Thursday 18 December 2014

Are Netbooks still a thing ?

A couple of days ago, I went over the road to a coffee shop for an offline discussion with a colleague. We were in search of some space where we could hide in plain sight to discuss some issues relating to a new project.

We chose the coffee shop next to Arts faculty, where you are as likely to find people discussing Aristophanes as their blocked sinks.

The atmosphere is reasonably hardcore and quite a few people had computing devices on the table. The students have long since departed for the summer taking their shiny iPads and Macbooks with them, so we can say that the devices on desks represented devices used by working academics and researchers.

As is my wont, I had a look around me while waiting to order to see what people were using.

There was, of course, the usual sprinkling of iPads and high end Android tablets, but strangely not that many MacBooks, with the MacBooks being outnumbered by Windows notebooks, of which none looked to be SSD based ultrabooks.

What there was though, was three people sat at separate tables using netbooks. Unfortunately I couldn’t sensibly (or politely) rubber neck to see what operating system was in use so I’ll assume windows.

Using a netbook makes some sense for someone that deals with words - the keyboards on a lot of netbooks were quite nice to type on, and if you have a windows desktop in your study, you can of course write your notes straght to dropbox, and then work on them later on your full size machine, yet have something reasonably lightweight with reasonable battery life to take to the library - as well as being next to the Arts building, the coffee shop is also opposite the Asian studies library - and being early summer people are probably trying to get on with their research.

Still it remains interesting that three or four years after netbooks dropped off the market they’re still in serious use …

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Wednesday 17 December 2014

handwriting, keyboards and effective notetaking

This morning I tweeted a link to a Guardian weekly article on the merits of handwriting versus keyboards for writing. Coincidentally I’ve just bought myself a fountain pen - my first for what must be close to forty years.

The pen is nothing special, just a twelve dollar Lamy with a steel nib, but it writes nicely on good quality paper, and more importantly my handwriting approaches legibility.

In the previous forty years I’ve used a mixture of quality rollerball pens such as Uniball and Edding fineline felt tips which have allowed me to handwrite - scribble really - notes quickly, but at the expense of legibility. I’ve never got on with cheap ball points or cheap paper - it’s why I still use a pencil for scratchpad work.

I’ve tried other things - handwriting recognition on a palm pilot was a notable failure of the early naughties, although the device was in many other ways a superb tool - so much so that I bought an external keyboard and used it for many years to take notes in meetings and seminars. I still have my old palm pilot, keyboard and docking cradle, and I used to promise myself that someday I would get jPilot configured on one of my linux machines and start using my Palmpilot again.

Realistically of course, that ship has sailed.

I have however continued to experiment. One of the most successful experiments was to use a no name Android tablet with a keyboard as a notetaker.

Type the notes in a semi structured form using a tool such a TextEdit, and email them to myself, clean them up and during the cleanup process reformat them as markdown (or wiki style syntax for wikidot), generate a pdf and put them straight into evernote, or indeed circulate the pdf as meeting minutes.

Very powerful, but flawed. Battery life was one issue, startup time was another, as was network dependence. All of them could be lived with and worked with.

I also found the seven inch keyboard a little tight for typing, hence my resurrecting my old Eee seven inch notebook. Doing this addressed the keyboard issue, and using Retext as a native markdown editor sped up matters but in fact I’ve usually ended up typing sets of oneline notes into abiword and converting them with pandoc to markdown or saving direct as a pdf to evernote.

But in all of this I’ve found a problem. Notetaking at best is an active exercise where you listen to what is being said, write down interesting things, draw arrows, reflect a little, write down questions and thoughts, link blobs together.

What I end up with is more a sort of mindmap. Especially when rather than a structured presentation it’s an ad hoc ‘draw on the wall’ session, or indeed a coffeeshop discussion.

Hence the fountain pen. Legible notes in a note book, scan them, send them to evernote, add comments, photographs of a whiteboard, all these things.

At the same time there’s definitely a role for taking notes straight into a computing device of some sort, especially in well structured seminars and presos. I guess my problem is that I havn’t yet found my ideal device - something fast enough, light enough and with decent enough battery life.

Until then it’s probably my old eee, or no name tablet, with a pen and notebook as backup …

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Wednesday 3 December 2014

2014 - what worked

In previous years I’ve done a ‘what worked’ post about this time.

I’m not doing one this year, for the simple reason that when I look back at the 2013 post, not much has changed.

To be sure, I’ve taken to using ReText for writing notes and the resurrected ookygoo as a writing machine, but truly not much has changed.

We have a better, more stable network connection and using the TP-Link box to allow failover to 3G when the adsl service goes away has been one of my better ideas, as has investing in a second portable 3G router for travel.

The real change this year has been in terms of media consumption - it’s the first year I have bought no music CD’s whatsoever - even managing to satisfy my love of Renaissance and early Baroque through downloads alone, and the first year that I have bought more ebooks than printed books. In fact I’d say that I have bought almost no new physical books - in fact I’d say two, and they were only bought as paperbacks because of the Amazon/Hachette spat, and happened to be on special.

I’ve still bought some second hand out of print books in dead tree format, but with the increases in the availability of digitised texts, even that’s been decreasing - I actually can see a time coming, say in five years time, when I might only buy ebooks …

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Thursday 27 November 2014

Apple knows you know

I have a work provided iPhone as well as my own personal phone.

I actually don’t really use my work phone - I have a work phone principally because I used to travel a lot overseas and in Australia and by giving me a phone it meant I could do the ET phone home thing when there was a problem without having to try and reclaim the cost of calls.

And smartphones allow you to do more - I’ve never quite been at the stage of a colleague who ssh’d into a recalcitrant box from his iPhone while transiting in Seoul - but you get the picture.

Now the iPhone ‘knows’ some things if you scroll down on the lock screen it will tell you the temperature and what events you have scheduled - and in the afternoons how long it would take you to drive home - strangely enough always 29 minutes.

Now I usually go to the supermarket to do the weekly shop on Wednesdays because we like to to the Farmer’s market and deli shopping together on Saturday mornings. So every Wednesday I’m off to Mawson to buy the staples plus some fresh salad, bread, OJ etc.

Yesterday for some reason I checked the outside temperature before leaving work on my iPhone rather than my personal phone. And I noticed that it said it would take you 23 minutes to drive to Mawson right now - ie my phone ‘knew’ it was Wednesday and that I go to a supermarket in Mawson that day.

Computationally quite interesting and slightly scary …

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Tuesday 25 November 2014

And can we make a decent open access reading list ?

I recently suggested that it might be able to put together an open access reading list for the classics.

So I did, purely as an experiment. I picked a very random (and very short) list of university classics departments and downloaded their introductory reading lists. Some were fairly short some were more oriented to summer reading (and the suspicion that most students would do little if any). I collated the Exeter, Tufts, Warwick and KCL lists and came up with the following:







KCL, Tufts

Adelaide e-books



Exeter, Tufts

Adelaide e-books



KCL, Tufts

Adelaide e-books







KCL, Exeter, Warwick

Adelaide e-books



KCL, Exeter

Adelaide e-books



KCL, Warwick

Internet Archive



Exeter, Tufts

Adelaide e-books




Adelaide e-books



Exeter, Tufts

Adelaide e-books


Lives of the Caesars




Letters from a Stoic


Internet archive




Adelaide e-books


True History


Adelaide e-books








Adelaide e-books


Nichormachean Ethics


Adelaide e-books


Daphne and Chloe


Internet Archive




Adelaide e-books




Adelaide e-books




Adelaide e-books




Adelaide e-books




Adelaide e-books

In the main I found the texts on the University of Adelaide's ebook sitse. Adelaide E-books ( is a paricularly good source of texts and in some cases has alternative translations, as well as links to wikipedia etc. It's not just classical texts, there's a good range of English literature texts as well.

All sites allow downloads in both epub and mobi format meaning that the books can be read on a kindle or on a tablet, including one of the cheap no-name Android tablets that can be picked up for less than a $100, in some cases considerably less.

I've made no attempt to assess the text for accuracy, but what this little paper exercise shows is that it is perfectly possible to create an open access reading list.

While you may argue that having to own a tablet is a barrier to access, most (potential) students already have a suitable device, and with a decent second hand paperback copy of Suetonius's Twelve Caesars costing around $10 with shipping we can argue that even if you have to buy a tablet the exercise is better than cost neutral ...

Open classics - a modest proposal

In the sciences one of the great current tropes is open access, ie publishing research papers in journals that do not require a subscription to access them, and equally importantly making research data available for re use and reanalysis.

There are other parallel movements such as open textbooks, open online courses etc.

Classics is also an area ripe for open access. Much of the material revolves around texts and the reanalysis of texts, and authoritative translations abound. I suspect that many classicists only know a number to texts from translations.

Acquiring the key texts and translations is not particularly difficult or costly - many have been around for years and reasonable second hand copies can be picked up through the various online second hand booksellers for a few dollars.

But of course, that does present a barrier for access - first of all one needs these few dollars and scronly one needs the time and the inclination to hunt for decent second hand copies and then wait for the postal systems of the world perform their miracle of nineteenth century technology.

Absolutely fine for a dilettante with a disposable income like me, less so for a student undertaking a course, especially one in a country such as Australia where the classics are most definitely fading.

So, to my proposal:

  1. Assemble a list of university reading lists
  2. Identify the most commonly listed items
  3. Identify suitable online (free) sources where possible
  4. Make the resource list available online

A very simple idea, and one that can be extended to other areas, for example medieval studies, English literature etc.

The virtue of this idea is that it works to reduce the cost of access, and also encourages ‘reading around’ a topic, ie don’t just read the set texts, read related ones, and get some understanding and insight.

In a time when books were paper and most university towns had a couple of second hand bookshops stocked with cheap second hand paperbacks, happenstance and reading around could be done very cheaply - forty years ago I used to play a game with myself on a Saturday afternoon - take my spare change after I’d attended to the week’s expenses, count it up, split it in half, and see what I could find in the way of interesting reading for half of what I’d got left of the week’s money.

Nowadays such a game wouldn’t be possible - second hand bookshops are mostly online which robs the exercise of the happenstance element - and happenstance is an important part of learning and discovery.

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Monday 10 November 2014

A distraction free writing machine

A week or so ago I upgraded my old EEEpc to Crunchbang linux - and I’m quietly impressed with its capabilities as a distraction free notetaker and writing machine.

Since the upgrade I’ve used it seriously for two or three meetings and to write a couple private documents, including an old style put in the mail letter. Performance has been more or less flawless.

With only ReText (for markdown) and AbiWord (for anything pretty) and no mail client other than Alpine for getting stuff off the machine this means you can focus on the text, or when using it as a note taker, on what’s being said. No other email, no twitter, no urge to distract yourself with wikipedia.

And it’s good. It’s fast (and fast to boot), and nicely responsive.

There are some downsides - the browser is a pain to use, though, with the export capabilities of both Abiword and Retext there’s no real need to use external services like MarkdowntoPDF or Cloudconvert.

Basically, documents are written on the machine and then either emailed off to Dropbox if they need more work or to Evernote to archive. I originally didn’t bother installing printing, but I’ve since added printer support just for the ease of producing bullet lists or handouts.

One of course needs to be realistic - it’s a five year old low power machine with a small non standard display - you cannot seriously expect to run anything and everything on it - for example I’d have doubts about running an R session on it, or doing any serious text manipulation.

Or indeed anything meaty written in Java.

But I have other machines for that. What I do have now is a small format machine that can fit in a man bag, has a decent keyboard and battery life, and being small and light can be taken along on a trip as a second writing machine …

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Tuesday 4 November 2014

Brisbane Altmetrics workshop

Over the past few months I’ve written about altmetrics and impact for example here and here

Yesterday I went to an ANDS sponsored workshop on Altmetrics and Impact in Brisbane - you can find my meeting notes online here - it’s an evernote share of a pdf, and you may be asked to click to view to get to the actual note.

As a calibration exercise it was incredibly useful - it convinced me that we’re roughly in the right place with altmetrics, namely

  • no one has a complete view on altmetrics, impact and engagement
  • attempts at quantification are partial at best
  • academic publishers are interested and investing in altmetrics due to change in their business model
    • attempt is by maintaining relevance and providing specialist services
  • impact is increasingly seen as an important alternative to classic citation rates
  • impact measurement tools are partial at best

So, altmetrics, bibliometrics or what have you will provide some interesting times. One interesting aside was that someone had used text analysis techniques on a set of pharmaceutical papers suggesting that one company may have an in house ghost writing team. This isn’t necessarily a bad thing - having documentation or writing specialists finesse text is by no means bad, although there has to be a question as to whether there may be an attempt to game the system by producing more readily citable papers.

Whether or not it is the case, I found it quite a nice use of the power of open access and being able to reuse documents as data for other analyses …

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Friday 31 October 2014

Reviving the ookygoo

A long time ago, 2009 to be exact, I bought an EEE pc 701SD linux netbook to use as a travel computer - and because of its kiddified UI we nicknamed it the Ookygoo.

UI restrictions apart it was truly excellent machine, and I used it for both work and recreational travel till 2012, by which time Asus had more or less lost interest in the netbook concept and upgrades to the OS and the installed software more or less ceased, meaning that though the machine still worked, things like the web browser were old, insecure, versions and quite rightly a lot of sites told me to upgrade or bugger off.

So it ended up in a drawer. I bought another windows netbook for travel, and a cheap Chinese tablet and keyboard combo for note taking. Well, the windows netbook has all the Microsoft problems of being slow to boot and pummelled by the upgrade cycle, and the note taking tablet has proved to be a little more erratic than I hoped even though I used it successfully for project scrum notes and client engagement meetings for a whole project.

So I always resolved that before the Eee went to the recycler I’d put a decent operating system on it. So last night I did just that.

Choice of operating system was a little tricky - the Eee has only 512MB (that’s half a gig) RAM, a slow early generation atom cpu, and an 8GB SSD.

There’s problem with some of the early SSD’s whereby they are quite prone to ‘fading’ after a lot of repeated write and delete operations, which means that using them for something very churny like a swapfile can bring on this ‘fading’ effect quite quickly.

When the Eee first came out, a lot of people put together dedicated distros but these are all long gone or hopelessly out of date.

After some googling I settled on Crunchbang, a distro I’d used extensively on a Virtualbox VM. I chose it because it was debian based, and debian has good in built support for the Eee 701, and has a very low memory footprint, meaning that you are unlikely to start swapping just running the window manager - and as it was a 2009 model I suspected that the SSD was probably a bit more robust that the SSD in the original 2007 version.

However, to keep things lightweight I decided to go distinctly old school - nano as a text editor and alpine as a mail client. My reasoning was that as a note taker, and given that I write most notes in Markdown, nano would be just fine. Markdown is so simple that you could write it using vi, but these days I find vi a little too hard core for day to day work - can never remember the bloody buffer commands. With a local install of pandoc I could generate odt and pdf versions of documents if necessary, and that alpine was good enough to email documents to myself - reckoning that it reality most notes get cleaned up before being circulated or archived.

Using Dropbox is an option but that adds to the memory usage. Using just nano and pine the machine is probably going to hardly ever swap, and of course it’s distraction free, leaving you to concentrate on what’s being said.

Installation was straightforward - it basically just worked.

I downloaded the iso of 32 bit version for older machines, used dd to write it to a USB drive and booted the Eee from the USB to test if everything (including wireless) worked.

Then I restarted it and ran the installer - there’s a bug in the installer which means that all you get is a flickering line when you start it - it’s a known Debian bug and the fix is nicely documented on Crunchbang’s website . Installation took around 45 minutes plus another 45 or so to apply updates, install pine and so on.

I havn’t used it in anger yet, but the machine seems stable, so the next step would be to give it an outing, and see just how useful it is in practice …

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Friday 17 October 2014

Yosemite ...

Normally I'm very cautious about OS upgrades but this morning I felt wild and impetuous and upgraded my work Mac to Yosemite, Apple's latest version of OS X - one of the advantages of living on the dark side of the world is we tend to get first go at updates.

The process basically just worked, although it took a bit longer than Apple claimed, and the system was pretty unusable during the post install optimization phase - budget at least a couple of hours, or perhaps a little  longer.

A few things needed nudging:

  • Dropbox needed a reinstall - just like after the 10.9.5 upgrade
  • Amazon Cloud drive broke and needed a java install
  • GanntProject (admittedly I was running quite an old version) broke and needed an update
Everything else seems to work, although switching between apps and app start times seems slow, but then it was with Mavericks, but once running everything seems reasonably responsive on what's now a four year old MacBook Pro with 4GB of RAM.

My only real gripe so far is the use of Helvetica Neue as a system font - yes it's legible, but it's a bit too heavy for my taste, but if that's the only annoyance, things are not too bad ...

Monday 13 October 2014

University rankings and altmetrics

I was on holiday last week, and we drove down to Victoria for a few days. On the way there I listened to the radio and someone (I forget who) was talking about the THES rankings and making the very good point that individually the various ranking tables don’t mean a lot as they all use different algorithms and tray and measure different things. but that if a university scores consistently high in a number of these tables it suggests that in some way it is better than one with either inconsistent scores or consistently low scores.

Better here means that its is good at teaching, good at research, and is effective in promoting this.

So with altmetrics, impact rankings and the rest. Individually the various scores don’t mean a lot, but collectively they are an indicator of engagement. I’ll say engagement because this is still a nebulous topic. There are people who publish highly cited research but don’t promote it. Typically these people are well known in their discipline. Then there are those who communicate well about their field and have an impact through teaching, through social media, and the rest. And of course there’s some people who are somewhere in between.

Like ranking tables, high scores are good. However before dismissing inconsistent scores (high say on social media, low on research impact) we need to actually ask a very difficult question: What are we trying to measure, and how will we know we’ve measured it ?

The first part is probably relatively simple to answer, the second one rather less so, as we need to decide on what we will accept as evidence and what it tells us about engagement

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Friday 26 September 2014

Almost instant ebook production

For reasons described elsewhere I was searching for pictures of Louise Bryant - who was a witness to some of the events following the 1917 revolution in Russia and was married to John Reed - best known for Ten days that shook the world but with a pedigree in left wing journalism and agitation in the US in the years before the first world war.
However, this post is only tangentially about my interest in the history of the Bolshevik revolution and subsequent civil war. While searching for pictures of Louise Bryant I came across an unpublished biography at (unsurprisingly), which I thought might be worth reading.
The biography is published as a set of long html pages - as if it was a set of blog posts, and I really wanted to read it offline using either a tablet or an ebook reader. So I decided to make it into an epub file for personal use.
It turned out to be really easy to so and as there’s quite a few other books and texts out there that have been transcribed and published as a set of web pages, so I thought I’d publish my recipe …
  • Using firefox download and save each of the web pages in the document
    as a file - choose web page as the format - this will save the html
    and also save any embedded images in a subdirectorynamed after the
    web file, eg if the first section of the book is called part_one it
    will save a file called part_one.html and create a directory called
    part_one_files containing the embedded images.
  • Then create a new blank document in libre office and using the insert command select and insert each of the files in turn into the document. This will give you a document containing the entire text.
    • Automagically the images will also be embedded in more or less the
      correct place.
  • Save the file as somefile.odt onto your dropbox
  • Go to CloudConvert and connect it to your
    dropbox account.
  • Select somefile.odt as your import document and choose either epub (for most generic ebook readers) or mobi (for kindle) as the output format.
  • Select save to dropbox as your output target, click convert and it
    will write the output file out to ~/dropbox/apps/cloudconvert/somefile.epub
    • (Under windows it will be in the apps\cloudconvert directory in My
    • If you chose mobi as the output format the output file will be
At that point you can then transfer your file to your chosen device such as either sideloading it or emailing it to your kindle, or opening the file on your tablet by using an ebook reader application and opening the file on dropbox.
The whole exercise took me about ten minutes.
I see no reason why this solution should not work equally well for other texts transcribed and published as web pages.

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Tuesday 23 September 2014

Digital Preservation Strategies ...

I came across a beautifully succinct quotation from National Records of Scotland:

‘If digital records are not captured there can be no preservation and
if there is no preservation there can be no access’

Which is a beautifully concise description of why we do data capture. If we don’t there is no way of retracing our steps, no way of of substantiating research, because we don’t have the original data.

And of course, if we don’t have the data all our arguments about preferred archival formats are moot. And in a very real sense they are anyway - formats change over time, and preferences change over time. Legal documents and court transcripts in Wordperfect from the nineties are a key example.

They may still have validity, but they are in a dead file format. No one when they created these transcripts knew that in twenty years the files would be in a dead format - they chose a widely used well documented format - it’s just that preferences changed.

Tools such as Tika, Pronom and Fido give us a chance on capture of also being able to record information about the file format, which gives us a clue about how we might read the file in the future.

And of course technology to read files changes as well, all we can do is try and make sensible decisions to make life easy for anyone who wants to access captured files.

File normalisation is one - what of course it really means is ‘convert files in a known proprietary format to an open format on ingest’ - usually using something like libre office in batch mode, and storing the converted file along with the original.

The idea is of course, that the converted file will be easier to read as it’s in an open format than a proprietary format. Of course, when we say proprietary format we mean Microsoft because we worry about its dominance of the file format ecology.

And we are of course most certainly wrong - there is just so much material in Microsoft formats that it is difficult to believe that there will be a future in which there are no applications to read these files - what one should be worrying about is the less well used formats such as Pages or AbiWord where there is a greater risk of losing access.

But the point remains, that unless we capture the files in the first place we will have no chance of reading them in the future …

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Tuesday 2 September 2014

Moving people away from commercial cloud services

A few days ago I posted an update on my thoughts about Eresearch support services .
One of the points I made was that no matter how desirable it was to move people off of commercially hosted services such as Dropbox, it wouldn't be easy

This ease of sharing and the fact that Dropbox is hosted 
outwith Australia is something that of course gives intellectual 
property managers the willies, but it is also a fact of life, and 
something that has to be dealt with - in other words, as Dropbox 
is already out there in the wild, and whatever is provided as a 
replacement has to be at least as good, and at least as flexible 
- which of course means it will bring the same intellectual property 

Dropbox, and the others, such as Evernote and Box, are in with the woodwork as they already have widespread adoption.

I’ve just had a real world example in which a researcher shared data with me via Dropbox that he wanted to have uploaded to our data repository, and have a Digital Object Identifier minted for that data so that it was citable.

In my conversations with him I followed the party line and suggested he use Cloudstor, AARNET’s file transfer service, which is based on FileSender to transfer the data to me.

As a service, it’s pretty easy to use. However, my client used Dropbox instead, simply because it’s what he was familiar with and he knew that it worked.

I am, of course, as bad as everyone else. I routinely share documents and notebooks stored in Evernote with colleagues, and share Google documents with colleagues, so I’m most definitely not going to complain about using Dropbox here - after all it’s exactly what I would have done, and as I’ve said before I’ve had publishers share material for review in exactly the same way.

Instead of complaining, I’m going to take this as a learning experience:
  • services like Cloudstor, are not going to succeed without a major educational campaign to raise awareness among the user community
  • competitor services like Dropbox are already well established and user have a high degree of familarity with them - any educational campaign needs to focus on cloudstor’s unique features
  • whatever value proposition is made needs to be relevant to the users - so if we want to build a unique selling proposition around keeping intellectual property onshore we’d better make it relevant and explain that as well
and the last point is something that we would need to think carefully about. My client was passing me his data as he wanted to not only to make it citable, but also open access, as he was publishing a paper in a journal that required this.

And if it were me my first question would be

If it’s open access does it matter it’s gone via Dropbox ?

And I must admit, I’d be hard pressed to find a reason why it mattered …
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Tuesday 26 August 2014

Eresearch services

About a year ago I posted my two cents worth on what an eresearch support service should look like.

A year or so on, and innumerable conversations with users, potential users and people who are interested I find my views are not much changed:

User wants can be broadly summarised as

  • storage
    • dropbox like sharing capability
    • lots of it
    • handling of diverse media types (agnostic)
    • assurance it is secure backed up and accessible
  • virtual machines
    • data analysis & manipulation
  • secure long term storage of data
    • publication of data for substantiation
    • digital object identifiers
  • advice on legacy data
    • format conversion
    • media conversion
    • digitisation
    • some bespoke programming, data wrangling etc

Dropbox is extremely popular because of its ease of use and universality, meaning people can share data from the field with colleagues, with colleagues overseas etc.

I have a second life in which I review books - it’s noticable that in the past year publishers have moved from sending you the epub or mobi version to sharing it with you via dropbox. I don’t see any reason why researchers should be any different in their habits.

This ease of sharing and the fact that Dropbox is hosted outwith Australia is something that of course gives intellectual property managers the willies, but it is also a fact of life, and something that has to be dealt with - in other words, as Dropbox is already out there in the wild, what ever is provided as a replacement has to be at least as good, and at least as flexible - which of course means it will bring the same intellectual property concerns.

And of course it’s not just Dropbox, we can say the same about Evernote, OneDrive, OneNote and Google Drive.

However in the course of my conversations one thing that comes up over and over again is the need for decent work in progress storage, and work in progress storage into which it is easy to load data, either by direct capture from instruments, or by some easy finder/file manager like process - people expect to be able to drag’n’drop and tellin them about some command line incantation with rsync doesn’t play.

There is an interest in data publication, but at the moment it’s basically driven by journals requiring that data has to be made available, but I expect that this will build as more and more journals require this. I also expect to see more interest in publishing source code and things like R scripts as part of the whole substantiation and open review thing.

There’s also an undercurrent of people wanting to return to research they did earlier and finding themselves locked out of their data because it’s been stored on media no longer in common use - such as zip drives, or in older data formats that made sense at the time. We could rehearse the open formats argument here, but that doesn’t fix the problem, which needs to be addressed. Allied to this is the need for a little bespoke programming or data wrangling to get data into a usable format, or to clean data.

So, one year on I’d say change hasn’t happened, but there’s nothing to say that it won’t …

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Wednesday 20 August 2014

Munich to ditch Linux ?

The internet has been all a-twitter today with the news that Munich was considering dumping Linux and going back to Microsoft.

I’m not surprised. Saddened perhaps, but not surprised. Much as Apple through the iPad owns the tablet space, Microsoft still owns the office desktop, and this means that if you want to do something different you have to not only do it as well as Microsoft, you have to do it better.

So let’s look at the Linux software environment and compare it with Microsoft. And of course when we’re talking about local government we’re largely taking about administrative and management tasks, which means word processing, spreadsheets, email and workflows - in other words office applications.

Libre Office and Open Office basically do everything Microsoft Office does, but slightly more clunkily and clever formatting in Office documents sometimes comes out a little wierd, especially if the original document has been edited with two or three different versions of Office, but in the main it’s perfectly usable. You’d be being snippy to say it wasn’t.

Ditto for evolution as a mail and calendar client. Not as polished as outlook but perfectly usable. And if you were a private individual or running a little home business there’s no reason why Linux wouldn’t work for you. The same argument applies to Macs and OS X. Or running anything with Google Docs.

And then there’s collaboration, workflows, business automation, call it what you will. Sharepoint does that pretty well. And in the Linux world?

Sure there are solutions but they usually involve keeping squads of wild eyed sandal wearing geeks in the basement - ie you can’t just license it, get some nice consultants in at inflated prices to configure it for you and leave it running the way you want.

And there’s lots of things out there to integrate. Useful things like invoicing and payment management solutions. Move to something definitely not mainstream and you have to re-engineer every damn thing …

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Wednesday 13 August 2014


I recently happened across an application called Multcloud.

To be honest, the manufacturers asked me if I was interested in reviewing it.

I declined, because, as a matter of policy I don’t write reviews on things I havn’t tested on myself by using them for real work, or for which payment (or some other inducement) is offered. I’ve always believed in eating my own dogfood, and I find that way I sleep better at night.

However, I was sufficiently curious to take a look.

The idea is quite simple - we all have multiple cloud based accounts, OneDrive, GoogleDrive, Box, and the rest and we all end up with files scattered across all of them, and if you’re like me have different machines that mount different subsets of these drives.

The idea is to provide you with a browser window into which you connect all your accounts, and then which allows you to search across them just as you would search the disks attached to your pc, and to copy files between them.

No a stupid idea - in fact quite a good idea. Obviously there’s a raft of security concerns but the vendors claim on their website that all authentication is by OAauth, and that no data is cached on their servers.

Now as I said, I havn’t tested this tool, and have no idea how well it performs. It’s also not the only such application out there - a little googling comes up with a list of alternatives. However this is a product that might well fill a need for some people. Remember that your mileage may vary …

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Monday 11 August 2014

Zotero, RefMan and Jabref

Zotero is a rather nice bibliography manager which can export references in a number of formats, including BibTex.

I was playing with reference managers last week trying to work out a set of workflows to get the information exported for reloading into a different solution - it’s the old problem of tracking people’s publication history and loading it into a research management system.

There’s a good little BibTex exporter for Zotero known as autozotbib that works as a plugin for both the desktop client and firefox that pushes the records out in BibTex as they are updated.

If you use dropbox for filesharing you can of course output the export file directly to Dropbox, which makes it readily accessible to a number of other reference management products, including JabRef.

In the course of playing about with this I also tried installing RefMan on my Android tablet, and telling it to read the Zotero output file - which it did.

Now I’m by no means a power Zotero user, but one thing I do sometimes need to do is check references and information, and something that increasingly I find myself going to a tablet to do so because of their extreme portability rather than using either a Chromebook or one of my aging netbooks. While I’ve only got one way synchronization - ie all the changes have to be made to the Zotero end of things, this little trick makes it comparatively easy to search reference lists with a native (and free) android app …

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Thursday 31 July 2014

So what do you use?

I've been a bit remiss posting on this topic - it's actually quite difficult given that I flit between platforms and devices, but I've managed to come up with the following table based on my principle activities:

Windows OS X Linux (Ubuntu) ChromeOS Android
WordProcessing LibreOffice LibreOffice LibreOffice GoogleDocs n/a

LibreOffice via
Lightweight document creation (MarkDown) Retext StackEdit MarkDrop

Retext via
Spreadsheets Libre Office Libre Office Libre Office GoogleDocs n/a

Excel via OneDrive
Email Web client Web client Web client Web Client Application
Twitter Web client Web client Web client Web Client Application
RSS Reader Web client Web client Web client Web Client n/a
Document Management Evernote Evernote Web client Web Client Evernote
PDF Viewer Acrobat Preview Evince Google viewer Acrobat
Epub Reader Calibre Calibre Calibre n/a n/a

This of course doesn't cover the devices used - for example I'me still using my old Cool-er ereader to read epubs offline, while my Kindle is used for recreational reading, and I still use my old noname 7inch tablet for notetaking.

I also find I use my full size windows laptop at weekends for more serious writing but prefer my Chromebook during the week for email, web and rss reading, plus writing the odd snippet. My newer Samsung tablet is used for email, online newspaper reading and online banking, but strangely I still like my original 10" Zpad for viewing images, even if it's a little slow these days ...

Monday 28 July 2014

Travelling with a 3G router

As I’ve written elsewhere, we’ve been on holidays, riding the train up to Cairns and driving back south through the edge of the western emptiness. During that trip we of course faced the great question of the twenty first century - how to get internet access.

Some of the places we stayed at provided complimentary internet, some did not, and some were simply out of range where there’s no coverage.

We couldn’t do a lot about a lack of coverge, but to combat the problem of small motels and rental cabins without the internet, we took our own, in the form of a little D-link 3G router I bought off of ebay for $18, an unlocked Huawei USB modem and one of these cheap data sim packages.

In the small towns of the bush it worked reasonably well allowing us to surf the web from an android tablet, check our email, and use internet banking and newspaper apps. In bigger, coastal places, such as Port Douglas, which was swamped with tourists, it didn’t do so well, probably because the 3G network was overloaded, meaning we suffered from dropped connections and timeouts.

Where we had good connection we even managed to have two tablets running at once - which was pretty neat.

It was fortunate though we’d taken tablets with us at the last moment, I’d originally planned to simply take the Chromebook and rely on phones for the rest.

Previously at home I’d successfully used applications on over a 3G link from my chromebook so I reckoned we’d get good enough performance.

In practice I didn’t. The Chromebook was tempremental - I’m guessing just too much back and fro to big G and time outs. Where we had a fast connection it was usable, where we didn’t it wasn’t, even though our tablets were. We’d have probably done better with the Windows netbook I took to Sri Lanka last year, and using postbox for email despite my various whinges about the netbook’s overall performance.

Spending blocks of time - four or five days off the net at a time also just revealed how dependent we’d become on the net for news and weather information - in the old days we’d have taken an AM/FM radio with us and listened religiously to the news and weather forecast on Radio National - well we still have the radio we used to take with us, but didn’t think to take it.

We also became extremely adept at spotting where there was working internet in a restuarant or a stop on the highway - where the internet worked people, starved of electronic interaction, sat and looked at their phones or tablets - where it didn’t they talked to each other, and there were payphones and people using them …

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Friday 27 June 2014

25 years of the internet in Australia

Australia’s been connected to the internet for twentyfive years now.
I of course don’t remember this, as I wasn’t here - I was working in a university computer centre in the UK, and in 1989 it was still all DECNet and Coloured books protocols.

(The UK had invented its own set of networking protocols, and connection to the rest of the world was either via complex email address translations or strange non interactive ftp incantations - something that I was a dab hand at - sending files to India via usenet etc…)

A couple of years later (I’ll say 1991, but actually I can’t remember) there was Project Shoestring which was a pilot migration to TCP/IP which recognised that Coloured Books was not going to make it globally and we’d better all move to TCP/IP - something that made the Unix people very happy (and Macintosh users - they could use Eudora for email and send each other BinHex encoded attachments).

Now we still used to run a student advisory service - this was a hangover from the days of batch programming but essentially what it was that one of the programming team sat in a booth and answered user queries as to why their batch job had gone stupid.

I was officially an analyst programmer which meant I had to do advisory even though I was singularly useless at it - rather than Fortran coding I knew about network transfers, document formats and these pesky new things called desktop computers. My principal contribution to human happiness at the time was explaining to US exchange students was how to email their girlfriend/boyfriend at or their mum or dad who had a compuserve account.

Anyway, one day shortly after we started a TCP/IP service, a visiting Australian academic turned up asking if we could help her access her email - she had thought to bring the numeric address of the mail server, so I fired up a VT100 emulator, connected to a terminal server, typed c tcp {server ip address}, and after a few seconds a login banner appeared, typed out at what looked like 300baud, she logged in and fired up elm to read her mail.

Clumsy for sure, but there it was, a connection across the planet …
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Thursday 26 June 2014

E-readers are (probably) dying

E-readers, as in dedicated devices for reading content are on the way out.

How do I know this - well, just by looking about. I’ve occassionally blogged about people’s reading habits on public transport in Canberra and even Singapore, but yesterday I was in Sydney for a meeting, and did something I hardly ever do these days - caught a peak hour train. The train was one from the CBD out past the airport to whereever the train goes once it’s past the airport, and being peak hour it was pretty full.

In between gawking at the sunset over the the Harbour Bridge (tip: try Circular Quay station at sunset for an excellent view) I looked around at my fellow passengers. The train car was pretty full and around three quarters of the people were reading something. A few oldies with paperbacks, but everyone else was using a tablet or a smartphone. Interestingly, young people of Asian experience seemed to mostly read on smartphones, while their western counterparts seemed to prefer 7” tablet. (I agree, they could be doing something else, but of those I could see clearly, what ever they were doing involved screenfuls of characters - which kind of looks like reading to me)

No one I could see was reading using kindle or other like e-ink grey screen device.

Now, e-readers have many virtues - especially Kindles - buy your book and it lands on your reader as soon as you have a wireless connection - long battery life and the rest - in fact they are very good at what they do. Proof of the pudding is that as well as my kindle I still use my Cool-er for reading public domain books from gutenberg as part of my unarticulated informal research into the nineteenth century colonial experience. Yes, of course I could use my kindle for this, but having two readers on the go means I can separate reading for interest from reading for fun - a bit like having two books on the go at once.

And I’m sure that a great many people will carry on using their readers, but if you’re carrying one device round with you, you’re more likely to carry a tablet, because of its versatility …

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Monday 23 June 2014

Curating Legacy Data

Data is the new black, everything seems to be about data at the moment and it’s desperately trendy. At the same time there is an entirely laudable movement towards researchers making the data that underlies their research available, for all sorts of reasons, including substantiation and reuse and recombination with other data sources.
This sometimes gets conflated with Big Data, but it should’t - outside of a few disciplines, most experimental data is pretty small, and even quite large sets of results will fit comfortably on a twenty dollar usb stick.
It’s important to remember that this is a recent phenomenon - only in the last five years or so has cloud storage become widely available, or commodity hard disks become large and cheap.
Before then data would be stored on zip drives (remember those) CD’s, DVD’s, or DAT tapes - all formats which are either dead or dying, and all of which are subject to maintainance issues. Basically bitrot due to media degradation.
Even if you’ve stored you data on an older external hard disk you can have problems - my wife did just that, and then lost the cable to a four year old external disk - it of course turned out to be a slightly non standard variant on USB, and it took us a lot of searching of documentation and cable vendors (including a couple of false starts) to find a suitable cable - when is a standard not a standard ? - when it’s a proprietary one.
Recovering this legacy data is labour intensive. It can be in formats that are difficult to read, and it can require conversion (with all that implies) to a newer format to be accessible - which can be a special kind of fun when it’s not a well known or well documented format (nineteen nineties multi channel data loggers come to mind).
So, what data should we convert?
Well most scientific publications are rarely read or cited, so we could take a guess and say that it’s probably not cost effective to convert the data underlying those - though someone did once ask me if I still had the data from an experiment I did back in the nineteen eighties - turns out they were having difficulty getting regulatory approval for their physiology study and thought that reanalysing my data might give them something to help their case. And I’m afraid I couldn’t help them, the data was all on five and quarter inch Cromemco Z2D disks, or else punch cards, and long gone.
So, what probably a legacy data curation strategy should do is focus on the data underlying highly cited papers - it’s probably of greater value, and there’s a chance it might have been stored in a more accessible format.
However even recovering data that’s been looked after still has costs associated with it - costs to cover the labour of getting it off the original source media and making it useful. And these are real dollar costs.
From experience, getting a half dozen nine track tapes read costs around fifteen hundred bucks if it’s done by a specialist media conversion company, and the administration, shipping, and making useful phase probably another fifteen hundred, less if some poor graduate student can be persuaded to do the work, but still is a reasonable chunk of money, and money that need to come from somewhere.
So, who pays, and is it worth it?

[Update 26/06/2014 : Notes of a meeting in Sydney on this very subject ...] 
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Monday 26 May 2014

Digital Humanities and Citizen Science

The humanities are going digital. This of course is not wholly true but those who study language and history - to name the two most obvious examples - have found the internet an unrivalled resource to provide access to digitized material.

No more trekking to obscure libraries and archives in the hope of finding material, it’s online, often as a result of various digitization and digital preservation initiatives. Even if the material is not online the archive’s catalogue almost certainly is, making the preliminary search something that can be done from home.

And then there’s archaeology - before the establishment of university archaeology departments in the sixties and seventies, a lot of excavations were sponsored by local archeological societies, and theire results never fully published. Digitization and initiatives such as the Archaeological Data Service in the UK have helped make that information available, findable, and searchable.
This is escpecially important in these financially constrained days where university archaeology departments are contracting and investigations are increasingly carried out by specialist sub contractors to mining and construction companies, meaning that there is no clear location for the deposit of results - digitisation, cheap storage, and a publication mechanism means that these results are less likely to be lost.

And there is of course what used to be called natural history - something that tends to fly under the radar these days but actually of great significance.

A lot of the fundamental information of species abundance and change is derived from the work of local natural history and field societies, good solid observational work that individuals find enjoyable to do, costs little, yet is of fundamental importance for assessing the impact of climate change or introduction of pest species. Truly citizen science.

Yet many of the results remain locked up in local society journals and botanical surveys yet it is of great potential. The digital humanities have shown the power of mass digitization, the field sciences have track record in citizen science - one can but wonder what would come out of putting the material collected by local societies online - time perhaps for Digital Ecology as a discipline ?
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Wednesday 21 May 2014

Apple iCloud and Oracle Comms server

I’m not an apple iCloud user - yes I’ve an account and I’ve tried the online version of pages, but that’s about it.

However, this morning I stupidly left my personal phone at home. Apart from the irritation factor it’s no big deal, except that it had the weekly shopping list on it and no, I hadn’t synced it anywhere sensible, like it’s a shopping list.

Once a week I go to the Mawson supermarket and buy all the boring bulk items like toilet paper and dry cat food. The list is more or less the same except for the extras such as dishwasher powder that we don’t need every week.

However I still have my work iPhone, so my quick fix was to recreate as much of the list as I remember on iCloud and sync the note.

Ok, so far so good. On a whim I also mailed the note to myself and dumped out the headers to look at the routing info. Ok, very geeky, but interesting.

In the middle of the routing data was the following:

Received: from ([]) by (Oracle Communications Messaging Server
7u4-27.08( 64bit (built Aug 22 2013)) with ESMTP id
<> for
d^^^^^@^^^; Tue, 20 May 2014 22:06:29 +0000 (GMT)

(I’ve obscured the name of the mailbox I was using by ^)

And there it was - iCloud uses Oracle communications server. Kind of interesting given that at work we changed from an older version, Convergence, to Office365 at the end of 2012 - obviously the Oracle product scales reasonably well …

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Tuesday 20 May 2014

Capacitive gloves

As I wrote a couple of weeks ago, I couldn’t resist springing a dollar for some Chinese iGlove clones - ie normal acrylic gloves with a little bit of capacitive material in the finger tip to allow you to use touch screens.

Well, my dollar gloves arrived and they do work. My only criticism is that the ‘one size fits all’ size only just fits my not particularly large male Caucasian hands - ie if you have big hands they may not fit you.

I’ve tested them on a variety of touch screen devices and they’re fine. They also work well on a standard laptop track pad, meaning you could use them for surfing with a laptop or a chromebook.

As always, I find typing with gloves akin to dancing wearing clogs, but if you were desparate, you could probably type on a chiclet style keyboard while wearing the goves and using the trackpad.

The pair of gloves only have capacitive thumb and forefinger tips - you can get ones with all five fingertips made of capacitive material and these might allow reasonable typing on an iPad or Galaxy virtual keyboard …

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Tuesday 6 May 2014

Chromebooks in daily use

If you’re a regular reader of this blog, you’ll know I’m a happy owner of an HP Chromebook and as previously a less happy owner of a different manufacturer’s offering.

I’ve been interested in thin clients since the mid nineties, but it’s always been something that was going to happen ‘next year’. Basically the problem was that the early NT derived solutions were hobbled by licensing restrictions and the later solutions, such as Sun’s solaris based solution were hobbled by not having a decent software base - this is of course why Sun bought Star Office, and indirectly why we have Libre and Open office today.

This is all so much ancient history. By the middle of the last decade we’d moved into a world where overwhelmingly applications and data were stored locally and if you were lucky backed up. The range of applications available was such that you could live and work on any platform and be independent of any central provision.

Now, while there had been some quite credible remote desktop solutions earlier, things changed when Google bought Writely and started being able to provide remotely hosted word processing and later spreadsheet and presentation services.

Google were not unique, there were some other competitors about such as Zoho, who are still with us.
At the same time Google started offering cheap storage and solutions such as Dropbox started to become available allowing syncing of content between devices.

This meant that manufacturers such as Asus could come out with low cost computers such as the 701SD, that while they had local applications could be used primarily as web access platforms using google docs, gmail and the like.

Such computers were ideal for travel and field work - almost stateless, capable of being used offline, low cost and robust. Our 701SD went on a number of overeas trips with us and and I used it extensively going to conferences and seminars.

At the same time I used an old recycled iMac as my main desk computer at home very successfully for a number of years - essentially because I only used web based applications plus a couple of local editors - something that proved to me at least that the browser was king and the host platform increasingly irrelevant. Data was of course stored elsewhere.

The real trouble with the netbook concept was that people didn’t really see it as an internet first device, and more as a low cost computer. That, plus both the FUD around Linux and Microsoft’s hobbling of Windows 7 Home Basic’s capablities stymied the netbook concept. Instead we took a left turn through tablet based computing - yet another application of low cost internet based computing.

Now, one of the things that is interesting about the iPad is just how many third party keyboard solutions there are, which is effectively a way of turning a tablet computer into a netbook - or since we’re using browser based applications, a netbook - and I emphasise net in netbook.

This time around public internet access is more common meaning that having an offline capability is useful, but not as essential as it once was.

So, what are they like in daily use?

Well if you have Chrome on your desktop and use gmail and google docs you already know the answer - it’s just the same. And you are not tied exclusively to Google, Zoho works just fine and if you have a Microsoft account you can use Microsoft’s online versions of Word and Excel - they’re not perfect but good enough for most cases where Google Docs import and convert doesn’t quite cut it. And of course you have’s hosted Open Office and Libre Office) if you’re doing something too fiddly for Docs, although in my experience niether fork copes well with some of the more complex formatting in Office documents when they’ve been created with (a) a complex style sheet and (b) been through one or two Office installs already - project proposals and the like where they have to be created using the standard template and have to go through a number of reviewers, with some back and forth being the prime example.

However for 90% of daily computing use they just work. And that’s because all the common applications you might use, such as Evernote and Wunderlist to name two have web versions and or clients for the Chromebook environment - there is very little that you can’t do in a web based enivronment - something for which we have to thank Steve Jobs and the iPad for making network centric computing mainstream.

Chromebooks mostly just work. And providing you have no problem about being dependent on the google ecology, provide affordable low cost computing with remote data storage. Yes, you are dependent on Google and the internet, but then you are anyway …
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