The document discusses various Web 2.0 technologies used for scientific collaboration and knowledge sharing, including blogs, wikis, and social bookmarking services. It provides examples of blogs in specific scientific fields like fungal genomics. Wikis are discussed as ways to collaboratively annotate genomes and organize laboratory information. Social bookmarking services like Connotea, CiteULike, and del.icio.us allow scientists to bookmark and tag web resources and publications for sharing.

1. Web 2.0 e ricerca
(Giovanni M. Dall'Olio – raduno molecularlab 2008)

2. Cosa é 'Web 2.0'?
•
Blogs
•
Rss Feeds
•
Wikis (wikipedia)
•
Social Bookmarking (del.icio.us)
•
Multimedia­sharing systems (Youtube ­> videos,
Flickr ­> photos, last.fm ­> music, ..)
These and others are called 'Web 2.0
Technologies'[1]

3. What is 'Web 2.0' ?
The common point in all web 2.0 technologies is
that they help people in sharing informations
and opinions.
●
Scientists also need to share and exchange their
informations and opinions[2].
●
Let's see a few examples of some of the Web 2.0
applications actually used in the scientific
community.

4. I - Blogs

5. I - Blogs
●
I blog sono l'equivalente di un diario personale, reso
pubblico su Internet.
●
Ognuno é libero di scrivere quello che vuole nel proprio
blog: storie personali, opinioni, etc.. [3]
●
Recentemente si sono diffusi i blog a contenuti
tecnico, in cui vengono trattati argomenti tecnici
anziché personali.
●

6. The fungalgenome.org Blog
●
fungalgenome.org é un blog sui funghi e sulla
genetica dei microrganismi unicellulari[5]
●
Ogni settimana gli autori postano qualche notizia su
questo campo: commentano un articolo pubblicato,
[6]
o una scoperta recente, etc.. .
●
Può essere più semplice tenersi aggiornarti sulla
genetica de funghi in questo modo, piuttosto che
seguire le riviste specializzate.

7. the fungalgenome.org Blog
(http://www.fungalgenome.org/blog)

8. programming4scientists.com
●
Blog di
bioinformatica,
programmazione per
scienziati
●
L'autore fornisce
consigli e tutorial su
come programmare,
per scienziati

9. Nature Blogs
●
Nature ha messo su
una rete di blogs
dedicati a
neuroscienze,
tecnologia, virologia,
genetica, etc..

10. Nascent
●
Blog sulla tecnologia
web appartenente al
circuito di Nature

11. II - Wikis

12. II - Wikis
●
A wiki is a website that
allows visitors to add,
remove, and otherwise
edit and change
content.
●
Like Wikipedia (
http://en.wikipedia.org
[7]
)

13. Wikipedia
(http://en.wikipedia.org)

14. Build your Lab's Wiki
●
The software that run wikipedia is called
MediaWiki and is released under a free license.
[8]
●
This means you can download it (the templates
of the wiki without its contents) to use it for
your own purposes.
●
So you can create a website with the same
functionalities and interface of wikipedia, but
with your own content.

15. Build your own wiki - examples
(Alternative Splicing Wiki[9])
Alternative splicing
analysis tools
Articles Databases
(This is a wiki I use on my laptop to organize my work about alternative

16. Build your own wiki - examples
(appunti di bioinformatica libera[10])
(http://bioinformatici.org/appunti - a wiki by some Italian students of

17. Wiki Technology in
Bioinformatics: Examples (I)
●
openwetware (http://openwetware.org) is a huge
wiki created in 2005 in the MIT institute, which
collects protocols, resources, courses, discussions,
about wet biology and bioinformatics research.
●
the annotation of 12 drosophila spp genomes has
been done by wiki (
http://rana.lbl.gov/drosophila/wiki/)
●
There have been some discussions about the use of
wikis to improve genome annotation (
2 articles on Nature, and on nodalpoint [11])

18. OpenWetWare
Resources (tutorials,
etc..)
Labs' home pages
Protocols (How to
make a PCR, how to
design primers, etc..)
(http://openwetware.org)

19. AAAWiki
(Annotation of 12 Drosophila spp genomes)
Announcements
Data
Papers
(http://rana.lbl.gov/drosophila/wiki/

20. Wiki Technology in
Bioinformatics: Examples (II)
●
WikiOmics (http://wikiomics.org) is a wiki for
the bioinformatics community, providing
tutorials and reviews.
●
Manatee (http://manatee.sf.net) is a genome
evaluation/annotation tool which allows
scientists to make functional assignments on
genes and sequences.
●
GenBank (
http://www.ncbi.nlm.nih.gov/Genbank/TPA­Inf
) offers a system to submit third­party
annotation to sequences)

21. WikiOmics
(wikipedia for bioinformaticists)
(http://wikiomics.org)

22. Wiki Technology in
Bioinformatics: Examples (III)
●
GONUTS (http://gowiki.tamu.edu/GO/wiki/) is a
wiki to provide third party annotation and
documentation to the GeneOntology (GO) terms.
●
EcoliWiki (http://ecoliwiki.net/colipedia/) is a
prototype of a wiki to annotate E.coli genome and
metabolic network.
●
The Fungalgenome website (
http://fungalgenome.org/wiki/ ) also has a wiki
to organize fungal genomes annotation.
●
The SynapticLeap (http://thesynapticleap.org/)
hosts some research communities.

23. Wiki Technology in
Bioinformatics: Examples (IV)
●
WikiReviews (http://tinyurl.com/26c6m8) at
OpenWetWare is to provide comments on
reviews.
●
The Saccharomyces Genome Database (
http://yeastgenome.org) has just started a wiki
for the community working on yeast (
[12]
http://wiki.yeastgenome.org/) .
●
BioWiki (http://biowiki.org) hosts other
bioinformatics projects.
●
WikiSurgery (http://www.wikisurgery.com/) is a

24. FungalGenome Wiki
Projects -
descriptions
Protocols
(http://fungalgenome.org/wiki)

25. III - Social-Bookmarking

26. III - Social-Bookmarking
● Social Bookmarking means:
– When I find an interesting website/article/document, I
share its address with other people – or with the other
members of the lab(s)[13];
– Other people can add their comments and tags to it;
– Eventually a third person can be in charge of organize
and curate those collections of bookmarks.

27. Social Bookmarking in Science
●
The most used services are:
– del.icio.us
– Connotea
– CiteULike
– Hubmed (Tags system)[14]

28. del.icio.us
●
It is the most known Social Bookmarking
Service.
●
It is not designed to manage publications, only
bookmarks.
●
Easy to configure and use (firefox/epiphany
extension)
●
Some scientists use it to bookmark RSS feeds
from connotea or pubmed/hubmed searches or
from other scientific websites[15].

29. Social Bookmarking – how does
it work?
●
You have to register to the website which offers
the social bookmarking service (e.g.: del.icio.us,
connotea, etc..)
●
you need to configure your web­browser, by
adding a special button to it (some firefox
extensions facilitate this)
● When you find an interesting article, you click on
that button and follow the instructions.
● Bookmarks are saved in a webserver (a publicly
accessible computer), where they are accessible to
everyone you allow.

30. Social Bookmarking in Science:
Connotea
●
Connotea is an online social bookmarking
service for scientists created by Nature
Publishing Group.
●
It allows to post articles as well as web
documents.
●
It automatically recognizes metadata like title,
author, abstract, when posting an article.
●
Slightly more difficult to configure and use (no
firefox extension)[16].

31. Connotea: Screenshots (I)
(main page)
(http://www.connotea.org)

32. Connotea: Screenshots (II)
(searching for tags)
Search Interface
Search Results
(http://www.connotea.org/search?q=%22alternative+splicing%22)

33. Connotea: Screenshots (III)
(posting an article)
(http://www.connotea.org - note the automatic recognition of title and authors.)

34. Social Bookmarking in Science:
CiteULike
●
CiteULike is another social
referencing/bookmarking tool for scientists.
●
It's not opensource, but it's not related to any
publishing group (e.g.: Nature).
●
Like Connotea, it allows to navigate into tags
and people, to import/export references in
BibTeX, etc..
●
CiteULike and Connotea have different databases
and users[17].

35. CiteULike: Screenshots (I)
(searching between tags)
(http://www.citeulike.org/

36. Connotea: Screenshots (II)
(posting an article)
(http://www.citeulike.org/ - note the automatic recognition of title and authors.)

37. IV Scientific Communities

38. Comunità scientifiche
●
Una comunità online é un luogo in cui ogni
utente é distinto da un proprio profilo
personale.
●
Esistono anche esperimenti di comunità
scientifiche, che si rifanno a facebook/myspace/
etc.

39. myExperiment
●
Su myExperiment I
ricercatori possono
mettere in
condivisione i loro
protocolli
bioinformatici
●
Scarica la sequenza
da ncbi ­> lancia blast
­> prendi i 10
migliori risultati ­>
etc...

40. Esempi di workflow da
myExperiment

41. Second Life
●
'Second Nature' é una
comunità scientifica
basata su Second Life,
un gioco multiplayer
online.
●
Si organizzano
conferenze ed
esposizioni virtuali, e
si può discutere con
altri esperti.

42. Molecularlab :)
●
Non esistono molte
comunità/forum
scientifici attivi
●
Molti sono semi­
abbandonati o con
poca frequenza
●
A volte si preferiscono
le mailing list

43. Scivee,

44. V - RSS Feed

45. V - RSS Feed
●
RSS Feeds are an instrument used by
webmasters to notify users about changes into
their website[18].
●
Imagine an online newspaper site: users can use
rss feeds to be notified when a new article
appears.
●
Rss Feeds can be also used to track new articles,
new results from a pubmed/hubmed search,
new blog posts, and so on.

46. how do I use Rss Feeds? I/II
●
When you see this symbol:
on a website, it means it offers rss feeds.
●
You can click on it and follow the instructions to
subscribe to the site's rss feeed.

47. how do I use Rss Feeds -
examples
Rss Feeds Button
(click on it to subscribe)

48. how do I use Rss Feeds -
examples
Rss Feeds Button
(click on it to subscribe)

49. how do I use Rss Feeds -
examples
Rss Feeds Button
(click on it to subscribe)

50. how do I use Rss Feeds? II/II
●
Do I need to install any program?
– Up­to­date browsers (Firefox, Opera, etc..) have
built­in capabilities to read rss feeds.
– Otherwise, you can use a Rss Reader application.
– Rss Readers Applications are more comfortable –
they have a better interface, they can show
notifications on your desktop, etc..
– Examples: Liferea, Blam, Mugshot, .... (see
http://en.wikipedia.org/wiki/Rss_reader)
● How to use RSS Feeds : [19]
http://www.answers.com/how%20to%20use%20rss%20feeds%20tu

51. Rss Feeds: instant notifications
of new articles on your desktop (I)
(liferea, a rss reader)

52. Liferea: an RSS Reader
(This is liferea, on my computer.)

53. Rss Feeds: instant notifications
of new articles on your desktop (II)
(mugshot, another rss

54. References
● [1] Def. Web 2.0: http://en.wikipedia.org/wiki/Web_2.0,
http://www.google.it/search?q=define%3A%22web%202.0%22&, http://www.answers.com/web%202.0
● [2] Web 2.0 and Science, discussions:
http://www.nodalpoint.org/node/1749 (Nature: The impact of quot;Web 2.0quot; on Science and publishing),
http://www.nodalpoint.org/2006/11/29/web_2_0_and_science_video_presentations_from_embl,
http://openwetware.org/wiki/Science_2.0 (Openwetware),
http://openwetware.org/wiki/Science_2.0/Brainstorming (Openwetware)
http://www.bmj.com/cgi/content/extract/333/7582/1283 (how Web 2.0 is changing medicine)
http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-1842.2007.00701.x (The emerging Web 2.0 social
software ...)
● [3] Def. Weblog: http://en.wikipedia.org/wiki/Weblog, http://answers.com/weblog,
http://google.com/search?q=define:weblog
● [4] Bioinformatics Blogs List: http://wiki.nodalpoint.org/blogs; I recommend Bio::Blogs (
http://bioblogs.wordpress.com/) and nodalpoint (http://nodalpoint.org).
● [6] A few discussions about the topic 'blog and science':
– quot;Blogsquot; and quot;Wikisquot; Are Valuable Software Tools for Communication Within Research Groups, Sauer et al.
2005 (http://www.blackwell-synergy.com/doi/full/10.1111/j.1525-1594.2004.29005.x?cookieSet=1)
– http://www.nodalpoint.org/node/1623 and others on nodalpoint.
● [7] Just in case: http://en.wikipedia.org/wiki/Wikipedia
● [8] Mediawiki is the software ran by Wikipedia. There are other softwares avaible for wiki, I suggest to read this
article: http://en.wikipedia.org/wiki/Comparison_of_wiki_software. However, almost all of the scientific wikis I
know use Mediawiki, with the advantage of having some additional plugins, like Biblio (
http://genome.imim.es/wiki/skins/monobook/external.png) to handle BibTeX references.
See also http://wikiomics.org/wiki/Ideas.

55. References (continued)
● [9] Alternative Splicing Wiki: Currently accessible only from my laptop, please ask me if interested.
● [10] 'Appunti di bioinformatica libera' means 'Notes of free Bioinformatics'. It's a project to collect tutorials and
resources about what it's possibile to do in bioinformatics using only free accessible resources ;).
● [11] Discussions and articles about using Wikis to improve genome annotation:
– http://nodalpoint.org/2007/02/12/genome_wiki
– http://fungalgenomes.org/blog/2007/02/wikis-for-genome-reannotation/
– http://genomebiology.com/2007/8/1/102
● [12] Yeast Genome Wiki: this has appeared on 12th of March, when I was still writing this presentation ;)
http://fungalgenomes.org/blog/2007/03/sgd-community-annotation/.
● [13] Discussions about using Social Bookmarking in Science:
– http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-1842.2007.00701.x, many on nodalpoint.
● [14] del.icio.us, connotea, citeulike, hubmed(tags): The hubmed tags system is actually a little experimental.
● [15] Scientists use del.icio.us to bookmark rss feeds: ehi, why don't you look at this discussion:
http://nodalpoint.org/2007/03/07/what_about_using_mugshot_in_bioinformatics ?
● [16] 'Configure connotea' tutorial: http://www.connotea.org/getting_started_other,
http://www.connotea.org/guide
● [17] Connotea and CiteULike have different users: ...
● [18] Rss Feeds: http://en.wikipedia.org/wiki/Rss_Feed