Science and the Web
Daniel Swan
Bioinformatics Support Unit
(http://twitter.com/nclbsu)
d.c.swan@ncl.ac.uk (http://twitter.com/d_swan)
(yes, even Twitter is a useful scientific tool!)
In the bad old days
 There was the internet
 But there was no web 
 No Facebook
 No iPlayer
 No Spotify
 No Google
 But we still managed to use it for awesome
science
 Yes, this really was the view of the worlds
sequence databases that we used to have!
But we had social resources
 Email newsgroups
 MUDs (kind of like a text only Second Life)
 Usenet Newsgroups
 A kind of forerunner of today's message boards
 Often un-moderated
 Full of spam
 All the science stuff of interest was under bio.* or sci.*
How the web was won
 The internet has been designed by scientists for
scientists pretty much since inception
 The internet ‘as we know it today’ arrived in the
1990s
 OK that’s just not true, but it’s what most people
associate with the internet
 Aka ‘The Web’
And this WAS about science
 (Sir) Tim Berners-Lee is a scientist
 The World-Wide Web (W3) was developed to be
a pool of human knowledge, which would allow
collaborators in remote sites to share their ideas
and all aspects of a common project
 Data, and pages could be linked together for
the first time with images, sounds, text
 As the data grew, it needed to be searched
 Search engines collated the data
And so Web 1.0 begun
 We got used to:
 Online shopping
 Having a homepage
 Getting our news online
 Guestbooks on websites
 Animated GIFs
 Wonderful colourschemes:
So wtf is Web 2.0?
 30% marketing nonsense to attract investors
 20% buzzwords designed to annoy old people
 ‘mashup’ etc.
 50% useful
 Specifically refers to ‘user generated content’
 High availability and access to data
 Networks of people and network effects
 Openness
 Tapping into the ‘wisdom of the crowds’
Concepts
 One of the social
concepts most
people are familiar
with now is tagging:
 And the ubiquitous
upvote:
How can we take this out of
Facebook and into
science?
We have a data overload
 How can you define what is important?
 And how can you deal with it subsequently?
Tagging is very useful
 Search and retrieval tool
 Can be applied to just about anything
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Browser bookmarks
Uploaded YouTube videos
Academic Papers
Uploaded Powerpoint presentations
And most importantly they can be SHARED with other
users
 We call these tags ‘folksonomies’
 “a system of classification derived from the practice
and method of collaboratively creating and managing
tags to annotate and categorize content”
Social bookmarking
 If you’re going to share your folksonomies, why
not share your bookmarks too?
 Maybe you don’t want to share everything you
have bookmarked in your browser…
 But what about the stuff that’s related to work?
 Many services exist for this, but the one that most
people know about is http://delicious.com/
Why share?
 Well you might as well ask
 Why go to a conference?
 “At a conference the most important things
happen in the coffee break” – Hans Ulrich Obrist
 Why talk to colleagues?
 The internet doesn’t have to be a distraction, it
can be an extension of your peer group. A
place to find and exchange relevant
information, build your profile and do your job
more efficiently
Case study 1: Publications
 Most people’s workflow for papers consists of

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

Download
Print
Stick in directory called ‘Papers’
Forget
 Maybe it might make it into Endnote!
 However online… you can do so much more
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Connotea
Cite-U-Like
Mendeley
Zotero
Connotea
Cite-U-Like
Mendeley
Zotero
Case study 2 – finding things
 No, not via Google
 One of the issues of information overload is
having to go to multiple sites in order to collate
the day to day information you might want to
read
 This is already a solved problem
 RSS
 ‘Really Simple Syndication’
Who has RSS?
 You can have RSS feeds from
 Journal publishers
 Search results
 Blogs
 Connotea, Cite-u-like, etc.
 Actually just about any dynamically updated web
resource.
 RSS is everywhere
 Pervasive, Useful, Centralised, Shareable
Case study 3 - presentations
 Even the humble Powerpoint slide has gone all
Web 2.0
 Scientists give talks, upload their slides
 Feedback given
 Even if you don’t share, it can be good to
consume
 Get ideas for presentations, formats etc.
Case study 4 – your work
 Yes, you can even share some of your work
 Protocols, early results, triumphs and tribulations
 Some scientists, keen to move from Web 2.0 to
Science 2.0 are using blogs, wikis and the internet
to publish their information outside of the limited
sphere of journals
 One of the largest sites for this in the world is
OpenWetWare
Science – being Open
 Already noted that biologists are good at openly
sharing primary data, in increasingly standardised
databases
 DNA sequence, protein sequence, microarray
experiments
 Increasingly happening with publications too
 PLoS (Public Library of Science) and
BioMedCentral (BMC) are two big players
 Rather than charging users for subscriptions, the
authors 'pay to publish'
Why is Open good?
 Your work is not behind a 'paywall'
 It can be very frustrating trying to get hold of papers
from journals or publishers that the University does
not have a site licence for
 Your work can be more widely read
 Hard to argue that this is not desirable!
 The full text of your article is preserved and can
even be analysed computationally to derive
even more knowledge
Publishing and Web 2.0
 Many publishers now offer the ability to comment
and ask for clarification on papers, especially in
the Open Access journals
 Authors can respond to comments and issue
rebuttals at the site the paper is downloaded
 Increases discourse on published papers, which is
very hard to do in a paper journal
 Certain publishers are building up quite
significant social networks around their published
content. Nature Group in particular with their
'Nature Network'
I can't keep track of it all!
 As we have alluded to already it's hard to keep
track of all the data that is out there and
available
 Whilst we can have email alerts and RSS feeds,
the issue is often one of separating out the signal
from the noise
 Whilst a regular review of the sources you take in
is a good way to do this there are other ways to
try and filter out what is coming to you
FOAF approaches
 FOAF is 'friend of a friend' – the online equivalent
of having someone come up and tell you about
a cool paper they have just read – or someone
has just told them about that might interest you.
 The success to FOAF approaches is being in the
right setting so that you are interacting with the
right set of people
 There have been many MANY attempts to build
'social networking for scientists'
 I'm only going to present one, and that's the one
that currently works for me
FriendFeed
 Friendfeed is like Google Reader, it sucks in RSS you generate
or pull in
 This display is updated in real time
 For instance I import - Cite-U-Like, Google Reader 'shared
items‘, activity on software development sites, Flickr photos
 They appear in everyone who has subscribed to me – a la
Twitter, only with threaded discussions where things percolate
up to the top the more they are 'liked' or discussed
 There 'rooms' that you can subscribe to where you will also
get content from on specific topics
 This is a GREAT way of seeing what other people are reading,
watching, viewing, talking about – and in a way that you can
leap right in and start discussing it with them.
Crowdsourcing & collaboration
 One of the coolest things I have seen FriendFeed
used for is 'crowdsourcing'
 This is where someone posts up a request for help,
and the community jumps in to help out
 Virtual collaborations spring up around the
community, from people who have never met
each other, and yet result in real scientific
publications
 Don't be afraid to ask for help online, and don't
be afraid to offer it either
Postgenomic – blog filter
From consumer to publisher
 The essence of Web 2.0 is that you provide the
content
 Whether you're uploading a video of an
experimental technique
 Whether you're releasing your slides onto
Slideshare
 Whether you're sharing what you're reading on
Connotea
 YOU are generating the content
Why should I produce content?
 It's a valid question
 Why should I blog?
 My blog is a mix of the personal and of work – that is
my decision
 Many people just blog about their work, on the
assumption your work life and your private life should
be kept very separate
 I think this is increasingly hard to do
 As soon as you have work colleagues and friends
mixed up on Facebook or Twitter, or whatever other
social networks you used the streams are polluted
Blogging work
 Blogging provides an opportunity to hone your writing
skills, rarely troubled outside of writing papers, end of year
reports and a thesis
 Sharpen your analytical skills by posting about the papers
your presenting at your lab meetings, and use
http://ResearchBlogging.org to reach an audience
 Part of your network building activities
 It's a continually updating, evolving CV – marketing YOU
 It helps you build a brand
 It gets your name up there in Google
 All of these are 'informal esteem factors'
Case study 5: Allyson
 Allyson adopted the following technologies as part of
her social workflow – blog, twitter, FriendFeed
 She started to attend conferences and blogged the
talks, which fed into FriendFeed
 People on FriendFeed appreciated being kept up to
date, and she became well known for it
 She has published 3 papers on using Web 2.0 to cover
conferences
 She has been paid for to fly to the USA and attend
conferences
 EVERYONE in her field, and some beyond – knows who
she is and this is PRICELESS
Why should I care?
 I heard a question on a podcast recently, that someone
who had published some stuff online in earlier, more
headstrong times that were now at the top of Google
wanted to know what the best way was to push this out of
Googles memory (off the front page effectively!)
 The suggestion was to generate content – good content
with your name attached, content that people want to
read, and enough of it to ensure that you come up top
every time on searching for your name
 What happens if someone decides to bad mouth you
online in the future?
 Just make sure they don’t have enough Google traction to
care
My experience
 Two years ago the first thing you got when googling my
name was an entertaining set of news stories about a
racist, redneck called Daniel Swan who had, in a drunken
state one evening, decided to plant a giant burning cross
in the front garden of a black family in his neighbourhood
 For various litigious reasons, his conviction was overturned
and his stupid grinning face was on every page you hit,
baseball cap on and leaning on his pickup
 2 years later, and the only person you will hit on the front
page is me and my grinning face instead – just regular
online interaction and content production means that I
get found first when my name is Googled
Your online brand
 As I alluded to earlier if you're going to publish content, in
this day and age a future employer is going to Google
you
 What you say and do in public forums is a matter of public
record, it’s ok to engage and discuss, but be wary of
getting mad
 You might want to have a look at what your Facebook
profile exposes to the world. It may be more than you
think.
 Whilst FB has many scientific groups, I don't think it's a
great platform for scientific discussion. Best to keep your
most personal life there, and your professional life
elsewhere.
 LinkedIn is a great place for an online CV and networking
LinkedIn
Licensing your content
 OK this is a dry topic and I won't go into it in too much detail
 Make sure that when you produce content online you state
which licence it is under
 I would advise people to look into Creative Commons
licencing for blog posts or anything extensive that you have
written and posted online
 Clear guidelines on what to use so that you can control
downstream what people do with your work
 Otherwise people may not have the right to reuse, redistribute
your work, or at the worst, will have the right to do so, but
won't have the requirement to credit you for it
 And you do want to be credited for your work!
In summary
 Please do share and tag your content with the world
 Think about how you can use the tools that are out there
to support your scientific workflow, so that the data is
there for YOU when YOU need it most
 Try to seek out like minded people in your field online and
interact with them, the University isn't your scientific world
– the world is your scientific world!
 Consider publishing your work in open access journals to
widen its readership
 Build a recognisable, trusted and centralised online
identity so when a potential employer starts to search for
information about you what comes back is positive,
intelligent and encouraging!
URLs

Delicious (social bookmarking) http://delicious.com/

JoVE (Journal of Visualised Experiments)
http://www.jove.com/
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Connotea (social reference manager)
http://connotea.org/
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PLoS (Open Access journal) http://www.plos.org/

Cite-U-Like (social reference manager)
http://www.citeulike.org/

BioMedCentral (Open Access journal)
http://www.biomedcentral.com/

Mendeley (social reference manager)
http://www.mendeley.com/

Nature Network (aggregation, scientific social
networking) http://network.nature.com/

Zotero (research tool, reference manager)
http://www.zotero.org/

FriendFeed (aggregation, scientific social networking)
http://friendfeed.com/

Google Reader (RSS reader) http://reader.google.com/ 

SlideShare (share Powerpoint slides)
http://www.slideshare.net/

ResearchBlogging (scientific blog aggregation)
http://www.researchblogging.org/
BioScreenCast (share videos on scientific software)
http://bioscreencast.com/
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LinkedIn (your online CV) http://www.linkedin.com/
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CreativeCommons (licensing online content)
http://creativecommons.org/
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OpenWetWare (protocols, lab wikis and more)
http://openwetware.org/wiki/Main_Page
Postgenomic (scientific blog aggregation)
http://www.postgenomic.com/