1. Science and the Web Simon Cockell (@sjcockell) Bioinformatics Support Unit (@nclbsu) http://bsu.ncl.ac.uk/ simon.cockell@newcastle.ac.uk

2. 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

3. Yes, this really was the view of the world’s sequence databases that we used to have!

5. 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.*

6. 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’

7. 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

8. And so Web 1.0 began We got used to: Online shopping Having a homepage Getting our news online Guestbooks on websites Animated GIFs Wonderful colourschemes:

9. So wtf is Web 2.0? 20% marketing nonsense to attract investors 20% buzzwords designed to annoy old people ‘mashup’ etc 10% missing vowels & capitalisation flickr, tumblr 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’

10. Concepts One of the social concepts most people are familiar with now is tagging: And the ubiquitous upvote:

11. How can we take this out of Facebook and into science?

12. Tagging is very useful Search and retrieval tool Can be applied to just about anything 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”

13. 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/http://delicious.com/ See also: diigo.com pintrest.com

14. delicious.com

15. Scientific Literature Scientific papers are as amenable to bookmarking as websites Needs specialized service http://pubmed.org/22522561http://dx.doi.org/10.1038/nm.2692 http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.2692.html

16. CiteULike A social bookmarking service for scientific literature Exactly like Delicious, but understands that different URLs can point to the same resource Allows you to exploit “network effects” Someone who reads lots of the same papers you do is probably interested in the same things They may have papers in their library you don’t know about You may be interested in those papers too

17. CiteULike

18. Mendeley Similar service to CiteULike Bookmark papers Define folksonomy Discover related literature Also – Manages PDFs Manages citations (plugins for Word etc) See also: Zotero (http://zotero.org)http://zotero.org Papers (http://mekentosj.com/papers)http://mekentosj.com/papers

19. Mendeley - App

20. Mendeley - Web

21. Mendeley - Citations

22. We have a data overload How can you define what is important? And how can you deal with it subsequently?

23. Knowledge Discovery 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’

24. RSS

25. Who has RSS? You can have RSS feeds from Journal publishers Search results (PubMed) Blogs CiteULike, etc. Actually just about any dynamically updated web resource. RSS is everywhere Pervasive, Useful, Centralised, Shareable

26. FOAF and Network Effects Already mentioned re: CiteULike FOAF = Friend Of A Friend Requires a network (obviously) Can be of things (ie papers) or people Have been loads of attempts to build ‘Facebook for Scientists’ Begs the question – how about Facebook?

27. On the (awesome) power of Twitter

29. Q&A Concept dates back to internet dark ages ‘Usenet’ groups, revolved around specific subject areas With the birth of the web, ‘forums’ proliferated Usability nightmare, hard to navigate, harder to search Then came expertsexchange.com That’s Experts Exchange dot com, not Expert Sex Change dot com Pay people to answer specific queries Results in *bad* content (people care about the money, not the content) Then came stackoverflow.com...

30. Stack Overflow

31. Stack Exchange

32. biology.stackexchange.com

33. academia.stackexchange.com

34. An example - BioStar

35. Half an hour later...

36. Online Collaboration (crowd sourcing)

37. Sharing your work Everything so far has been about sharing knowledge Things you read Things you’ve seen Things you know Some people go further and share all their work So-called ‘Open Science’ While this is an extreme, it can have benefits Some aspects of open science are becoming mainstream Open Access publishing Data sharing (now required by many funding bodies)

38. #arseniclife

39. If this data was presented by a PhD student at their committee meeting, I'd send them back to the bench to do more cleanup and controls. “

40. #arseniclife

41. Open Access publishing 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

42. “ Increasing pressure to share data BBSRC expects research data generated as a result of BBSRC support to be made available with as few restrictions as possible in a timely and responsible manner to the scientific community for subsequent research. Applicants should make use of existing standards for data collection and management and make data available through existing community resources or databases where possible. http://www.bbsrc.ac.uk/organisation/policies/position/policy/data-sharing-policy.aspx

43. Data Sharing Many services for specific data types GEO/ArrayExpress for microarrays PRIDE for proteomics SRA for high-throughput sequencing Also now facilities to share more generic research data: FigShare

45. 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

46. Your online “brand” In this day and age a future employer is going to Google you Own what Google “says” about 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 Be consistent and professional in your online ‘persona’ You might want to have a look at what your Facebook profile exposes to the world - it may be more than you think LinkedIn is a great place for an online CV and networking

47. Things we haven’t had time for... Loads more useful sites and services: Nature Network OpenWetWare LinkedIn SlideShare Prezi BioScreenCast Google Plus/Groups/Docs DropBox ResearchBlogging