MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'ensembl'. Sat, 03 Sep 2011 02:32:06 +0100 http://www.medworm.com/index.php?rid=3408575&cid=t_177846_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F03%2F26%2Fbiomart-and-biomart%2F I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a gene. These are called filters. They have values – for example, HGNC symbols. You want to retrieve other identifiers – attributes – for your objects. You can use BioMart as a web application called MartView. However, R users should check out the biomaRt package, part of the Bioconductor suite. Here’s a couple of examples. Example 1: fetch Ensembl gene identifiers given HGNC symbols Let’s start with a simple example. You have a CSV file in which one of the fields is a HGNC symbol (w... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3408575 Fri, 26 Mar 2010 07:23:18 +0100 3408575 http://www.medworm.com/index.php?rid=2018352&cid=t_177846_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F12%2Fpublic-data-sets-on-aws-amazon-web.html "AWS hopes to provide researchers across a variety of disciplines and industries with tools to enable more innovation, more quickly" [Public data on AWS]If you are interested in cloud computing and storage then you will be delighted that Amazon offers support to the science community. Though appreciated, do I think that the information provided for the data sets is very sparse, e.g. which conformer generation was used for the chemistry data sets? How exactly was the UGI dataset created?Anyway, this sounds similar to the computing and storage solution of Google, called MapReduce and GFS. I do not know enough about it to understand the technical differences between the frameworks of Amazon and Google, but both are used to work with tons of data. As announced by Amazon would users (or compan... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2018352 Sat, 06 Dec 2008 16:43:00 +0100 2018352 http://www.medworm.com/index.php?rid=1759889&cid=t_177846_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fencode---understanding-our-genome.html%3F_c%3Dfeed-rss Ewan Birney Keynote Talk, Afternoon Session, 3 September (11th MGED Meeting, 1-4 September, 2008) ENCODE There are 4418 TSS with multiple lines of evidence supporting them. This is ~10 fold more than the number of genes. Only 38% would be tradit... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=1759889 Wed, 03 Sep 2008 14:52:27 +0100 1759889 http://www.medworm.com/index.php?rid=1370782&cid=t_177846_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2008%2F04%2F14%2Fensemblog_the_ensembl_weblog The Ensembl Weblog provides news, views and announcements about the Ensembl Genome Browser. The blog has been going for a few years now, but I’ve only just become aware of it thanks to a recent Ensembl Genome Browser Tutorial by Bert Overduin. Catching up on posts from Ensemblians this year, Ewan Birney wrote a piece about The Gene Love-in last week and Paul Flicek briefly described the 1000 Genomes project back in January. The Ensembl Weblog is fairly low traffic, so if you don’t already read it, it’s worth considering subscribing to the feed. And it’s good to see more scientists using blogs to communicate. Long may this trend continue! read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=1370782 Mon, 14 Apr 2008 17:16:06 +0100 1370782 http://www.medworm.com/index.php?rid=1368869&cid=t_177846_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F269197633%2F Ewan Birney and Ensembl (the other/original genome browser depending on if you are a UCSC junkie) have started blogging a bit more about what is going on under the proverbial hood over there in Hinxton.  There are some great nuggets talking about what are some of the current problems.  These bite-sized comments should be a great glimpse into what is going on without drowning in the deluge that is ensembl-dev.   This is a recent post on the challenges of gene annotation coordination among "manual" and "automated" annotation of gene structure of groups at the same institution.   Scale that up among multiple genomes, genome centers, quality of prediction programs and assemblies, and you can see why the fungal genome comparisons could use a little bit more help. It is great to hear what ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1368869 Sun, 13 Apr 2008 03:00:48 +0100 1368869