices *must* be able to encrypt data at rest for Research Ethics (and basic confidentiality) reasons.
I extract audio interviews from the devices as quickly as I can, usually adding them to my iTunes library (with the Mac's hard drive set to encrypt at rest).
For transcription, I tend to listen once and try to identify the times where interesting things were said that I'd want transcribed. For my PhD, I'd then go and manually transcribe (usually to paper, first, then typing those notes in a word processor; this was done to just etch in my mind the important things that were said while letting me search them in the future). Now I ensure that my grants include transcription budgets and so I send audio files out to be transcribed at the times I note in the first listen. I ensure appropriate confidentiality and data security standards are in any contract with a transcription company before securely delivering audio files to them.
# Draft Writing
Drafts that are planned for less than 35 pages tend to be written in Google Docs because I like the redundancy it provides, and find the austere nature of the writing environment conducive to rapid drafting. It also (at this point) exports reasonably well to other standards to subsequently revise and edit. Google Docs is particularly important for collaborative writing (which I do a lot of); the ability to have all authors working on the same document and not worry about revision controls is an absolute blessing. Also, Google Docs is cross platform, meaning the software versions people use, or the operating systems, and so forth doesn't matter at the initial stages of writing.
Footnotes, at this stage, are just typed in sufficiently to later find and complete them (or get an RA to find/complete them).
# Revision Writing
To date, I've revised almost all of my publications using Word. But the thing is, I *hate* word. It's clunky, tends to crash with a large number of tracked comments, and is just generally bloated. Nevertheless, I've used it to crank out a lot of words. But I hate it.
To this end, I've just started playing with Pages. Most of my writing is pretty basic; I don't use graphics very much, no advanced tables or charts, or include equations. As such, Pages is something I'm trying out with a pair of pieces that are under a Revise order. Thus far I've been struck by how much cleaner it is (and faster!) when adding comments or tracking revisions.
# Notekeeping
Like many academics, I have notes everywhere. Historically I used a huge whiteboard to map out articles as well as to capture bits of data/notes, but my new office lacks a whiteboard. As a result I'm kind of struggling: Evernote's never worked for my academic writing needs, and most of the other 'digital' tools I've tried lack the physicality that I need when working through ideas. So I'm back to a small Moleskine notebook that travels with me, as well as some larger pads of paper in my office. I try to go through all the notes every 3 months or so and then re-identify what remains pertinent, and which can just be crossed off/destroyed.
# Data Redundancy
I tend to maintain data in a host of locations, always operating on the assumption that a fire or other emergency could occur that would simultaneously destroy one backup locations *and* my primary computer. As such, I have encrypted-at-rest data backups at work and at home (using Apple's Time Machine) and also have a set of encrypted bundles that I store in various clouds that hold 'high priority, low sensitivity' files.
I had one computer literally burn up on me during the final stretch of my dissertation; the ability to be back online in about 6 hours (time to go to Futureshop, buy a new mac, and restore from Time Capsule at home) has demonstrated to me that this multiple-redundancy model is a good idea. Also, during my BA and MA I supported faculty members' computing environments and saw firsthand multiple mid- and senior-scholars lose their computers and decades of research they'd digitized. I *do not* want a similar thing to ever happen to me.
I don't have a decent 'backup' solution for the Moleskines, though I'm toying with the idea of hiring an RA to digitize (i.e. type out) what's in them. But I don't know that it's a terribly useful way to spend money and sounds like a useless/terrible RA job.
My workflow tends to include the following:
# Desk Research
I usually download articles into a common folder ('unread articles/chapters') and then either read them on the screen (shorter than 15-20 pages) and digitally annotate as I go after sucking them into Papers, or print and annotate on paper. Regardless, I then transfer notes from the digital or analogue medium into a set of Moleskine notebooks that I've been building up for years and that contain notes on everything of importance that I've read over the past 8 years or so.
# Fieldwork Research
A key component of my work involves interviews, usually in a semi-structured format. I try and bring a pair of recording devices to each interview; my mobile phone at the time and, typically, my tablet of the day as well. It clutters things up a bit but ensures that if one of the devices dies I'm unlikely to lose the interview. Given that, for many of my subjects, I'm likely unable to get ahold of them face-to-face again sometimes for years, this redundancy is critical. Moreover, devices *must* be able to encrypt data at rest for Research Ethics (and basic confidentiality) reasons.
I extract audio interviews from the devices as quickly as I can, usually adding them to my iTunes library (with the Mac's hard drive set to encrypt at rest).
For transcription, I tend to listen once and try to identify the times where interesting things were said that I'd want transcribed. For my PhD, I'd then go and manually transcribe (usually to paper, first, then typing those notes in a word processor; this was done to just etch in my mind the important things that were said while letting me search them in the future). Now I ensure that my grants include transcription budgets and so I send audio files out to be transcribed at the times I note in the first listen. I ensure appropriate confidentiality and data security standards are in any contract with a transcription company before securely delivering audio files to them.
# Draft Writing
Drafts that are planned for less than 35 pages tend to be written in Google Docs because I like the redundancy it provides, and find the austere nature of the writing environment conducive to rapid drafting. It also (at this point) exports reasonably well to other standards to subsequently revise and edit. Google Docs is particularly important for collaborative writing (which I do a lot of); the ability to have all authors working on the same document and not worry about revision controls is an absolute blessing. Also, Google Docs is cross platform, meaning the software versions people use, or the operating systems, and so forth doesn't matter at the initial stages of writing.
Footnotes, at this stage, are just typed in sufficiently to later find and complete them (or get an RA to find/complete them).
# Revision Writing
To date, I've revised almost all of my publications using Word. But the thing is, I *hate* word. It's clunky, tends to crash with a large number of tracked comments, and is just generally bloated. Nevertheless, I've used it to crank out a lot of words. But I hate it.
To this end, I've just started playing with Pages. Most of my writing is pretty basic; I don't use graphics very much, no advanced tables or charts, or include equations. As such, Pages is something I'm trying out with a pair of pieces that are under a Revise order. Thus far I've been struck by how much cleaner it is (and faster!) when adding comments or tracking revisions.
# Notekeeping
Like many academics, I have notes everywhere. Historically I used a huge whiteboard to map out articles as well as to capture bits of data/notes, but my new office lacks a whiteboard. As a result I'm kind of struggling: Evernote's never worked for my academic writing needs, and most of the other 'digital' tools I've tried lack the physicality that I need when working through ideas. So I'm back to a small Moleskine notebook that travels with me, as well as some larger pads of paper in my office. I try to go through all the notes every 3 months or so and then re-identify what remains pertinent, and which can just be crossed off/destroyed.
# Data Redundancy
I tend to maintain data in a host of locations, always operating on the assumption that a fire or other emergency could occur that would simultaneously destroy one backup locations *and* my primary computer. As such, I have encrypted-at-rest data backups at work and at home (using Apple's Time Machine) and also have a set of encrypted bundles that I store in various clouds that hold 'high priority, low sensitivity' files.
I had one computer literally burn up on me during the final stretch of my dissertation; the ability to be back online in about 6 hours (time to go to Futureshop, buy a new mac, and restore from Time Capsule at home) has demonstrated to me that this multiple-redundancy model is a good idea. Also, during my BA and MA I supported faculty members' computing environments and saw firsthand multiple mid- and senior-scholars lose their computers and decades of research they'd digitized. I *do not* want a similar thing to ever happen to me.
I don't have a decent 'backup' solution for the Moleskines, though I'm toying with the idea of hiring an RA to digitize (i.e. type out) what's in them. But I don't know that it's a terribly useful way to spend money and sounds like a useless/terrible RA job.
Have you tried Skim? I found it good for annotating PDFs as it keep the comments separated from the PDF files.
I find DEVONThink the best tool for searching PDFs.
If you read articles in PDF, then you should take a look at these tools.
I don't do field research, so I cannot help you there.
I tend to use Microsoft Word for both. Many times I find out that it is not worth to use different software for drafting and revising as there may be differences in formatting and I would lose a lot of time on that. As I would have to submit the file in Word anyway, then I use Word most of the time.
In addition, I think that Word has some very useful tools such as grammar check, thesaurus, cross-references, and many others that most word processors lack, and that make writing much faster and more straightforward.
I am, of course, talking about Word 2013 for Windows, which is great. Word 2011 for Mac is just another piece of software, bloated and buggy.
Pages is OK, but it lacks Word's features. And if you use footnotes, then you will realize that Pages cannot split footnotes in two pages, making it useless for people who needs that.
You keep them on paper? Well, try something else. Lots of note-taking apps for any platform...
I just use Dropbox. And now I am starting to use OneDrive. Very simple to keep things on the cloud.
A question perhaps a bit unrelated to the software itself, do you tend to remember most information when annotating it on screen, or when you do so on paper? This has been my main issue in regards to the academic workflow: I can't keep a sufficient number of elements in my head to write a lengthy paragraph at once, and end up with a time divided like 10% writing, 90% shuffling through notes. It's annoying and I would readily accept a more efficient workflow.
Down your post, you mention Moleskine notebooks, but do you actually sort info before writing into them (as these are expensive notebooks), or jolt ideas down the way they come in your mind?
What tablet or phone is able to encrypt data-at-rest? I mean, now we do know there's no such thing as unbreakable encryption, especially if used with default settings.
What is the encryption standard required by your ethics board anyway? Would a TrueCrypt container be accepted? The reason for me asking such a question is we also know TC, AFAIK the only cross-platform encryption utility, mysteriously disappeared from the Web without an explanation.
I wish my lab were as thorough as you are with data. We didn't even have lab logs. Otherwise, are you sure you don't spend too much time on each interview? I mean, transcribing twice must take a helluva time. Oh, I never knew there were transcription companies out there. Seems like the US still hosts the most niche-catering companies.
So interviews must be encrypted but drafts can roam freely?
At a time, I had a MacBook, encrypted with FileVault. I ended up disabling it because it would restrict the SSD to SATA 1.5Gbps, and besides, the Time Machine backups were in the clear.
Question is, how did you manage to get an encrypted TM? Are your bundles created through Mac OS X utility, or a third-party tool?
I see your PhD is well-funded. I am envious :$
Were they stupid enough to keep only one copy of their work on a fragile medium? As one I heard about who kept all of her thesis and data on a single USB key throughout the years?
Well if it's all text, you could always dictate it. I have been told Dragon is pretty good, and probably faster than typing.
If transcription is important for your research, look into software such as ELAN (free, open source) that specializes on time-aligned transcriptions. It's java based and while its interface might look a bit archaic, it's very powerful once you learn how to use it.
When it comes to writing, I use latex/plain text only so I can't comment on the WYSIWYG processors as we don't get along very well. (I do have opinions on them and proprietary document formats but that's probably not for this thread.)
I've paid for papers and it seems to work; my needs tend to be pretty minimal (some annotation, authoritative match functions to get citation data, basic search functionality for journals etc). For longer/more detailed pieces (like law journal articles....) I tend to rely on print as I just can't maintain attention reading on a laptop screen with long articles.
I just find Word oppressive to do primary work in (hell, even when I'm doing final revisions it can be unpleasant), though I am referring to the Windows version. Most things I publish for are word-count based, and my writing is pretty basic (i.e. footnotes and the very, very odd graphic). I've never really bothered with citation systems because so many journals have their own bizarre styles (to say nothing of book presses) and find that relying on them just leads to further back and forth with editors.
Fair enough; I've not had to deal extending footnotes for style-guide reasons thus far.
It's not an accident; I just don't remember things that I type as well as hand-written notes. I just don't slow down enough to really retain it. I understand the value of search etc etc, but the hard-copy is as much a memory device as it is anything else.
My method is ridiculously unhelpful: I figure out the generalized structure of the argument or paper (takes a while, but I tend to need the conceptual stuff sorted in my own head before it's worth the time to write) and then go through 'key' sources that I know are likely relevant. For some I know them like the back of my hand and so there's no need to re-read/skim them, for others I go through and remind myself of what's in them. I try and group various articles/chapters/reports/etc for each section, so that I can quickly reference them as I write the section at hand. So I can't say that I necessarily remember everything but I do my best to put it in one place so I can quickly recall the various articles.
I have different Moleskines for different tasks. One set is just for collecting readings (i.e. key arguments, elements of an argument, quotations, etc), another is for project development (papers to write, ways of structuring data, means of working with various parties to advocate for access to new data, etc), yet another is for miscellaneous ideas/paper ideas/brain farts, and another is for...well...whatever doesn't fit in the others.
I've toyed with getting an Evernote-branded Moleskine, but I really doubt that I'd use it the way that's intended. And I find Evernote's UI unattractive enough that I don't really want to rely on it routinely (regardless of the program's utility).
Last time I was doing fieldwork I had a Blackberry Playbook and Blackberry Bold, which I'd also set up to do remote wipes. It wasn't unbreakable, but it's reasonably secure. For the next interviews in a few months I'll be shifting over to an iPhone and iPad. I have Android devices, now, and won't take them out for field research for security reasons.
A lot of my interviews are with senior executives who I guarantee personal anonymity to (generally cite them as 'senior executive in [nation] [industry type]') because I'm more interested in understanding the politics of a given issue than attributing direct quotations to individuals. Other interviews are with members of the Intelligence Community, and others with government officials who *absolutely cannot* be identified by their managers or department heads. So the encryption gives rest to everyone, while cutting down on the risk of data in transit. It also makes the ethics board process go a lot more smoothly.
To explain my (very!) particular circumstances, I've been in situations where I was threatened with confinement if I didn't give up my data. Fortunately they chose note to confine me when I refused their demands, though there are (now) certain nations that I avoid transiting through. Unfortunately my own country is sometimes hostile during transit, so for particularly sensitive travel I leave all my key electronics home and get someone to lend me what I need wherever I land or, alternately, temporarily purchase (and return before leaving the area of research) a laptop off-the-shelf to ensure that it isn't compromised in transit.
I try to identify the bits (now) that are more valuable to transcribe and avoid full transcription. I tend to only have handfuls of interviews (typically 30-50) so it's only a few weeks of time a year. For some stuff I can't get a third-party to do the work, but for others (e.g. executives speaking with permission) it's fine to get someone else to do that grunt work.
Depends on the draft, but generally, yes, because I've taken care to de-identify what is said and avoid quoting information that would positively identify someone I spoke with.
Depends on the sensitivity. FileVault is a default I enable (and never provide recovery information to Apple), and the time capsules are just encrypted with the default functions within OS X. That said, anything sensitive is stored in a True Crypt Volume, and then the HDD itself is also encrypted. It means that an attacker can ascertain that there is a secondary line of encryption, but I haven't seen a reliable attack that would let an attacker decrypt True Crypt that's also shielded by HDD full disc encryption. For extremely sensitive data we have a safe in the Lab where I can store USB keys that are designed to destroy themselves if an incorrect password in typed in a few times.
I spent -- and still spend -- a lot of time writing grants (to the tune of around 10-20% of my time...FML.) So I've enjoyed reasonable funding but it's always been hard work to get it
Well, they didn't really understand what they were doing. And it bit them in the ass. And it was always terrible to break the news to them
Fair enough.
I prefer long articles in PDF, so I can search the text. But each to its own.
Well, I find Word very useful. For a first draft, I can use its outlining features as well as the grammar check and thesaurus, which are both great.
If you ever have to rely on footnotes, then you will realize how bad Pages really is.
Unhelpful as it doesn't have to do with a specific method, but just a better working memory. I guess I'll have to curb my ADD through methylphenidate
While working I tend to skim through a ton of articles before finding the useful ones, and since I usually don't have as much time as I wished I had, this turns out rather inefficient. And I don't have any hint on whose articles are likely relevant, unfortunately, and when they are, it's usually for more than one given section. I'd still get advice on that particular aspect, too.
Similar here. I tend to draw quick figures and arrows when taking notes, more efficient than pure text, and not easily done in any computer application. Must be a heavy bag with all these notebooks
Are iOS devices encrypted? I knew they can lock the content and erase it if a bad password was entered more than 10 times, but I never got this function to actually work. And given what Snowden has revealed, even reputed vendors may not be trusted when it comes to encryption as they may have planted backdoors unbeknownst to the end-used. Even open-source software is not immune, as the mysterious TrueCrypt discontinuation suggests.
Sounds "exciting" but worrying at the same time. I heard once about a Canadian student who was extensively searched and scrutinized because of its sensitive research topic. I guess he wouldn't settle for anything less than zero-knownledge encryption.
It seems that the speed trade-off is necessary in your application. Are you using the well-known IronKey? And the encryption option, only available on Time Capsules? I never seen one for a regular, FireWire-attached HDD.
I'll still call you lucky. Even seasoned researchers in my university spend more like 50% writing grant proposals and doing administrative tasks unrelated to research itself.I spent -- and still spend -- a lot of time writing grants (to the tune of around 10-20% of my time...FML.) So I've enjoyed reasonable funding but it's always been hard work to get it
On another hand, I still wonder how people can rise so high in knownledge missing even basic cautious behavior. Call me unlucky, but in three years, I went through 5 hard drives (These Scorpio Black must have a defect!), so I know why backups are important. Doing my masters, I always had three copies of all the data in different places, excluding the lab as I didn't have a fixed spot.Well, they didn't really understand what they were doing. And it bit them in the ass. And it was always terrible to break the news to them
Makes sense, but how do you shuffle through a long article? On screen or on paper?
I always found that Word's grammar check was pure crap. Have you heard about any *real* grammar / orthograph checker for the English language?
Thanks so much for the comments on my blog. Unfortunately, I can't keep it up anymore, but if you'd like to write a guest post, please feel free.
To the bold? I don't know. I do have a tendency to spread across what is probably too many apps. I'm thinking about how to simplify my workflow, but when it comes to cutting out apps, I always find that I drift back to them after a while. The ones that have a stable role in my workflow are Scrivener, Bookends, EndNote, DevonThink and CPN. Everything else varies a bit
And Word, of course, for finalising papers, but that's really only out of necessity. In terms of formatting, I just do most of it in Word towards the end of the writing process and keep things as simple as possible up to that point. I work with unformatted EndNote references until I'm in Word.
I'm definitely not returning to Windows as my main writing app. I only work on a mac and I find MW 2011 for mac generally annoying, and use it as little as possible. But since I work in a Windows environment, as little as possible is quite regularly.