Managing PDF books and papers

I have a small collection of mathematical and computer science books and papers as PDF files. Some are stashed in Google Docs, others in Read it Later and others as links in email, etc. It would be nice if:

• all documents were organised together


• I could access the documents from all my devices - work and home macs and iPad


• adding / removing documents automatically synchronised across all devices


• there is a record of the url each document came from


• document contents are searchable

A cloud solution with device specific apps would be a good start. I would be happy to pay an annual price similar to flickr and Remember the Milk for a good product. From memory these are about USD$25 / year.

All the solutions I have come across are intended for academic bibliographic management. Most of my documents were collected adhoc from the web, without access to restricted channels such as the ACM Digital Library. The tools are geared towards searching the popular open and paid publication repositories and extracting bibliographic details automatically. I can see how this would be very useful if you have access, but I found it problematic in matching my documents when I don't have access. Given my requirements this became more hassle then it was worth.

Some solutions integrate social networking. Being able to share your reading and observe what others are reading might be quite useful. Warrants future investigation.

I don't have any need to annotate, highlight or add notes to the PDF files at present.

Papers
A Mac application (USD$42) featuring document synchronisation with the corresponding iPhone and iPad apps (USD$17.99). Storing the database and documents on Dropbox should also enable sharing between Macs. Metadata and content are searchable and the full screen reading mode is great. You can add notes to documents, but not annotate or highlight portions. At work I am behind a strict corporate firewall and proxy. Papers gave a spurious error about internet connectivity and disabled all online actions. Following this forum post fixed things up.

I had high hopes for Papers. The iPad synchronisation is very compelling, but otherwise it currently doesn't do enough for me to warrant paying money for (and putting my data in) Mac only software. If I end up regularly using the supported repositories then I will probably reconsider.

Mendeley
A web application with a companion Mac/Windows/Linux desktop app. There is no iPad app, although it is apparently in the works. The desktop UI looks like it is Java and is a bit clunky on the Mac.

The desktop app is orientated around managing your documents and associated files. You can add your files, set their metadata and sync with your website account. Synchronisation is initiated manually via a UI button. There is a full screen viewer, although I couldn't figure out the zoom and navigation keys. Alternatively you can open documents with the default external application. Document annotations, highlighting and notes are all supported, as well as full text searching. Unfortunately the network proxy settings aren't automatically detected from System Preferences and I need to manually edit them when taking the MacBook Pro between work and home.

On the website you can manage your references and notes and view your files, but I couldn't figure out how to upload files or see annotations and highlighting. Otherwise, the web site is all about social networking. You get 500MB of personal storage space and 500MB of shared space. The first upgrade is USD$4.99/month for 3.5GB + 3.5GB.

To make it attractive for me, Mendeley needs to tidy up the desktop app, automatically sync in the background, make the full screen view useful, release a synchronised iPad app and lower the price.

BibDesk + Dropbox + Skim + GoodReader
BibDesk is a Mac BibTex editor and reference manager. I can record as much metadata as is convenient, associate url's and PDF files, organise and search. By storing the BibDesk database file and PDF files on Dropbox, both content and metadata is automatically synchronised between all Macs. Dropbox provides 2GB of free storage, which is a great to get started. Skim is a PDF reader with a decent full screen mode on the Mac. GoodReader (USD$1.19) is a PDF viewer with Dropbox integration on the iPad. Although it is much quicker to transfer documents to GoodReader via iTunes.

The main downside with this setup is the lack of BibDesk support on the iPad and that all documents aren't automatically synchronised locally to the iPad. It is sufficient for me now though, as I am currently only adding new documents periodically.

CiteULike
Web site sponsored by Springer. I haven't investigated it properly, but it looks like you can add references from the major publication repositories or add your own, upload the associated documents and setup social connections. There are no Mac or iPad apps, so you need to manage your local files and how to view them yourself.

QOTD

Do not have the mind set that the day you release version 1.0 is the finish line, it’s the starting line, so hurry up and get there.

-- Sam Howley

From: Lessons learned from 13 failed software products via @ericries

QOTD

It's not that people cannot think mathematically. It's that they have enormous trouble doing it in a de-contextualized, abstract setting.

-- Keith Devlin

From In Math You Have to Remember, In Other Subjects You Can Think About It

Masters to Graduate Diploma

In 2008 I commenced a coursework Masters in mathematics at the University of Queensland. I have downgraded this to a Graduate Diploma and should officially graduate in a few weeks.

My original goal for commencing postgraduate study was to improve my knowledge in programming languages and make the current research more accessible. Unfortunately the local universities teach very little (relevant) theoretical computing science, so I enrolled in mathematics with a focus on discrete mathematics, logic and abstract algebra. After the first year I discovered that there is no real future in programming language research here in Brisbane. I had achieved my goal in the context of the courses available and so switched my study to statistics as data analytics is both interesting and hopefully more viable locally.

To complete the Masters I need to do the equivalent of four courses in research. As I am enrolled in a coursework masters, I pay 2-3 times the standard undergraduate fees. The last course cost $2010. Therefore there is approximately $8000 in fees remaining.

I would enjoy the remaining Masters research component if could find the right supervisor and topic. However employment as a researcher now generally requires a PhD, not a Masters and while a PhD is longer, it also has no fees. So if the circumstances were right to do the Masters research it makes more sense to consider a PhD anyway.

The value proposition for completing the Masters is too low. I have fulfilled the requirements for a Graduate Diploma and so will finish with that.

Education is not linear

And we have sold ourselves into a fast food model of education and it's impoverishing our spirits and our energies as much as fast food is depleting our physical bodies.

-- Ken Robinson

Brief summary of iPhone Flickr apps

I use Flickr to store my photos. Now that I have an iPhone, I would like to use it as a mobile photo album as well as uploading photos taken from the camera. I don't want the added complexity of using iPhoto as a middleman, so I did a rough survey of iPhone Flickr apps.

Flickr 1.1.3 (free).

• Loads photos fast. Caching works well if you have already viewed a photo.


• View photos full screen and swipe to navigate.


• No zoom.


• If you take photos with the inbuilt Camera app and upload them sometime later, it doesn't set the map location and time taken to the original values.


• Uploaded photo file size seems larger than with Mobile Fotos or syncing with iPhoto.

Darkslide 1.6.2 (free add-supported version)

• Slow load times (even for previously viewed photos).


• No swipe to nagivate photos.


• No zoom.

Flickit 2.0 (free)

• Only does uploading. The Pro app ($5.99) is a full client.


• If you take photos with the inbuilt camera app and upload them sometime later, it doesn't set the map location and time taken to original values. Found an explanation from the developer.


• Compresses photos significantly. I could only see small differences compared with the same photo uploaded via alternative means. Developer was helpful when I asked about this.

Mobile Fotos ($5.99)

• Upload correctly sets the map location and time taken to the original values for photos taken with the inbuilt Camera app.


• View photos full screen, swipe to navigate and pinch to zoom.


• Slideshow.


• Uploaded photos have washed out colours.


• Can't select from your tags when uploading, need to type in each time.


• Had one case where photos were shown as a blank screen. Cleared cache and problem was resolved.


• Developer was responsive when I asked questions.

Reflections ($5.99) and Photo Wallet: Flickr ($3.99) both look interesting in their own right, but neither offer zoom. The developer of Photo Wallet answered my question via twitter quickly to.

In summary, none of the Apps I tried are ideal for uploading to Flickr. This leaves me importing into iPhoto and uploading via the standard web uploader.* Mobile Fotos has the best viewing experience and I would also use it for uploading if the colours and tagging were fixed.

* The iPhone saves GPS information into the EXIF data. I had to set the "Import EXIF location data" privacy setting for the Flickr map location to be set. The privacy implications of this need further investigation.

Math is not linear

Math is not linear on Prezi