O'Really?

December 14, 2012

Born Digital, Born Mobile or Born Slippy?

Born Digital

Born Digital? Mobile, mobile, mobile! Creative Commons licensed image via Youth and Media

Thoughtworks is an Information Technology consultancy which started in Chicago and now has offices all over the world. This year they’ve been running some interesting events called Quarterly Briefings which discuss topical technology, with the help of some case studies.

So for example, back in October some Google Guys ‘n’ Girls looked at Big Data. Following on from this, last Wednesday tackled the emotive issue of mobile with Move Over Desktop, Mobile is here! looking at agile software development using the mobile part of LastMinute.com as a example.

These events are fun, good for networking, handy for keeping abreast of what’s happening – all lubricated with free food and drink – what’s not to like?

Two of the speakers, John Crosby (LastMinute.com) and Renee Hawkins (Thoughtworks.com), offered lots of food for thought, more than I can document here. However, three things stuck in my head:

  • Renee pointed out twenty-somethings often have the best ideas, innovation comes from Generation Y. Senior staff, decision makers and leaders in many organisations are often baby boomers or Generation-Xers. When they think of software applications, they often think of web first, then mobile. The current generation of undergraduates and graduates from our Universities were born after the invention of the web. They aren’t just born digital [1,2], they’re born mobile too, iPhones and Androids aren’t new – they’re just normal. Desktops and web-applications are old school to them, its tablets and mobile smartphones where all the action is – that’s what many of them are now growing up with. So it shouldn’t be surprising that Generation Y often have good ideas in science & technology.
  • Renee also talked about doing agile vs. being agile: many organisations claim to be doing agile software development: they have the stand-up daily scrum meetings, kanban boards covered in post-it notes and practice pair-programming but they’re often just ticking the boxes – they’re not actually able to deploy software quickly. They look agile, but really they are doing agile, not actually being agile.
  • John quoted Googler Eric Schmidt on mobile first from a few years ago, who said something like organisations should put their best software developers on mobile projects. Schmidt said this a while back, and many people at the time thought, “Hmmm, yeah maybe”. The current trajectory of mobile technology is proving Schmidt right…[3] despite the strange Android Engagement Paradox.

So when it comes to software applications, are you born digital, born mobile or born slippy? The latter drink too much and are usually Gen-Xers or Baby Boomers…

…and if you’re interested in attending similar events to the above in your area keep an eye on join.thoughtworks.com/events and thoughtworks.com/radar.

References

  1. John Palfrey and Urs Gassey (2008) Born Digital: Understanding the First Generation of Digital Natives (ISBN:0465018564) Basic Books
  2. Sean McLane (2012). What Is It With These Kids? – A Generational Insight into Student Workers and Customers SIGUCCS’12 DOI: 10.1145/2382456.2382481
  3. Mary Meeker (2012) Internet Trends @ Stanford, Kleiner Perkins Caufield & Byers

May 8, 2012

BBC Connected Studio: Get involved in shaping digital content at the Beeb

BBC: The Olympic Broadcaster

Olympic broadcasting by the BBC from Quay House, Salford Quays, Manchester

The BBC is currently seeking external partners for collaborative innovation around BBC Online. This is happening through a series of events called BBC Connected Studio. It’s open to small, medium and micro businesses, individuals and digital agencies from the creative sector who want to work with the BBC developing new functions, features or formats for online audiences.

The first studio was held in Manchester last Friday focusing on Home Page, Search and Navigation (HPSN), a part of the Beeb that gets around 9 million (and up to 40 million) unique visitors every week from the UK alone. International visitors to this page get sent to bbc.com which is completely separate. Here are some rough notes on the event from a non-BBC outsiders perspective.

The basic format of the day goes something like this:

  • You are given a brief
  • There is an introduction from various people to kick things off
  • You have access to experts within the BBC, to pick their brains
  • There is time to work up your ideas on the day
  • Then you pitch an idea in ~2 minutes (like a much friendlier version of Dragons’ Den) to an assembled audience of about 80-ish people collected on the day.
  • There is time for questions and feedback
  • Successful pitches are notified after the event with the opportunity to build a functioning prototype and potential pilot project

For the event last Friday, the studio was kicked off by introductions from Ralph Rivera and Adrian Woolard, James Thornett and Clare Hudson.

During the day, there was expert advice available, formally at Speakers’ Corner and informally via conversation. This covered a wide range of topics including Simon Williams on audiences, Tim Fiennes on market analysis, Tom Broughton on homepage technology, Steve Gibbons on user experience and Phil Poole on personalisation.

Following this there was time to work on concepts and plan presentations, including a very useful audience feedback session with some real users of the BBC home page.

At the end of the day there were just over 20 open public pitches and 9 closed private pitches (those with sensitive intellectual property rights). I teamed up with Nick Drummond (of ATilla the AT-AT pet fame) to pitch an idea called Show Me More – providing links to BBC content directly on the home page (bbc.co.uk).

What worked well

The event went well, especially since this was the first one of the series. The audience feedback sessions and speakers corner were well organised and well attended. Whatever the outcome, this was a good opportunity to bid for work, see what goes on at the BBC and meet some of the people behind the BBC online. There was lots of advice available on how to work up a pitch, the audience was friendly and respectful. It was enlightening to watch other people’s presentations. The fifth floor of Quay house at MediaCityUK (pictured above) is an ideal venue for this kind of event with lots of different sized spaces for collaborating, thinking, eating, drinking and enjoying the fine views of Manchester from an elevated perspective.

How it could be improved

There was (inevitably?) a fair amount repetition in the 20 pitches as everyone was pitching to the same brief. It might be better next time to have fewer pitches and encourage people to work in slightly larger groups and reduce duplication. You can’t say very much in two minutes but perhaps that’s the idea…

As an aside, I’d love to see a public open API to BBC content, as far as I know there isn’t really one (yet). An open API would allow innovation by opening up content and services to organisations and businesses outside the BBC. Something along the lines of the Twitter API, Flickr API or Google Maps API would be great. An API seems to fit squarely with the needs of it’s constitution as a public service broadcaster. I asked about this at Speakers’ Corner and on twitter (speakers’ corner of the interwebs). There are security issues (as usual) but:

I think there might be a BBC SPARQL endpoint somewhere (there certainly used to be), which is an API of sorts but can’t find the exact location at the time of posting this.

All in all, BBC Connected Studio was informative and fun, thanks to Adrian Woolard and everyone at the BBC for your excellent hospitality. If you’re interested in taking part, it’s well worth joining in.

How to get involved

If you’d liked to get involved in BBC Connected, there are various events scheduled in 2012 on different products at the Beeb including: Weather & Travel, CBeebies, UX&D, CBBC, Sport, TV / iPlayer, News, Knowledge & Learning, Radio & Music. For more info subscribe to the BBC Internet blog, follow tweets @BBC_Connected or visit BBC Connected Studio.

July 27, 2010

Twenty million papers in PubMed: a triumph or a tragedy?

pubmed.govA quick search on pubmed.gov today reveals that the freely available American database of biomedical literature has just passed the 20 million citations mark*. Should we celebrate or commiserate passing this landmark figure? Is it a triumph or a tragedy that PubMed® is the size it is? (more…)

July 6, 2009

Ship-shape and Banksy Fashion

Filed under: web — Duncan Hull @ 9:07 am
Tags: , , , , , ,

Britannia Rules the CCTV

Graffiti artist or blogger?

So I was passing through Bristol the other day, a fine city that has given the world many things. Perhaps one of the best known (apart from the trip-hop and slavery) is the renegade graffiti artist called Banksy who during July and August has an exhibition of work on at the Bristol City Museum and Art Gallery. This show is well worth a visit – take a look at banksy.co.uk and the links below for a taster. A book of Banksy’s work also has plenty of thought provoking content in it, not least, a quote from the artist on where to publish:

A wall has always been the best place to publish your work.

To my mind the worlds of graffiti and blogging have much in common. As art forms, they both have a low barrier to entry – all you need is a can of spray paint – or an internet connection. Both blogging and graffiti are often frowned on by The Establishment™. Some of this is probably due to the highly variable quality of blogs and “street art” but when they are done well, they are both worth paying attention too. Last but not least, the Web is like a big public wall where pretty much anyone can scribble, spray and scrawl anything they like, which can be powerful stuff. As one graffiti artist once put it – the can is mightier than the sword – and the Web is mightier than the sword too.

The mighty exhibition Banksy vs. The Museum has been incredibly popular and a huge success, with large queues every day especially at weekends. So if you’re interested in going, get there ship-shape, Bristol fashion and early before it opens at 10am each day and finishes on 31st August 2009.

[Britannia Rules the CCTV above - one of the works from the exhibition by Banksy]

References

  1. Banksy (2006) Wall and Piece (isbn:1884137872)
  2. Miranda Sawyer (2009) Review of Banksy at Bristol City Museum (The Guardian)
  3. Serena Davies (2009) Review of Banksy versus The Museum (The Daily Telegraph)
  4. BBC News (2009) In pictures: Banksy’s Bristol Show
  5. Ship-shape and Bristol Fashion means “in first class order” according to phrases.org.uk

September 5, 2007

WWW2007: Workflows on the Web

Don't PanicThe Hitch-hiking novelist Douglas Noel Adams (DNA) once remarked that the World Wide Web (WWW) is the only thing whose shortened form – ‘double-you double-you double-you-dot’ – takes three times longer to say than what it’s “short” for [1]. If he were still with us today, there is plenty of stuff at the 16th International World Wide Web conference (WWW2007), currently underway in Banff, that would interest him. Here are some short, abbreviated notes on a couple of interesting papers at this years conference. They are relevant to bioinformatics and worth reading, whichever type of DNA you’re most interested in.

One full paper [2] by Daniel Goodman describes a scientific workflow language called Martlet. The motivating example is taken from climateprediction.net but I suspect some of the points they make about scientific workflows are relevant to bioinformatics too. Just like the recent post by Boscoh about functional programming, the paper discusses an inspired-by-Haskell functional approach to building and running workflows. Comparisons with other workflow systems like Taverna / SCUFL are drawn. Despite what they say, Taverna already uses a functional model (not an imperative one), it just hasn’t been published yet. The paper also draws comparisons between Martlet and other functional systems, like Google’s Map-Reduce. It concludes that the (allegedly) new Martlet programming model “raises the interesting possibility of a whole set of new algorithms just waiting to be discovered once people start to think about programming in this new way”. Which is an exciting possibility.

Another position paper [3] (warning: position paper = arm waving) by Anupriya Ankolekar et al argues that the Semantic Web and Web-Two-Point-Oh are complementary, rather than competing. Their motivating examples are a bit lame (Blogging a movie? Can’t they think of something more original?) …but they make some interesting (and obvious) points. The authors think that aggregators like Yahoo! Pipes! will play an important role in the emerging Semantic Web. Currently, there don’t seem to be too many bioinformaticians using Yahoo! pipes, perhaps they just don’t share their pipes / workflows yet?

Running in parallel to all of the above is the Health Care and Life Sciences Data Integration for the Semantic Web workshop, where more detailed discussion on the bio semweb is underway. As its a workshop, there are no full or position papers, but take a look at The State of the Nation in Life Science Data integration to get a flavour of what is going on.

Wether functional, semantic, Web-enabled or just buzzword-friendly, there is plenty of action in the scientific workflow field right now. If you’re interested in the webby stuff, next years conference, WWW2008, is in Beijing, China. I wonder if they will mark the 10th anniversary of the publication of that Google paper at WWW7 back in 1998? The deadline for papers at WWW2008 will probably be sometime in November 2007, but around 90% of submitted papers will be rejected if previous years are anything to go by. If you’re thinking of doing a paper, DON’T PANIC about those intimidating statistics, because bioinformatics is bursting full of interesting and hard problems that challenge the state-of-the-art. The kind of stuff that will go down well at Dubya Dubya Dubya.

(Photo credit: Fire Monkey Fish)

References

  1. Douglas Adams (1999) Beyond the Brochure: Build it and we will come
  2. Daniel Goodman (2007) Introduction and Evaluation of Marlet, a Scientific Workflow Language for Abstracted Parallelisation doi:10.1145/1242572.1242705
  3. Anupriya Ankolekar, Markus Krotzsch, Thanh Tran and Denny Vrandecic (2007) The Two Cultures: Mashing up Web 2.0 and the Semantic Web doi:10.1145/1242572.1242684


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November 7, 2006

People 2.0: Pioneers of the next generation Web

UK news-rag The Grauniad has a series of interviews with some of the people behind the next generation web, so-called Web 2.0. After reading these interviews, I can’t help wondering, who are the equivalent pioneers in bioinformatics?

The interviews include…

  1. Wikipedian Jimmy Wales
  2. WordPresser Matt Mullenweg
  3. Technorati’s Dave Sifry

…and several others too. Most of the interviews are worth reading, I particularly enjoyed Mullenweg’s which contains a wonderful quote:

Q: What is your big idea?

A: I don’t have big ideas. I sometimes have small ideas, which seem to work out.

So who is currently pioneering the “Web of Science”, Bioinformatics 2.0 if you like? Ensemblian Ewan Birney? Ian Holmes at Berkeley? Or somebody else?

[Image credit: Picture from Steve Jurvetson, this post originally published on nodalpoint with comments]

November 1, 2006

Bioinformatics Impact Factors

B of the Bang (in Big Bangchester)There are all sorts of flaws with using impact factors for judging the quality of biomedical research. Love them or hate them, just getting hold of impact factors for journals in bioinformatics and related fields is much harder than it should be, so I thought I’d reproduce some statistics I gathered here. The rankings, which you should use with caution [1,2], are correct as of June 2006 (and apply to citations in 2005) courtesy of Journal Citation Reports®, part of Thomson ISI Web of Knowledge. JCR has a pretty horrible clunky web interface when compared to some of its rivals [3,4], maybe one day they’ll make it better. Anyway, this is not a comprehensive list, just a fairly random selection of bioinformatics and computer science journals that publish articles I’ve been reading the last few years.

Journal ISI impact factor
Science 30.927
Cell 29.431
Nature Reviews Molecular Cell Biology 29.852
Nature 29.273
Nature Genetics 25.797
Nature Biotechnology 22.378
Nature Reviews Drug Discovery 18.775
PLOS Biology 14.672
PNAS 10.231
Genome Research 10.139
Genome Biology 9.712
Drug Discovery Today 7.755
Nucleic Acids Research 7.552
Bioessays 6.787
Plant Physiology 6.114
Bioinformatics (OUP) 6.019
BMC Bioinformatics 4.958
BMC Genomics 4.092
Proteins: structure, function and bioinformatics 4.684
IEEE Intelligent Systems 2.560
Journal of Computational Biology 2.446
Journal of Biomedical Informatics 2.388
IEEE Internet Computing 2.304
Artificial Intelligence in Medicine 1.882
Comparative and Functional Genomics 0.992
Concurrency and Computation: Practice and experience 0.535
Briefings in Bioinformatics (OUP) not listed
PLOS Computational Biology not listed
Journal of Web Semantics not listed

One point of interest, cheeky young upstart BioMed Central Bioinformatics (going since 2000) seems to be catching up on traditional old-school favourite OUP Bioinformatics (going since 1985), which as mentioned on nodalpoint, has been publishing some dodgy parser papers lately.

May 24, 2006

Dub Dub Dub 2006

WWW2006
The 15th International World Wide Web conference is currently underway in Edinburgh, Bonny Scotland. As usual, this popular conference has some good papers, only 11%* of submissions are accepted. One particular paper caught my eye: One Document to Bind Them: Combining XML, Web Services, and the Semantic Web. This paper has probably been selected because it will wind people up (sorry I mean “spark a debate”) so its an entertaining and sometimes enlightening read.

In this paper, Harry Halpin and Henry Thompson make some observations about the state of the web in 2006:

But, according to the authors, it doesn’t have to be this way…

  1. Many (but not all) web services are functions that are available on the web,
  2. The semantic web gives us an elaborate type system, using ontologies, which can extend what we already have with XML Schema
  3. The combination of the first two, gives us Semantic Web Services which are typed functions. This allows us to invoke web services not just by their URI (e.g. http://xml.nig.ac.jp/xddbj/Blast for a Blast service), but by the type of information they have. E.g. you have an output of type BLAST_report or perhaps InterProScan_report, what services will take this as input? What operations can be performed on this data? This sounds a lot like BioMOBY, with bells on.

What Harry and Henry propose is tying all this together using a single XML vocabulary, called Semantic fXML, to put “a unified abstraction of data, types and functions” so that the web can compute. This is all a bit pie-in-the-sky vision of the future stuff, but what might it mean for your average bioinformatican? It would be seriously useful if we could make the current molecular biology web services easier to use, but agreeing on and using an ontology for annotating the types of the inputs and outputs of all the services is non-trivial task. Bioinformaticians already have a (somewhat limited) universal type system for describing all data in bioinformatics, its called string. Persuading them to use something more powerful is not easy unless the benefits are immediately obvious.

At the moment, it is difficult to tell if sfXML will ever have any impact on bioinformatics but who cares? Despite this, the paper is enjoyable reminder of what is interesting about services on the Web. They transform the web from a place where we can merely search and browse for data (sequences, genes, proteins, metabolic pathways, systems etc), into “one vast de-centralised computer” a bit like the one described in can computers explain biology? This, in my humble opinion, is what makes the web and bioinformatics an exciting place to work in 2006.

* Footnote: Of nearly 700 papers submitted: only 81 research papers were accepted (11%). This is a 25% increase on the number of submissions last year to www2005 in Chiba, Japan.

References

  1. Harry Halpin and Henry S. Thompson (2006) One Document to Bind Them: Combining XML, Web Services, and the Semantic Web in Proceedings of the 15th international conference on World Wide Web, Edinburgh Scotland DOI:10.1145/1135777.1135877
  2. This post originally published on nodalpoint with comments

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