Blogs Web feeds Take home messages References Information overflow? Stay tuned with a click Use blogs and RSS for your research Part of the EMBL Centre for Computational Biology talks series Novel concepts and easy-to-use web tools for biologists Konrad F¨orstner, Bork Group, EMBL http://konrad.foerstner.org May 23rd, 2006 Blogs Web feeds Take home messages References What is this talk about? This talk will introduce you to blogs and web feeds and their usage as tools for scientists. Blogs Web feeds Take home messages References Outline 1 Blogs 2 Web feeds 3 Take home messages 4 References Blogs Web feeds Take home messages References Motivation - Why reading/writing blogs? with blogs you can easily get other’s opinions share your opinion Blogs Web feeds Take home messages References What is a blog? blog - abbreviation for ”web log” (via ”we blog”) basically an online diary Blogs Web feeds Take home messages References Brief history and current developement History middle of the 90s: first blog appeared end of the 90s: easy-to-use service started, boom began 2004 Merriam-Webster’s Online Dictionary declared blog as the word of the year 2005: entimated over 60 Millions blogs worldwide (May) Current (tracked by Technorati) 35.3 Million weblogs (not all blogs are tracked by Technorati) the blogosphere is doubles in size every 6 months 75,000 new weblogs per day 55% of the new weblogs are still posting after 3 month over 1.2 Million posts per day Blogs Web feeds Take home messages References Brief history and current developement History middle of the 90s: first blog appeared end of the 90s: easy-to-use service started, boom began 2004 Merriam-Webster’s Online Dictionary declared blog as the word of the year 2005: entimated over 60 Millions blogs worldwide (May) Current (tracked by Technorati) 35.3 Million weblogs (not all blogs are tracked by Technorati) the blogosphere is doubles in size every 6 months 75,000 new weblogs per day 55% of the new weblogs are still posting after 3 month over 1.2 Million posts per day Blogs Web feeds Take home messages References Structure of a blog Common elements of blog title current blog entries short info about the author (link) blogroll - links to other blogs archive web feed Blogs Web feeds Take home messages References Structure of a blog entry Common elements of blog title body permalink - URL to individual entry date of posting Additional elements comments - written by readers category/tags - the topic(s) of the entry trackback Blogs Web feeds Take home messages References Structure of a blog entry http://pbeltrao.blogspot.com/2006/05/little-bit-of-this-little-bit-of-that.html Blogs Web feeds Take home messages References Types of blogs an incomplete list of blog types litblog - literary blog watchblog - watching media and commenting critically corporate/business blog linkblog - mainly collection of links photoblogs/phlog liveblog - real-time commentary podcast/audioblog - audio files are posted videoblog/vblog - video files are posted moblog - content is produced on a mobile device (cellphone, pda) edublog - teaching blog scienceblog - ... guess Blogs Web feeds Take home messages References The blogger person writing the blog blog of a single person vs. blog of a community blogger is anonymous vs. blogger is known hobby blogger vs. semi-professional vs. full-time blogger Blogs Web feeds Take home messages References Writing a blog Hosting a blog service provider like blogger.com, twoday.net on your own server e.g. using blog engines like WordPress, b2evolution Entry editing web interface web-browser/email-client plugin (e.g. Performancing, Deepest Sender for Firefox) standalone applications like blogtk Blogs Web feeds Take home messages References Writing a blog Hosting a blog service provider like blogger.com, twoday.net on your own server e.g. using blog engines like WordPress, b2evolution Entry editing web interface web-browser/email-client plugin (e.g. Performancing, Deepest Sender for Firefox) standalone applications like blogtk Blogs Web feeds Take home messages References Writing a blog http://www.blogger.com Blogs Web feeds Take home messages References Writing comments Writing comments to blog entries can also be a very fruitful contribution to the community. Blogs Web feeds Take home messages References Finding/exploring blogs Tool for exploring the blogosphere searching with blog search engines: technorati.com blogs.google.com using technorati tags blogroll of blogs you know Blogs Web feeds Take home messages References Blogs for scientific communication Compared to classical scientific communication (publications) + much faster + cheaper + more accessible ± no filtering – not yet accepted as valid contribution in job/grant decisions etc. Blogs Web feeds Take home messages References Selected scientific blogs www.biopeer.com Nature blogs sciencepolitics.blogspot.com www.scienceblog.com www.scienceblogs.com digitalbio.blogspot.com (postgenomic.com) Blogs Web feeds Take home messages References biopeer http://www.biopeer.com Blogs Web feeds Take home messages References Referee defends his position Note from the Biomass - http://binf.twoday.net/stories/1680766 Blogs Web feeds Take home messages References Postgenomic - aggregation of life science blogs http://postgenomic.com Blogs Web feeds Take home messages References Postgenomics - aggregation of life science blogs http://postgenomic.com Blogs Web feeds Take home messages References Postgenomics - aggregation of life science blogs http://postgenomic.com Blogs Web feeds Take home messages References Using blogs as labjournals group internal or for the whole scientific community would increase transparency of research dramatically feedback could improve the experimental procedure unnecessary redundancy could be avoided Blogs Web feeds Take home messages References Using blogs as labjournals Publishing data in a blog first http://biocurious.com/a-protein-aggregation-puzzle Blogs Web feeds Take home messages References Motivation - Why using web feeds? The web feeds technology makes it possible to keep track of changes of websites in a very easy and time saving way. It can be used for websites like news sites, journal homepages, wikis or blogs. Blogs Web feeds Take home messages References What are web feeds Web feeds contain the current content and metadata of a website in machine readable format XML based file format RSS (Really Simple Syndication) Atom only the content is sent, the layout is determined by your reader software The glue of the internet - bringing services together Blogs Web feeds Take home messages References RSS readers online reader (like bloglines.com, shortwire.com) browser/email-client plugins (e.g. Sage for Firefox) stand-alone reader (e.g. AmphetaDesk, Liferea, FeedReader) Blogs Web feeds Take home messages References Example of a reader http://sage.mozdev.org Blogs Web feeds Take home messages References Where do I find the feed of a page? Blogs Web feeds Take home messages References RSS of PubMed/HubMed searches http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed Blogs Web feeds Take home messages References RSS of PubMed/HubMed searches http://www.hubmed.org Blogs Web feeds Take home messages References Handling web feed collections OPML Outline Processor Markup Language mainly used for the exchange of web feed collections also an XML based file format most aggregators can export to / import from OMPL makes moving from one reader to another easier (interesting project: share.opml.org) Blogs Web feeds Take home messages References Take home messages Blogs are already useful sources of information and a complementary channel to traditional scientific communication. They have much more potential which can be used when they are accepted by the majority of the scientific community. The use of web feeds is a very efficient way to keep track of rapidly changing web content. Blogs Web feeds Take home messages References Take home messages Blogs are already useful sources of information and a complementary channel to traditional scientific communication. They have much more potential which can be used when they are accepted by the majority of the scientific community. The use of web feeds is a very efficient way to keep track of rapidly changing web content. Blogs Web feeds Take home messages References Take home messages Blogs are already useful sources of information and a complementary channel to traditional scientific communication. They have much more potential which can be used when they are accepted by the majority of the scientific community. The use of web feeds is a very efficient way to keep track of rapidly changing web content. Blogs Web feeds Take home messages References Acknowledgements Thanks to Peer Bork Pedro Beltrao for lots of input. Anne-Marie Glynn and Evagelia Petsalaki for the very contructive feedback. You for your attention Blogs Web feeds Take home messages References Blogs Web feeds Take home messages References References http://en.wikipedia.org/wiki/Aggregator http://en.wikipedia.org/wiki/Atom %28standard%29 http://en.wikipedia.org/wiki/Blog http://en.wikipedia.org/wiki/OPML http://en.wikipedia.org/wiki/RSS %28file format%29 http://en.wikipedia.org/wiki/Trackback http://en.wikipedia.org/wiki/Web feed http://en.wikipedia.org/wiki/Blog software http://sciencepolitics.blogspot.com/2006/04/publishing-hypotheses-and-data-on-blog.html http: //www.politik-digital.de/edemocracy/netzkultur/blogger/jschmidtBlogger-Studie060214.shtml http: //www.blogherald.com/2005/05/25/world-wide-blog-count-for-may-now-over-60-million-blogs http://www.sifry.com/alerts/archives/000432.html http://blogtk.sourceforge.net http://liferea.sourceforge.net/ http://www.disobey.com/amphetadesk http://www.feedreader.com http://www.mozilla.com/firefox/ Blogs Web feeds Take home messages References Created in LaTeX using the beamer class, pdfLaTeX, emacs. All programs run on OpenBSD. www.latex-project.org latex-beamer.sourceforge.net www.tug.org/applications/pdftex www.gnu.org/software/emacs www.openbsd.org Published under the Creative Commons Attribution-NonCommercial-ShareAlike 2.5 License creativecommons.org/licenses/by-nc-sa/2.5.