Sunday, 22 February 2015

Xubuntu webcam fun

My configuration of my MSI Wind notebook as a Xubuntu based machine is coming along quite nicely. I still don't have an answer to offline blogging, but yesterday I added skype and dropbox, dropbox so I can access all my files, and skype so I can call home.

Dropbox just installed. Skype needed a dpkg -i command but installed without issue - or so I thought until I tested it.

No webcam.

So I tried cheese - again no webcam device detected. I assumed (wrongly) that the device driver was missing or incorrect and set out on a hunt for the correct driver.

Luckily I didn't find one.

Instead I found a slew of posts from people with similar problems and no answer, and finally a post with a reply that fixed the problem.

And it was a facepalm moment.

Apparently the MSI has privacy switch controlled by the F6 key to disable the web cam, and - you guessed it - the default startup state is off.

Hit the key, the webcam is enabled, and everything works. Colours are bit crappy, but it's a webcam.

I can live with that ...

Thursday, 19 February 2015

Experience atlases ...

Last night I came across the concept of the ‘experience atlas’.

It comes out of the HR world but despite taht it’s quite an interesting idea. People’s job titles often don’t reflect what they do, especially if they work in a fast moving field, and they’ve been in post for a few years.

A recruiter looking at someone’s resume might just look at the job titles and qualifications and take a very narrow view of someone’s experience and allow their pre-conceptions to guide them as to the usefulness of someone’s experience.

For example between 1984 and 1986 (I’m deliberately choosing an episode a long time ago as it doesn’t matter either way) I was employed as a ‘Computer Officer’ at a field research station.

Officially I looked after the computers, provided enduser support, some help with data management, data analysis,  liaised with the parent computer centre and bought things.

Nothing remarkable there, and I did do all of these things. But I also did a whole lot of other things.

For example, as I’d previously held a Medical Research Council studentship, and knew about ethics approvals and experimental protocols, I ended up managing botanical survey teams.


Well you had to have procedures in place about what to do if someone was chased by a bull or in a traffic accident while they were out doing their work, and that looks a hell of a lot like an ethics approval for experiments on human beings.

There were also rules and compliance requirements regarding rare plants, and indeed if the surveyors accidentally came in contact with rare animals.

I also did some work with insectivorous bats at the time - which again involved obtaining clearances and approvals, as bats are scheduled in the UK and only people holding an appropriate clearance can handle them.

For example, anyone can watch bats fly out of a medieval church, but if you want to catch tag and release some to track movement between colonies it’s got to be done by approved people with appropriate clearances - ie it takes you to a whole new level of management and paperwork.

And the medieval example is appropriate - wildlife people might have one view of the presence of the colony while heritage people might well have another view, and the local vicar usually just wanted to get on with his pastoral work and not have to deal with things, meaning that you could well end up trying to negotiate and reconcile matters between who we would now call stakeholders. And you can’t contribute usefully unless you know about what’s involved - so having an interest in history and archaeology was a plus.

Now, I don’t want to exaggerate what I did, but instead make the point that this is valuable experience that’s not reflected in my cv.

Likewise when you come to annual reviews, basing you next year’s kpi on your resume is often narrow and inappropriate - an experience atlas gives a broader view of someone’s competences and capabilities.

The downside of course is that they’re a pain to compile - too much information, but a structured format with defined questions to build up a portfolio might be a way forward ...

Wednesday, 18 February 2015

Linux replacements for Windows Live Writer ... (not)

When I upgraded to Xubuntu, one of the downsides was that I lost the use of Windows Live writer, a free and nifty offline blogging client from Microsoft that plays nicely with both blogger and wordpress.

Given that my xubuntu machine is used while travelling, offline capability is useful as it lets me blog in these moments while waiting for something to happen, or while travelling on a train or plane.

Now the real usefulness is that once you get to somewhere with internet you can simply click on ‘Publish’ and it’s published.

The obvious workaround of writing the draft post in an editor and cutting and pasting it into a blog window on the web isn’t quite so slick, especially if you have links or some complex formatting like a table.

Yes it can be done, but it can be a little more time consuming.

So this lunchtime I did a bit of googling, and there’s certainly clients out there such as Drivel and Blogilo but they have a set of problems - basically there’s not been a lot of development of these applications in recent years, which means that they havn’t kept up with api changes for example QTM looks promising, but actually can’t post to a recent Wordpress install.

In fact I had a happy hour building and testing those that looked promising, and basically none of them really did the job.

All very frustrating, but basically it means writing the text in an editor of your choice (and exporting the file as html if there’s any complexity involved) and pasting into blog site ...

Monday, 16 February 2015

Netbook Xubuntu ....

Long term readers will remember that I bought myself a Windows 7 netbook back in 2012 to replace my Linux based Eeepc as lightweight machine to take travelling.

I won't rehearse why, but I still find that while tablets are good there are some things that just work better on a 'normal' computer.

However, increasingly I’ve grown dissatisfied with the performance of my Windows 7 netbook. Just too slow to boot, start a browser etc.

The original rationale was to have a windows device and use it with a 3G stick while travelling but I’ve kind of circumvented that by buying a portable 3G wifi hot spot. The other advantage was to have a recent version of skype, as the linux version was always several releases behind, but these days I can always circumvent that by packing a tablet.

The only other things I would lose that I actually used were the quite nice Windows Live offline blog writing tools, the nice Postbox application for Gmail, and Evernote.

While Nixnote works well enough it’s never been a substitute for the Evernote desktop client, but more recently Evernote’s web client has improved vastly in terms of user experience, even if the splash screen seems to feature slightly freaky looking people who have just been struck by some form of divine rapture.

Evolution will certainly substitute for Postbox for offline mail composition. The Microsoft web tools are a little more tricky, and I don’t have an answer other than Focuswriter or Retext with a bit of pandoc plus some cutting and pasting.

Other applications don’t really matter - I always used abiword as a word processor anyway, and everything else can be done via the web, and there’s quite a nice dropbox client for linux should I want to sync and share content.

But which distribution?

It’s a netbook with only 1GB of memory so the full standard Ubuntu might have been too much of an ask. I could have used Crunchbang, which I’m very happy with on my revived Eee, but development has recently ceased, so it looked like a lighter weight version of Ubuntu might be the goal.

I couldn’t decide between Lubuntu and Xubuntu, so I built myself a couple of VM’s to see if I really disliked either of them, and I found myself marginally more comfortable with Xubuntu, which I’d used a long time ago when I used an old ppc based imac with Xubuntu 6.06 as my main desktop machine at home.

Next, I made myself a bootable USB and then tried Xubuntu on the machine in ‘live CD’ mode to make sure that everything worked and that performance was adequate.

It was, so a sticky Saturday afternoon, I installed Xubuntu. I chose not to keep my Windows 7 home basic install reckoning that I’d probably never use it, and there was no content on the machine that wasn’t synced elsewhere.

Installation took a couple of hours - really because I also needed a slew of post install system updates, plus I wanted to install my extra apps. But at the end I had a working machine.

Speed and responsiveness is pretty good, and it doesn’t seem to swap excessively.

As always with new builds it takes time to get a feel for how fast (or slow) the machine is but it certainly seems more than reasonable ...

Friday, 30 January 2015

Software and reproducibility

In my career I've seen two cases where errors in the processor hardware or support environment caused problems in reproducing results - one was a GFLOAT bug in Vax microcode, the other was Intel's infamous Pentium floating point bug.

So if someone asked me how likely a problem reproducing a set of results was due to a firmware or hardware problem, I'd say pretty unlikely.

Unfortunately I can't say the same about software. Libraries change, compilers have interesting features, and increasingly these days code is dependent on third party libraries and extensions, all of which conspire to make reproducing results a nightmare.

Through in powerful environments like R and python iBooks and one has a verification problem. It's also unrealistic to expect a researcher to document all the libraries and dependencies involved - it's not their core competence.

Just like one expects Word or Open Office to open the previously saved draft of a research paper one expects that R will open a previous notebook and run the job.

However, if a few years have elapsed and the dependencies and performance of a particular library have changed, or one's running ostensibly the same version in a different computing environment there's a risk that things might not work the same.

The risk is small, and for computationally light research, say botanical work on plant morphology, can be ignored. However the problem is rather more significant in the case on computationally heavy research such as genetics, or in rerunning complex models, such as are found in climate research.

In the case of less intensive work, the sort of work that can be run on a laptop, creating, saving and documenting a VirtualBox image might be a solution - we're assuming that VirtualBox images are future proofed, but at least we can guarantee that state of the machine, in terms of libraries and so on is identical to that run by the original researcher, and whats more saves anyone trying to reproduce the research the travail of building an identical environment.

This of course does not scale in the case of computationally intensive work. Cloud computing and Docker are perhaps our saviours here. Most 'big' computing jobs are run in the cloud these days, or at least in a cloud like environment. Likewise, Docker, which was designed to simplify application portability can be our friend by allowing us to save the stat of our computing environment - an idea recently put forward in an paper by Carl Boettiger.

This actually is quite a neat idea. As the Docker container is digital object we can archive it and manage it in the same way as we manage other digital objects using some form of data repository solution with all the capabilities such solutions have to guard against bitrot.

It also as a solution allows the archiving of valuable interactive resources such as websites particularly those driven out of a database such as a lot of language resources.

I like the idea of containerization as an archiving tool - it neatly sidesteps a lot of the problems associated with archiving software and interactive environments ...

Tuesday, 27 January 2015

It's never actually over you know ...

A long time ago, early to mid nineties to be precise, I used to provide a file transfer service at the university I worked at.

5.25" floppies to 3.5", Mac system 7 to PC, Wordstar to Word, NotaBene to WordPertct, in fact just about anything to WordPerfect as we had a WordPerfect 5.1 service running on Vaxes as a student wordprocessing service. WordPerfect had this nice feature that the Vax file format was directly compatible with the PC file format. Macs were slightly more problematical and used their own format, but the Macs came bundled with a file export option to write files as PC format files.

However, this was before PC's were cheap and affordable. People used to turn up with weird machines and files in odd formats. Special dedicated word processors, little KayPro CP/M laptops and the rest. There was a hunger out there for cheap reliable worprocessing

King of the weird  was the Amstrad PCW. Wildly popular with graduate students due to its low cost, it used a non standard 3" disk format and came bundled with Locoscript, which was compatible with just about nothing.

To get the data off the machine we had a serial interface and used kermit to upload it to one of the vax machines and then convert it into a text file for the user to convert and restructure. Later on the uploads were to a Unix host but the data cleaning was still not much better than stripping off the top bit and filtering out control characters. Good enough for basic text but played hell with someone who'd discovered they could embed Byzantine Greek text in their document.

Due to the fact that the fastest we could reliably drive the serial interface was 9600 baud, files took forever to upload and were truly painful to do.

By about 1995 (I can't remember, but if I'm out it's only by a year) the PCW phenomenon had died and we stopped offering file upload/conversions.

And that was the last time I saw a 3" disk.

Until today - apparently our archives division have found some in a box of uncatalogued material ...

Sunday, 11 January 2015

Focuswriter on the Eee

A couple of days ago I wrote about FocusWriter, a distraction free writing tool for a range of platforms. At the time I hadn't used it in  anger, but true to my word I installed it on my revived EEEpc 701 SD.

Installation was trivial - a minute or two at most, and in use the application was efficient and responsive, giving just the write amount of control to write fluently. I was sufficiently enthused to use it to knock out the first draft of a book review, some thing I'd normally do using AbiWord or ReText.

The writing experience was pretty good, and pretty fluid - I'm actually quietly impressed by FocusWriter and will certainly be using it alongside of my trinity of preferred Markdown writing tools