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

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]

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.

I - Blogs

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.
●

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.

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

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

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

Nascent
●
Blog sulla tecnologia
web appartenente al
circuito di Nature

II - Wikis

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]
)

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

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.

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

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

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])

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

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

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)

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

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.

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

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

III - Social-Bookmarking

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.

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

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].

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.

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].

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

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

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

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].

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

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

IV Scientific Communities

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.

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...

Esempi di workflow da
myExperiment

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.

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

Scivee,

V - RSS Feed

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.

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.

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

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

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

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

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

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

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

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 \"Web 2.0\" 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':
– \"Blogs\" and \"Wikis\" 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.

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