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| nodalpoint.org - A bioinformatics weblog http://www.nodalpoint.org Nodalpoint is a bioinformatics weblog. en Science blogging at the Royal Institution, London http://www.nodalpoint.org/2008/08/27/science_blogging_at_the_royal_institution_london <p><span style="border:medium none;float:right;margin-left:0.5em;font-size:10px;font-weight:normal;color:#666666;"><a title="sciblog" href=""http://www.flickr.com/photos/dullhunk/2713449932/"><img" src=""http://farm4.static.flickr.com/3261/2713449932_13272ce803_o.gif"" alt="sciblog" /></a></span>Nature Publishing Group are organising a <a href=""http://upcoming.yahoo.com/event/942826/">workshop" on science blogging, this Saturday 30th August 2008</a> at the <a href=""http://www.rigb.org/">Royal" Institution of Great Britain</a> in London. Why would you care? Because there are:</p><ol><li><a title="sciblog attendees" href=""http://www.nature.com/natureconferences/sciblog2008/attendees.html">Lots" of interesting people</a>...</li><li>...<a title="sciblog programme" href=""http://www.nature.com/natureconferences/sciblog2008/programme.html">talking" about a range of interesting subjects</a> ...</li><li>.. in a <a title="sciblog@citeulike" href=""http://www.citeulike.org/tag/sciblog">distinguished" venue</a> that has recently been refurbished. It is also home to the <a href=""http://en.wikipedia.org/wiki/Royal_Institution_Christmas_Lectures">fantastic" Christmas lectures</a> and much more besides.</li></ol><p>To cap it all, I think it will be great fun too. So if you're going, see you there. If you're not, it is never too late to publish your <a href=""http://www.genome-technology.com/issues/blog/general/148817-1.html">fantasy" science funding</a> entry. Much of the conference will be televised and blogged, making it available online too.</p><br class="clear" /><p><a href=""http://www.nodalpoint.org/2008/08/27/science_blogging_at_the_royal_institution_london">read" more</a></p> http://www.nodalpoint.org/2008/08/27/science_blogging_at_the_royal_institution_london#comments London NPG rigb Royal Institution sciblog Wed, 27 Aug 2008 04:07:17 -0400 Duncan 2368 at http://www.nodalpoint.org Let's play Fantasy Science Funding! http://www.nodalpoint.org/2008/08/14/lets_play_fantasy_science_funding <p><span style="border:medium none;float:right;margin-left:0.5em;font-size:10px;font-weight:normal;color:#666666;"><a title="Donald Trump and Melania by Boss Tweed" href=""http://www.flickr.com/photos/bosstweed/254102797/"><img" src=""http://farm1.static.flickr.com/85/254102797_b594d0fde7_m.jpg"" alt="Donald Trump and Melania by Boss Tweed" /></a></span>Fantasy Science Funding is a fun game that anybody can play. You select a Science funding body of your choice, imagine yourself as its all powerful chief executive, and decide which areas of scientific research you would "hire and fire". What could be easier? <a href=""http://network.nature.com/blogs/user/duncan/2008/08/14/lets-play-fantasy-science-funding">Here" is how Fantasy Science Funding works...</a></p><br class="clear" /><p><a href=""http://www.nodalpoint.org/2008/08/14/lets_play_fantasy_science_funding">read" more</a></p> http://www.nodalpoint.org/2008/08/14/lets_play_fantasy_science_funding#comments chief executive Donald Trump fantasy fantasy football fantasy science funding fun funding sciblog Thu, 14 Aug 2008 09:39:02 -0400 Duncan 2366 at http://www.nodalpoint.org How History Affects Pattern Matching Inside The Genome http://www.nodalpoint.org/2008/07/25/how_history_affects_pattern_matching_inside_the_genome <p>In a recent Science magazine article, Löytynoja-Goldman showed that all current Multiple Sequence Alignment algorithms – the bread-and-butter algorithm for biologists studying similarities in genes across different species – completely fail to detect independent insertions in the alignment of sequences, and thus, erroneously mismatches regions of evolutionary volatility. In their improved MSA algorithm, PRANK, they use history itself to improve the performance of this basic algorithm. [<a href=""http://boscoh.com/protein/how-history-affects-pattern-matching-inside-the-genome">more...</a>]</p><br" class="clear" /> http://www.nodalpoint.org/2008/07/25/how_history_affects_pattern_matching_inside_the_genome#comments sequence alignment bioinformatics algorithms evolution phylogenetics Fri, 25 Jul 2008 18:28:33 -0400 bosco 2363 at http://www.nodalpoint.org Tree of Life http://www.nodalpoint.org/2008/07/02/tree_of_life <p><span id="picture-right" style="border:none;float: right; margin-left:0.5em; font-size:10px; color:#666666;font-weight:normal;"><a href=""http://www.flickr.com/photos/phitar/89279817/"" title="3 monkeys in a tree by Phitar"><img src=""http://farm1.static.flickr.com/28/89279817_fcd95b6b59_m.jpg"" alt="3 monkeys in a tree by Phitar"/></a></span>I'm not much of an evolutionary biologist, but <a href=""http://phylogenomics.blogspot.com/2008/06/calling-all-evolutionary-biologists.html">Jonathan" Eisen asked for help</a> and I can't resist. So, in the name of Science, and via the goodness of nodalpoint, here is some deserved <a href=""http://www.catb.org/jargon/html/G/google-juice.html">Google" Juice</a> for various Trees of Life on the Web.</p><ul><li><a href=""http://phylogenomics.blogspot.com/">Jonathan" Eisen's "Tree of Life" blog</a></li><li> <a href=""http://www.tolweb.org/">Tree" of Life Web Project</a> </li><li> <a href=""http://en.wikipedia.org/wiki/Tree_of_life_%28science%29">Tree" of life (science) - Wikipedia, the free encyclopedia</a> </li><li> <a href=""http://ucjeps.berkeley.edu/TreeofLife/">Green" Tree of Life at Berkeley</a> </li><li> <a href=""http://aftol.org/">Fungal" Tree of Life Project</a> </li><li> <a href=""http://insects.oeb.harvard.edu/ATOL/">Beetle" Tree of Life project</a> </li><li> <a href=""http://www.inhs.uiuc.edu/research/FLYTREE/">Fly" Tree of Life project</a> </li><li> <a href=""http://mammaltree.informatics.sunysb.edu/">Mammal" Tree of Life project</a> </li><li> <a href=""http://bio.slu.edu/mayden/cypriniformes/home.html">Cypriniformes" Tree of Life project</a> </li><li> <a href=""http://www.biology.duke.edu/bryology/LiToL/">Liverwort" Tree of Life Project</a> </li><li> <a href=""http://www.fieldmuseum.org/research_collections/zoology/zoo_sites/early_bird/">Early" Bird Tree of Life project</a> </li><li> <a href=""http://www.flmnh.ufl.edu/angiospermATOL/">Angiosperm" Tree of Life project</a> </li><li> <a href=""http://cnidarian.info/">Cnidaria" Tree of Life Project</a> </li><li> <a href=""http://decapoda.nhm.org/">Decapoda" Tree of Life Project</a> </li></ul><p>There, I've done my bit for Science, now it's your turn. Spread the ❤ link love ❤,and since we will soon be <a href=""http://www.darwin200.org/">celebrating" the 200th anniversary of the birth of Charles Darwin</a>, why not marvel at the <a href=""http://phylogenomics.blogspot.com/2008/06/top-five-metaphors-darwin-considered.html">coral" / shrub / lungs of life too</a>?</p><p>(CC-licensed Tree of Life picture by <a href=""http://www.flickr.com/photos/phitar/">Phitar</a>)</p><br" class="clear" /><p><a href=""http://www.nodalpoint.org/2008/07/02/tree_of_life">read" more</a></p> http://www.nodalpoint.org/2008/07/02/tree_of_life#comments Charles Darwin Comparative genomics Darwin Darwin 200 evolution Google Juice jonathan eisen phylogenetics Tree of Life Wed, 02 Jul 2008 18:44:17 -0400 Duncan 2361 at http://www.nodalpoint.org Hunting for cytochrome p450 genes in Maize http://www.nodalpoint.org/2008/06/03/hunting_for_cytochrome_p450_genes_in_maize <p><span id="picture-right" style="border:none;float: right; margin-left:0.5em; font-size:10px; color:#666666;font-weight:normal;"><a href=""http://www.flickr.com/photos/swamibu/1265918839/"" title="Bicolour maize by swamibu"><img src=""http://farm2.static.flickr.com/1099/1265918839_51746c5cac_m.jpg"" /></a></span>Hello, Just wondering if anyone on nodalpoint is in a position to help with gene hunting for cytochrome p450 genes in Maize (just for fun)?</p><p>Some more details at <a href=""http://www.openhelix.com/blog/?p=388">whether" maize carries the protective cytochrome p450 or the “defective” version of the gene</a> and <a href=""http://jeremycherfas.net/wp/Archive/2008/05/25/framing-a-defect/">Researchers" Identify Genetic “Fix” for Problem in Some Sweet Corn Hybrids</a>.</p><p>This is for a long lost friend of mine <a href=""http://jeremycherfas.net/wp/about/">Jeremy" Cherfas</a> who is a biologist, but computer literate. He writes <a href=""http://www.nodalpoint.org/2006/08/10/bio_ignorance">good" books about the human genome</a> (for example) and is just curious to do some experimental and exploratory bioinformatics, just for kicks but with a <a href=""http://agro.biodiver.se/">special" interest in Agricultural Biodiversity</a>.</p><br class="clear" /><p><a href=""http://www.nodalpoint.org/2008/06/03/hunting_for_cytochrome_p450_genes_in_maize">read" more</a></p> http://www.nodalpoint.org/2008/06/03/hunting_for_cytochrome_p450_genes_in_maize#comments Help! biodiversity corn cyp gene hunting herbicide Jeremy Cherfas maize p450 zea mays Tue, 03 Jun 2008 08:19:16 -0400 Duncan 2359 at http://www.nodalpoint.org Eureka Science News - intelligent science news aggregator http://www.nodalpoint.org/2008/05/10/eureka_science_news_intelligent_science_news_aggregator <p><a href=""http://esciencenews.com">Eureka" Science News</a> just launched - it's an intelligent science news aggregator based on machine learning (for classification) and clustering of recent news from all major science sources - I'm a microarray analyst, so I used the same techniques I use to cluster genes, but this time to cluster news! It's fun to use skills in other contexts - I hope you will enjoy the site!</p><br class="clear" /> http://www.nodalpoint.org/2008/05/10/eureka_science_news_intelligent_science_news_aggregator#comments Clusters hierarchical clustering Machine Learning naive bayesian News Science 2.0 science news Sat, 10 May 2008 14:49:37 -0400 FiReaNG3L 2357 at http://www.nodalpoint.org I Still Haven't Found What I'm Googling For http://www.nodalpoint.org/2008/05/09/i_still_havent_found_what_im_googling_for <p><span style="border:medium none;float:right;margin-left:0.5em;font-size:10px;font-weight:normal;color:#666666;"><a title="Irish Google" href=""http://www.google.com/holidaylogos05.html"><img" src=""http://www.google.com/logos/stpatricks_05.gif"" alt="Irish Google" /></a></span>Twenty one years ago this month, in May 1987, Irish rockers U2 released their classic Joshua Tree single, <a href=""http://en.wikipedia.org/wiki/I_Still_Haven't_Found_What_I'm_Looking_For">I" Still Haven't Found What I'm Looking For</a>. Those twenty one years have seen incredible technological change: the adoption of desktop computers, mobile phones, the birth of the Web and the widespread use of search engines like Google. So with sincere apologies to Bono, The Edge, Adam and Larry, it's time we updated the lyrics for the 21st century. So, I give you "<a href=""http://duncan.hull.name/2008/05/09/i-still-havent-found-what-im-googling-for/">I" Still Haven't Found What I'm <i>Googling</i> For</a>" (21st anniversary, 2008 webby edition)...</p><br class="clear" /><p><a href=""http://www.nodalpoint.org/2008/05/09/i_still_havent_found_what_im_googling_for">read" more</a></p> http://www.nodalpoint.org/2008/05/09/i_still_havent_found_what_im_googling_for#comments Bono Data management Google googling Ireland joshua tree lyrical search technology u2 web Fri, 09 May 2008 05:48:48 -0400 Duncan 2356 at http://www.nodalpoint.org Introducing the eyeLIMS project http://www.nodalpoint.org/2008/05/03/introducing_the_eyelims_project <p>Scientists usually share information with collaborators from all around the world. For that purpose, eyeOS (<a href=""http://www.eyeos.org"" title="www.eyeos.org">www.eyeos.org</a>) provides an invaluable system to access and share documents, create and save data files or store crucial personal and professional information.</p><p>To see eyeOS widely used by scientists all around the world, we initiated the eyeLIMS project ! eyeLIMS is a community-driven project which aims at providing a Free, web-based, Open Source Laboratory Information Management System (LIMS) powered by eyeOS.</p><br class="clear" /><p><a href=""http://www.nodalpoint.org/2008/05/03/introducing_the_eyelims_project">read" more</a></p> http://www.nodalpoint.org/2008/05/03/introducing_the_eyelims_project#comments Bioinformatics Bioinformatics Data management Free LIMS Open Bioinformatics Open Source Open source software Science 2.0 web-based XML Sat, 03 May 2008 11:22:57 -0400 amejat 2355 at http://www.nodalpoint.org Ensemblog: The Ensembl Weblog http://www.nodalpoint.org/2008/04/14/ensemblog_the_ensembl_weblog <p><span style="border:medium none;float:right;margin-left:0.5em;font-size:10px;font-weight:normal;color:#666666;"><a href=""http://www.flickr.com/photos/dullhunk/2413271562/"" title="Pongo pygmaeus abelii"><img src=""http://farm4.static.flickr.com/3144/2413271562_d5e7eedf04_o.png"" width="150" height="200" alt="Pongo pygmaeus abelii" /></a></span>The <a href=""http://ensembl.blogspot.com/">Ensembl" Weblog</a> provides news, views and announcements about the <a href=""http://www.ensembl.org">Ensembl" Genome Browser</a>. The blog has been going for a few years now, but I’ve only just become aware of it thanks to a recent <a href=""http://duncan.hull.name/2008/03/19/genomes-to-systems-2008-day-two/">Ensembl" Genome Browser Tutorial by Bert Overduin</a>. Catching up on posts from Ensemblians this year, Ewan Birney wrote a piece about <a href=""http://ensembl.blogspot.com/2008/04/gene-love-in.html">The" Gene Love-in</a> last week and Paul Flicek briefly described the <a href=""http://ensembl.blogspot.com/2008/01/ensembl-and-1000-genomes.html">1000" Genomes project</a> back in January. The Ensembl Weblog is fairly low traffic, so if you don’t already read it, it’s worth considering <a href=""http://ensembl.blogspot.com/feeds/posts/default">subscribing" to the feed</a>.</p><p>And it’s good to see more scientists using blogs to communicate. Long may this trend continue!</p><br class="clear" /><p><a href=""http://www.nodalpoint.org/2008/04/14/ensemblog_the_ensembl_weblog">read" more</a></p> http://www.nodalpoint.org/2008/04/14/ensemblog_the_ensembl_weblog#comments ensembl ensemblian Ewan Birney orangutan Paul Flicek Mon, 14 Apr 2008 13:16:06 -0400 Duncan 2341 at http://www.nodalpoint.org Taverna tutorial and version 2.0 preview http://www.nodalpoint.org/2008/04/09/taverna_tutorial_and_version_2_0_preview <p><span id="picture-right" style="border:none;float: right; margin-left:0.5em; font-size:10px; color:#666666;font-weight:normal;"><a href=""http://www.flickr.com/photos/ciordia/245106485/"" title="Taverna menu by Andy Ciordia"><img src=""http://farm1.static.flickr.com/90/245106485_6aaae74bb9_m.jpg"" alt="Taverna menu by Andy Ciordia" /></a></span>There are a few remaining places left on the <a href=""http://www.mygrid.org.uk/index.php?module=pagemaster&PAGE_user_op=view_page&PAGE_id=110&MMN_position=139:86:105">Building" Scientific Workflows for Bioinformatics and Systems biology using Taverna</a> course held in Manchester, UK on 15th April 2008. Attendance at the workshop is free, but participants will have to cover their own travel costs. Due to the hands-on nature of the workshop, numbers are limited to 30, so there is a ‘first-come, first-serve’ policy on bookings. Book now to avoid disappointment!</p><br class="clear" /><p><a href=""http://www.nodalpoint.org/2008/04/09/taverna_tutorial_and_version_2_0_preview">read" more</a></p> http://www.nodalpoint.org/2008/04/09/taverna_tutorial_and_version_2_0_preview#comments Bioinformatics mygrid systems biology taverna tutorial workflow Wed, 09 Apr 2008 11:39:35 -0400 Duncan 2340 at http://www.nodalpoint.org |
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