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Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

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Short presentation on some web 2.0 technologies that could be help for scientific research.

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Web 2.0 e ricerca scientifica - Web 2.0 and scientific research

  1. 1. Web 2.0 e ricerca (Giovanni M. Dall'Olio – raduno molecularlab 2008)
  2. 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. 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. 4. I - Blogs
  5. 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. 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. 7. the fungalgenome.org Blog (http://www.fungalgenome.org/blog)
  8. 8. programming4scientists.com ● Blog di  bioinformatica,  programmazione per  scienziati ● L'autore fornisce  consigli e tutorial su  come programmare,  per scienziati
  9. 9. Nature Blogs ● Nature ha messo su  una rete di blogs  dedicati a  neuroscienze,  tecnologia, virologia,  genetica, etc..
  10. 10. Nascent ● Blog sulla tecnologia  web appartenente al  circuito di Nature
  11. 11. II - Wikis
  12. 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. 13. Wikipedia (http://en.wikipedia.org)
  14. 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. 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. 16. Build your own wiki - examples (appunti di bioinformatica libera[10]) (http://bioinformatici.org/appunti - a wiki by some Italian students of
  17. 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. 18. OpenWetWare Resources (tutorials, etc..) Labs' home pages Protocols (How to make a PCR, how to design primers, etc..) (http://openwetware.org)
  19. 19. AAAWiki (Annotation of 12 Drosophila spp genomes) Announcements Data Papers (http://rana.lbl.gov/drosophila/wiki/
  20. 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. 21. WikiOmics (wikipedia for bioinformaticists) (http://wikiomics.org)
  22. 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. 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. 24. FungalGenome Wiki Projects - descriptions Protocols (http://fungalgenome.org/wiki)
  25. 25. III - Social-Bookmarking
  26. 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. 27. Social Bookmarking in Science ● The most used services are: – del.icio.us – Connotea – CiteULike – Hubmed (Tags system)[14]
  28. 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. 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. 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. 31. Connotea: Screenshots (I) (main page) (http://www.connotea.org)
  32. 32. Connotea: Screenshots (II) (searching for tags) Search Interface Search Results (http://www.connotea.org/search?q=%22alternative+splicing%22)
  33. 33. Connotea: Screenshots (III) (posting an article) (http://www.connotea.org - note the automatic recognition of title and authors.)
  34. 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. 35. CiteULike: Screenshots (I) (searching between tags) (http://www.citeulike.org/
  36. 36. Connotea: Screenshots (II) (posting an article) (http://www.citeulike.org/ - note the automatic recognition of title and authors.)
  37. 37. IV Scientific Communities
  38. 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. 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. 40. Esempi di workflow da myExperiment
  41. 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. 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. 43. Scivee,
  44. 44. V - RSS Feed
  45. 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. 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. 47. how do I use Rss Feeds - examples Rss Feeds Button (click on it to subscribe)
  48. 48. how do I use Rss Feeds - examples Rss Feeds Button (click on it to subscribe)
  49. 49. how do I use Rss Feeds - examples Rss Feeds Button (click on it to subscribe)
  50. 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. 51. Rss Feeds: instant notifications of new articles on your desktop (I) (liferea, a rss reader)
  52. 52. Liferea: an RSS Reader (This is liferea, on my computer.)
  53. 53. Rss Feeds: instant notifications of new articles on your desktop (II) (mugshot, another rss
  54. 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. 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

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