MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Flags and Lollipops - Bioinformatics Blog' source. Sun, 09 Nov 2008 14:50:52 +0100 http://www.ghastlyfop.com/blog/2008/10/academiaedu.html I like academia.edu. The academic family tree idea is pretty cool (I know that the concept has been around for a while in various guises but their implementation is pretty slick) and I like the fact that new visitors can arrive and be interacting with the site within minutes. It's also nice to see an academic networking site that, well, doesn't look like Facebook.I'm also impressed by the speed at which they've been throwing up refinements and bug fixes... and by the adverts on PhD. Canny marketing (good work poorly paid but well fed intern)! The academia.edu team are a smart bunch of people which is probably how they got funding in the first place.For balance what's not good about it? The flash freezes my mac on an empty cache... and the .edu TLD is really only for educational institution... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1907702 Sat, 25 Oct 2008 22:43:00 +0100 1907702 http://www.ghastlyfop.com/blog/2008/05/disappointed-with-popfly.html Popfly is the mashup editor that Microsoft released last year. The idea is good. The 3D graphics are good. Silverlight is a bit buggy in Firefox (sidebars don't always redraw properly) but that's OK.If you're going to create a web 2.0 mashups builder, though, don't you think it's be a good idea to provide some Atom support? (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1467011 Sat, 24 May 2008 21:46:00 +0100 1467011 http://www.ghastlyfop.com/blog/2008/05/meta-analysis.html The journal platform team here at NPG just rolled out machine readable metadata for the papers we publish in Dublin Core, PRISM (good PRISM, not to be confused with evil PRISM) and Google metadata formats.No more scraping to automatically get the citation for a paper, it's all in the HEAD:<meta name="citation_journal_title" content="Nature" /><meta name="citation_publisher" content="Nature Publishing Group" /><meta name="citation_authors" content="Paul Schenk, Isamu Matsuyama, Francis Nimmo" /><meta name="citation_title" content="True polar wander on Europa from global-scale small-circle depressions" /><meta name="citation_volume" content="453" /><meta name=&... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1467012 Mon, 19 May 2008 16:08:00 +0100 1467012 http://www.ghastlyfop.com/blog/2008/04/nice-work-pedro.html Noticed while leafing through today's Nature that Pedro has a paper out (Isalan et al., Evolvability and hierarchy in rewired bacterial gene networks).There's more on this over at Public Rambling. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1467013 Fri, 18 Apr 2008 10:41:00 +0100 1467013 http://www.ghastlyfop.com/blog/2008/04/ian-owes-me-pint_17.html (update: Gavin Bell at Nature gave up one of his app spots so that I could put this live, which I did: only to discover that Google App Engine is even more unforgiving of timeouts than Facebook. Currently trying to work out how to make the bookmarking process, for now it doesn't work very well. Also the search is broken, though that's Google's fault and not mine.)I bet Ian earlier that I could rewrite Connotea on App Engine in six hours. I can't remember why. Probably ego (mine, I mean). He didn't actually bet me a pint but he should have done...... because the original estimate was a tad optimistic (ahem). After twelve hours I've produced pycite, though, which is pretty good going I think. I'll admit it: Python is actually very cool.pycite is three hundred lines of logic and a set of html... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1467014 Thu, 17 Apr 2008 15:34:00 +0100 1467014 http://www.ghastlyfop.com/blog/2008/04/ian-owes-me-pint.html I bet Ian earlier that I could rewrite Connotea on App Engine in six hours. I can't remember why. Probably ego. He didn't actually promise me a pint but he should have done.The original estimate was a tad optimistic (ahem) but after twelve hours I've produced pycite, which is pretty good going I think. I'll admit it: Python is actually very cool.Anyway, pycite is three hundred lines of logic and a set of html templates that implements a (very simple) social bookmarking service. Sadly I don't actually have an App Engine account so it's not live on the web anywhere (I'll buy whoever does have an account and puts it up first a pint - let's spread the love), you'll have to download it and run it locally to see it in action.What you can do with it:run it without owning a server of your ownlog i... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1362444 Thu, 10 Apr 2008 03:26:00 +0100 1362444 http://www.ghastlyfop.com/blog/2008/04/gaggle.html I hadn't heard of Gaggle before but both Deepak and Sutee Dee (who needs a homepage.. ;)) from the ISB mentioned it last week so I figured it was worth a look. It's a system built by Paul Shannon at the ISB in Seattle to share data between different bioinformatics applications on the fly. It has been around for a while, I think - there was a BMC Bioinformatics paper describing the system in March 2006.A small server program (the ´Gaggle Boss´) provides communication among analysis and display programs (the ´geese´) which are modest and minimal adaptations of existing (or novel) bioinformatics and computational biology programs, and web resources. The Boss and the geese all run as separate programs on the user´s desktop computer, communicating with each other, at the user´s behest, by... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1354049 Mon, 07 Apr 2008 13:26:00 +0100 1354049 http://www.ghastlyfop.com/blog/2008/04/why-you-should-try-online-dating.html (you can jump to the short answer here, if you're feeling impatient)Onto the psychology of social media. Kristin Stecher of the University of Washington and Dave Evans of Psychster LLC both gave interesting talks about profile pages.Psychster is a consulting company dedicated to "the social science of social networking". Recently they've been looking at interpersonal perception (how does person A perceive person B? How close is that to B's self perception?). Most research into this uses 'fake' people - i.e. A is given a detailed written description of B and works off of that, rather than meeting anybody face to face.To try and get a large 'real people' dataset Psychster created a Facebook application (and later a website) where users could fill out a questionnaire that rated their personal... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1349626 Thu, 03 Apr 2008 23:22:00 +0100 1349626 http://www.ghastlyfop.com/blog/2008/04/do-you-use-language-differently-when.html Can you tell if somebody is clinically depressed by analyzing their use of language? I'm not a psychologist, so take the background info below with a pinch of salt but the topic came up at ICWSM (more on how later) and I thought it was fascinating.In 2001 Stirman et al compared the collected works of nine poets who eventually committed suicide and nine poets who didn't (as a control set). Their theory was that the depressed (and eventually suicidal) poets would use more first person singular (I, me, my) and words related to hopelessness and desperation (hate, worthless, death, grave) and that was supported by the data.Rude et al later found something similar when they compared essays (on a common topic - "coming to college") written by college students. Depressed students used "I" and nega... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1349627 Thu, 03 Apr 2008 18:32:00 +0100 1349627 http://www.ghastlyfop.com/blog/2008/04/analyzing-myspace-profiles.html This morning James Caverlee presented his study of almost two million (well, two sets of ~ one million - one set of profiles picked at random and one gathered by traversing the social graph) MySpace profiles. It was interesting stuff. Some bits and pieces below.MySpace users live up to gender stereotypes, rather disappointingly:.nobrtable br { display: none }Words most frequently appearing in MySpace profilesWomenMenlove, people, dancing, life, shopping, can, girl, family, hearts, being, have, notebook, are, dance, favourite, thingsdating, sport, networking, metal, serious, football, relationship, sh*t, single, wars,straight, band, video, f*ck, guitar, gayAnd geographic ones (didn't manage to write all of these down in time):users in Oregonusers in Alabamacamping, hiking, pixies, snowboard... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1344317 Wed, 02 Apr 2008 01:26:00 +0100 1344317 http://www.ghastlyfop.com/blog/2008/04/tossed-salad-and-scrambled-eggs.html I'm in Seattle for the ICWSM. The first day just finished and I'm going to blog about the more interesting talks tomorrow when I'm more awake. In the meantime: Crowdvine for conferences is actually pretty useful Lions for Lambs is terrible St Trinians is actually quite good The Century of the Self is brilliant Seattle looks really nice from the air Note to self: US Milky Way bars = UK Mars bars, tricksy bastards Steak + beer + bay views = awesome (thanks Deepak!) More Starbuckses than normal Everybody is disconcertingly friendly. People keep offering to take me skiing. And to see waterfalls. People here big on waterfalls MS Live Labs are hiring Brad Fitzpatrick is a great speaker but I found his talk disappointing - too much hand waving about OpenID / OAuth / XMPP / XRDS. Dude, it's a room... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1340655 Tue, 01 Apr 2008 05:43:00 +0100 1340655 http://www.ghastlyfop.com/blog/2008/03/dawkins-officially-bigger-than-jesus.html I've run all of the posts from Scienceblogs.com in 2007 through the ClearForest API. ClearForest extracts entities - people, places, organizations - from plain text.I'm in the process of pulling things together for a visualization, but here's a quick answer to the 'who are Sciblings talking about?' question. The 'count' is the number of times that each entity was seen (could be multiple times in the same post) across 2007.+-----------------------------------------------+-------+| term | count |+-----------------------------------------------+-------+| Michael Egnor | 1855 | | Richard Dawkins | 1737 | | Bush | 1669 | | Congress | 1430 | | Charles Darwin | 1226 | | Michael Behe ... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1314163 Wed, 19 Mar 2008 11:31:00 +0100 1314163 http://www.ghastlyfop.com/blog/2008/03/science-streaming.html Michael Barton has a nice post up:I currently use Subversion to back up my project files, and I noticed Twitter status updates are very similar in length to subversion log messages. I created a short script so that every time I do a subversion repository check in, the message is also sent to Twitter.I'd like to see activity aggregators accept arbitrary update - sort of like Facebook's Beacon updating people's News Feed, but done properly. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1312403 Wed, 19 Mar 2008 00:39:00 +0100 1312403 http://www.ghastlyfop.com/blog/2008/03/nature-archive-visualized.html I'm using up my annual carry-over vacation days by taking some time off work this week. Normal people probably use this valuable breathing space to bond with their loved ones, play badminton and learn exciting new hobbies. So far I've sat alone in my flat for thirty six hours straight writing Processing sketches *. So... here's a draft visualization (14mb MP4, should play in your browser with Quicktime) of the key words and phrases found in Nature journal over the past thirty years.The video starts with the phrases from 1970 and continues until 2007.Phrases appear on the right in the year that they were first seen, then travel leftwards, disappearing in the year they were last seen.The size of each phrase is related to how often it was seen relative to all the other phrases.The hue of each... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1309074 Tue, 18 Mar 2008 03:08:00 +0100 1309074 http://www.ghastlyfop.com/blog/2008/03/seattle.html I'm going to be in Seattle the first week of April for the ICWSM.There are a whole bunch of awesome looking talks and one or two wild cards. Wild cards like:Spontaneous Inference of Personality Traits from Online ProfilesKristin Stecher, Scott CountsWhich sounds interesting, anyway.Let me know if you're in the area and fancy meeting up for lunch or a drink. I'm in town from the 29th of March to the 5th April. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1294444 Tue, 11 Mar 2008 10:44:00 +0100 1294444 http://www.ghastlyfop.com/blog/2008/03/new-jove-blog-commenting-on-papers.html Anna Kushnir's new blog for JoVE is up and running (actually it has been up and running for a while, I'm a bit behind with blogging. Those January Open Science posts are coming at some point, too). It's a nice mix of content.Of particular interest are a couple of interesting entries talking about the online participation - or lack thereof - of scientists. See also Noah Gray's take on neuroscientists and web 2.0 and David Crotty's 'why web 2.0 is failing in biology' post.Did you skip over all those links? You shouldn't, really. At least read David Crotty's.So, yeah, anyway, why scientists don't comment on papers - my take is that being too busy and being afraid of the consequences don't come into it. Sure, they're valid concerns - but everybody is busy at work and everybody realizes that wh... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1292282 Mon, 10 Mar 2008 23:11:00 +0100 1292282 http://www.ghastlyfop.com/blog/2008/02/hot-diggity.html The Collective Intelligence Foo Camp looks awesome, especially if you're into blogs and recommender systems (and who isn't, right? Right...? Everybody?). Some particularly cool attendees: Greg Linden (worked on Amazon's recommender system, great blog) Matt Hurst (ex of Nielsen BlogPulse, now at Microsoft, great blog) Niall Kennedy (ex of Technorati, Microsoft, bunch of other places, great blog) Bernardo Huberman (also talking at ICWSM '08 next month, sad lack of blog)(via Greg Linden) (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1246634 Thu, 21 Feb 2008 01:09:00 +0100 1246634 http://www.ghastlyfop.com/blog/2008/02/uh-lazyweb.html I know it was only a month ago that you were invoked here last. But... Freebase. It's killing me (I was inspried to finally build something using it by Pierre, whose examples I have sadly failed to adapt :( ).What MQL can I use to get *all* of the information about *all* people with profession of 'author'?I have{ "query" : [ { "*" : [ {} ], "guid" : null, "limit" : 5, "name" : null, "profession" : "author", "type" : "/people/person" } ]}(thanks to Pierre for pointing out a syntax error here originally, oops)Which should list all of the properties for 5 authors, right? But I only see properties from the /people/person schema.How do I get all the author properties too? (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1241945 Tue, 19 Feb 2008 14:18:00 +0100 1241945 http://www.ghastlyfop.com/blog/2008/02/publishing-house-scale-of-web-server.html Kevin Burton recently checked to see which operating system the websites of different US presidential candidates are built on. The executive summary: Democrats use lots of Linux while Republicans (Ron Paul excepted) mainly use Windows.Some have suggested a correlation between Windows web server usage and being evil. This makes sense as only somebody with no soul could love ASP. Does the theory hold true in the publishing world? PLoS run Linux Nature run Linux Science run Linux Wiley run Solaris Elsevier run Windows 2000 Springer run Windows 2003So from a purely progressive science on the web point of view.... yeah, sort of.Springer, Elsevier and Wiley are pretty big companies and have lots of different sites, so maybe it's doing them a disservice to assume that whatever serves their root d... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1237771 Sun, 17 Feb 2008 15:22:00 +0100 1237771 http://www.ghastlyfop.com/blog/2008/02/nature-on-facebook.html It's in my Nature.com is Nature's splendid new Facebook group (there's a fan page, too, with a selection of fresh Nature.com content on it in case you need a quick fix of science news without leaving the 'book). Anyway, it's splendid because it's a chance to interact with NPGers on an informal level - or rather a chance for us to interact with students & scientists on an informal level. The group started out as a mini-project run by a couple of Facebook early adopters and while it has picked up a lot of advice and support from within the company since then it's still a friendly place where everybody knows your name*.Some of that company support has come in the form of free Nature-header-red iPods, so sign up and keep an eye out for giveaways in the near future.(if you haven't seen it alrea... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1226774 Tue, 12 Feb 2008 21:24:00 +0100 1226774 http://www.ghastlyfop.com/blog/2008/02/where-i-lazily-recycle-news-from.html Geoff Bilder over at CrossRef has announced that their citation plugin for MT and WordPress is now available for download. CrossRef is the shadowy cabal that runs the DOI system for journals. Shadowy because despite the fact that DOIs underpin academic publishing who outside of publishing tech circles has ever heard of them? Anyway, they've been doing a lot of cool science 2.0 stuff recently, probably because of Geoff, for whom I have a lot of respect. He does need to update his blog more often, though. ;)(via OpenHelix)Also at OpenHelix is a writeup of Gene Characterization Index: Assessing the Depth of Gene Annotation, published in PLoS One at the end of last year. It's a nice project.One (very) minor niggle: the whole genome dataset they provide looks like this:Gene ID GCI2 10.019 10.02... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1220858 Sun, 10 Feb 2008 14:36:00 +0100 1220858 http://www.ghastlyfop.com/blog/2008/01/viral-spread-visualized.html Viral spread of Facebook app from Stew on Vimeo.The movie above is a (blurry when streamed, try the 3.6mb MPEG download) visualization of the signup and invite data from Bookshare from July 18th of last year to now. As users sign up they are geolocated and plotted on the map. More users signing up in a particular location mean bigger, brighter spots. Invites from one user to another are drawn as snaking lines that travel from the city of the inviter to the city of the invitee.It's written in Processing.I'd love to hear from anybody who owns a large Facebook application and has kept id / install date / invitee data (bearing in mind Facebook's data privacy rules...). See also this.First draft available here (1.6mb MPEG) (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1152559 Tue, 15 Jan 2008 05:00:00 +0100 1152559 http://www.ghastlyfop.com/blog/2008/01/viral-spread-visualized.html Application spreading virally from Stew Potte on Vimeo.The movie above is a first draft visualization of the signup and invite data from Bookshare from July 18th of last year to now. As users sign up they are geolocated and plotted on the map. More users signing up in a particular location mean bigger, brighter spots. Invites from one user to another are drawn as snaking lines that travel from the city of the inviter to the city of the invitee.It's written in Processing and suffers a bit from being compressed and streamed - here's a slightly higher res version (1.6mb MPEG).I'd love to hear from anybody who owns a large Facebook application and has kept id / install date / invitee data (bearing in mind Facebook's data privacy rules...). See also this. (Source: Flags and Lollipops - Bioinfor... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1150701 Tue, 15 Jan 2008 05:00:00 +0100 1150701 http://www.ghastlyfop.com/blog/2008/01/lazyweb-i-invoke-thee.html Dear maths geeks,On Bookshare each user owns a set of books. The same book can be owned by multiple users.What algorithm can I use to find the smallest possible set of books that contains at least one book from each user? (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1146426 Sun, 13 Jan 2008 05:00:00 +0100 1146426 http://www.ghastlyfop.com/blog/2008/01/lamp-performance-for-dummies.html I've spent the last six months combing Google for 'slow mysql' results. It was enlightening. Now in the spirit of giving back to the community I give you:Euan's Top Tips For Medium Sized LAMP Powered Web AppsWhere 'medium sized' means you have four or five concurrent users on ten tables with around half a million rows each and 'top' means that you've already done all the basic stuff - picking table types, adding indexes, designing the database properly in the first place etc.Some are common sense. Some are not appropriate for all situations. Use at your own risk. If most operations are reads turn the MySQL query cache on. Don't use mysqldump for backups. Users don't like five minutes of being unable to write anything to the database because the tables are locked. Use mysqlhotcopy or an LVM... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1146427 Fri, 11 Jan 2008 05:00:00 +0100 1146427 http://www.ghastlyfop.com/blog/2007/10/facebook-code-on-bebo.html Yes, nothing to do with bioinformatics, but social networking:Bebo announced that it'd support Facebook style apps as well as OpenSocial late last year. They've launched properly now.The documentation has been up for a while already and there aren't any real surprises, though there's a couple of new Bebo specific tags (which seems like a bad idea to me; I mean, the whole point is code compatibility between multiple systems).One major omission is Javascript support; there's no equivalent to FBJS (Facebook's sandboxed Javascript version). This means that a lot of the bigger apps will hold off moving over, I'd have thought - though it's not a problem for simpler quizzes and Flash based stuff like Scrabulous.There are a couple of OpenSocial containers now but I haven't heard of any Facebook se... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1146428 Thu, 10 Jan 2008 05:00:00 +0100 1146428 http://www.ghastlyfop.com/blog/2008/01/diversions-excuses-etc.html OK, so it's going to be a week of open science spread out over the month. Probably. I've been distracted by: Silverlight: actually it's quite cool - writing simple multimedia apps is a cinch. Shame that it's probably not going to catch on... it's not that much better than Flash. All that Zed Shaw ragging on the Rails community stuff - mainly cause I think Rails is overhyped (though definitely has its place). I also liked his quote about implementing the semantic web over existing web infrastructure: "Einsteins brain on a crack whores body isn’t going to happen". I disagree but made me laugh... BioMoby (via Egon's delicious bookmarks) Hangovers (there is no cure). Mass Effect - incredibly cheesy sci-fi plot. Naked alien ladies. Voice acting from Seth Green and Lance Henriksen. Had to buy ... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1131710 Sat, 05 Jan 2008 05:00:00 +0100 1131710 http://www.ghastlyfop.com/blog/2007/12/open-notebook-whats-disease-again.html Is there a super-semantic-web-enabled phenotype database out there*? I want to ask a question like 'give a list of monogenic disorders whose locus has been confirmed by at least two labs, broken down by type of causative mutation type' and get an answer.(* on a tangent: is 23andMe's gene book thing freely available?)OMIM falls quite a long way short of this... it never set out to be a resource for programmatic access so you can't really blame them. The morbid map is available for download and contains all of the gene -> disorder mappings in their database.A couple of issues:OMIM's weird entry categorization system (#*%+...) is very confusing. There are 2229 'phenotypes' (note: not 'Mendelian phenotypes') with a known molecular basis in the database, apparently, but only 386 genes with a ph... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1123345 Mon, 31 Dec 2007 05:00:00 +0100 1123345 http://www.ghastlyfop.com/blog/2007/12/open-notebook-pt1.html I've decided to get back into 'proper' science. For a week, anyway, I'm not stupid (well, stupid enough to do this in my spare time, but yeah...). Here's the plan: ask an interesting yet niche and relatively simple question use bioinformatics tools and awesome science 2.0 websites to find answer keep track of progress on this blog put together manuscript and submit to Precedings use backdoor into Nature Genetics manuscript tracking system to get paper acceptedThis may not make for exciting reading - we'll see. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1121738 Sat, 29 Dec 2007 05:00:00 +0100 1121738 http://www.ghastlyfop.com/blog/2007/12/open-notebook-pt2-question-theories.html The questionMonogenic (classically mendelian) disorders are caused by mutations or errors in a single gene. Many of these gene -> disesase mappings have been discovered and are listed in OMIM, the Online Mendelian Inheritance in Man database.There are ~ 1,000 'disease' genes (genes that give rise to a particular monogenic disorder when mutated in particular way) listed in OMIM. If you compare this set to other genes some interesting differences become apparent [1, 2] (only two paragraphs before reference to own paper; this is just like a real writeup!). Check out the table below from [1]:Median gene length (*) is particularly interesting; disease genes have a median length of 27k while the control set sits at 19k. Why?(* the longest known transcript of each gene was used)Some plausible sou... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1121737 Sat, 29 Dec 2007 05:00:00 +0100 1121737 http://www.ghastlyfop.com/blog/2007/12/come-work-for-web-publishing.html NPG is recruiting (a publishing / managerial role): Head of Community Business DevelopmentThis person will play a central role in NPG's evolution as a scientific communication company. They will be based in London or New York and will report to the Publishing Director, Nature.com. This role will focus on using online approaches to develop a better understanding of, and deeper relationships with, each of our users. By serving them better we intend ultimately to attract attention and usage from all professional scientists, and by using these services as the foundation for new businesses we intend to continue NPG's rapid evolution as an online scientific communication company. This role will involve line management responsibility for our existing social software teams, as well as the appointm... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1111870 Sat, 22 Dec 2007 05:00:00 +0100 1111870 http://www.ghastlyfop.com/blog/2007/12/userscripts-for-life-sciences.html Egon and Noel have a paper in BMC Bioinformatics this month describing userscripts for the life sciences... nice work, guys.Last year there was a discussion over at Pedro's of the merits of publishing individual userscripts after Ben Good's paper about a Greasemonkey based iHOP enhancement appeared in BMC. This is more of a review.We discussed the possibility of hosting a science mashups / web services wiki at NPG - sort of like ProgrammableWeb, but listing only the APIs, databases and tools relevant to science. This sort of ties in with the post over at Nodalpoint that Alf wrote about documenting bioinformatics APIs. There's enough stuff available nowadays for it to be a useful resource, I think.Incidentally: I started writing this post BEFORE I read it properly and realised that I got a ... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1111871 Sat, 22 Dec 2007 02:02:48 +0100 1111871 http://www.ghastlyfop.com/blog/2007/12/second-life.html via Alf's delicious bookmarks - Linden Lab has released a beta version of the Second Life client that uses Windmark's 'atmospheric rendering technology'. Big difference, no? (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1079756 Fri, 07 Dec 2007 05:00:00 +0100 1079756 http://www.ghastlyfop.com/blog/2007/11/first-steps-with-opensocial.html I got access to the Orkut Developer's sandbox this morning (at the moment Orkut is the only place where you can test Opensocial apps - Ning also has an implementation but it's far too buggy to work with).I like the idea behind Opensocial a lot. It had to happen, sooner or later.The problem is that in this case, IMHO, Google have gone for 'sooner' a bit too soon. My Opensocial experience has been rubbish. I'm all for release early, release often but the whole thing seems half-baked to me.I'm not talking about the API itself, just the implementation, though the API also has issues (for example: no way of identifying app visitors who aren't logged-in members of the social network you're hosted on).First off: the Orkut sandbox sucks, big time. It becomes marginally more usable once you discove... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=1002800 Mon, 05 Nov 2007 05:00:00 +0100 1002800 http://www.ghastlyfop.com/blog/2007/10/three-stories.html This ("three stories about science and the web") - in particular Mike's reply to the first comment - cheered me up today. Heh. Got me thinking. Journals carrying lonely hearts ads aren't a terrible idea. I mean, people who read the same niche journals have similar professional interests, probably go to the same conferences... Anyway, Bioinformatics Zen is full of good stuff. Check it out if you haven't already. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=964600 Fri, 19 Oct 2007 04:00:00 +0100 964600 http://www.ghastlyfop.com/blog/2007/10/activity-aggregation.html Over at Nascent I just blogged about a pet project - building an aggregator for scientific contributions outside of the literature. This idea came out of conversations within NPG and has been gestating for a while. I had a rough prototype at Scifoo but things haven't progressed very far since then. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=935299 Mon, 08 Oct 2007 04:00:00 +0100 935299 http://www.ghastlyfop.com/blog/2007/10/connotea-postgenomic-complaints.html I was catching up on my Bloglines subscriptions and came across Tiageo's 'Pissed with Connotea' post about some complaints he had about some NPG products. I was going to reply in a comment but figured that T's points are worth addressing here, too.1. [Connotea] Performance and downtime: Sometimes to submit a citation takes ages, or the service is down (although, regarding downtime, it seems to be getting better).Yeah. This is something that has plagued Connotea recently though it is getting better as you say. Unfortunately the solutions aren't as easy as you might think. Ian Mulvany - who runs the site - was saying earlier that they're looking at adding a new server this week, which should help.2. Postgenomic: When I tried to use it, it was mostly down. Want anedoctical evidence? If you se... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=934024 Mon, 08 Oct 2007 04:00:00 +0100 934024 http://www.ghastlyfop.com/blog/2007/08/scifoo-1.html So Scifoo was awesome. We've set up an aggregator at Nature.com that'll collect post-foo posts, photos and news articles as they come out, to go along with Andrew's Planet Scifoo. It's at www.nature.com/scifoo.Something I haven't seen mentioned in any other blog posts - on Friday night Nikita Bernstein from JoVE set up a Digg style 'prototype initiative' where campers could submit ideas for collaborations. A couple of ideas that got discussed at the conference are up there now.One of my favourites is Carl Bergstrom's Fantasy Journal League:Create the rules and web infrastructure for a game of "fantasy journals" analogous to the fantasy baseball and fantasy football leagues that are so popular among sports fans. Scientists could draft papers for their own fantasy journal, and then compete t... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=786745 Wed, 08 Aug 2007 04:00:00 +0100 786745 http://www.ghastlyfop.com/blog/2007/07/simpsons.html Wouldn't normally plug Nature content here, but there's an interview with Al Jean in this week's Nature Podcast that's worth a listen (it's only five minutes long). It'll also appear in the print edition.Piltdown angel: In "Lisa the Skeptic" an almost complete human skeleton with angel's wings pits science — Lisa and guest star Stephen Jay Gould — against faith, as defended by Ned Flanders: "Science is like a blabbermouth who ruins a movie by telling you how it ends. Well I say that there are some things we don't want to know. Important things!" - from the top ten science moments in the SimpsonsDidn't think much of the trailer but apparently the film is brilliant.Physics World covered science in the Simpsons too. A quick Google search also turns up this introduction to physics that use... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=758692 Thu, 26 Jul 2007 04:00:00 +0100 758692 http://www.ghastlyfop.com/blog/2007/07/improving-science-blog-platforms.html I've posted on Nascent asking for a wishlist of plugins and tweaks to make blogging software more scientist friendly.I'm pretty sure that lots of 'one coder and a free weekend could save thousands of (wo)man hours of blog gruntwork' type scenarios exist in science blogging in general. Let's find them...Seeing as I'm a stone-age Blogger.com user I'm probably missing out on all sorts of cool stuff, of course. We only got tagging a couple of months ago. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=740494 Tue, 17 Jul 2007 04:00:00 +0100 740494 http://www.ghastlyfop.com/blog/2007/07/easypg.html Pierre Far from BlogSci has written an excellent WordPress plugin called EasyPG that helps you mark up blog posts for Postgenomic (and Chemical Blogspace).Now we just need to find somebody who can write MoveableType plugins... (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=721355 Mon, 09 Jul 2007 04:00:00 +0100 721355 http://www.ghastlyfop.com/blog/2007/07/crossref-metadata-for-all.html (via Code4Lib) CrossRef currently has a competition running. Submit a proposal for an innovative service that uses CrossRef data and if you're selected you can get an account for free (giving you access to the CrossRef database, which normally costs $$$).In case you haven't heard of CrossRef:CrossRef's specific mandate is to be the citation linking backbone for all scholarly information in electronic form. CrossRef is a collaborative reference linking service that functions as a sort of digital switchboard. It holds no full text content, but rather effects linkages through Digital Object Identifiers (DOI), which are tagged to article metadata supplied by the participating publishers. The end result is an efficient, scalable linking system through which a researcher can click on a reference... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=711735 Tue, 03 Jul 2007 04:00:00 +0100 711735 http://www.ghastlyfop.com/blog/2007/06/precedings-pt2.html We're going to try using groups and forums on Nature Network as places to discuss Web Publishing products. The idea is that Network's limitations will become apparent very quickly (well, not very quickly, it's well written - but complex and still relatively new) and we'll be able to prioritize fixes and new features better. This makes sense. Before anybody mentions it in the comments I think that Network needs RSS too. AFAIK it's on the to-do list.Anyway, Precedings has a group there which you can use to request new features, discuss the issues surrounding biomedical preprints, ask questions about the site, etc. Hilary Spencer (who runs Precedings) has already posted about submitting research to Precedings vs just posting it on your blog. It's interesting stuff - wasn't there a similar dis... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=683208 Wed, 20 Jun 2007 04:00:00 +0100 683208 http://www.ghastlyfop.com/blog/2007/06/publishers-trackbacks-and-shared-data.html The elevator pitch version of this post: if you're a science publisher interested in the web then let's talk about collaborating on a shared system that will stimulate online discussion, kickstart commenting and recognize the sometimes valuable contributions already being made every day by science blogs.I'm a strong believer in allowing commenting on online papers. This is something under serious discussion at Nature (the question is how to do it properly). The vast majority of researchers read, organize and discover papers online; we should give them the tools and opportunity to discuss papers online, too.It's easy to be dispirited by the lack of comments on early adopters - though what would an appropriate number of comments on a paper be? Is one comment pointing out a critical error wor... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=683210 Mon, 18 Jun 2007 04:00:00 +0100 683210 http://www.ghastlyfop.com/blog/2007/06/precedings.html launched officially last week. Pedro has blogged his impressions with the closed beta already. Egon and Deepak both had posts about it too. It's now open to everybody.The thirty second overview: it's a preprint server for the life sciences. Submitted manuscripts gets a DOI and are citable. There's no peer review (though you can leave comments). (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=683209 Mon, 18 Jun 2007 04:00:00 +0100 683209 http://www.ghastlyfop.com/blog/2007/06/facebook-as-platform-pt2.html I thought that it might be useful to blog my experiences with the new Facebook Platform API. For the past two weeks I've been working on Bookshare in my spare time. Bookshare is a book review site with social networking features (feel free to sign up and let me know what you think).Anyway....Facebook makes you think about scalabilityHere was my first harsh Facebook lesson: apps can spread fast. Not necessarily exponentially but always faster than you can iterate over your code optimizing it. Quick hacks come back to bite you in the ass hours after you implement them, rather than months, because your userbase can double overnight.Here's a fictional but in no way implausible scenario: imagine that you wrote an application that shows lolcats on people's profile pages to try out the Facebook A... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=676015 Wed, 13 Jun 2007 04:00:00 +0100 676015 http://www.ghastlyfop.com/blog/2007/06/scintilla.html We're doing some pre-launch tweaking of Scintilla, a new science aggregation product, at Nature. It's a something that Alf and I have been working on recently (well, Alf has been working on it, I mostly just complain and then swoop in to take credit by sending out invites at the last minute ;)).You're welcome to check it out and send any comments, suggestions or bug reports to scintilla@nature.com. We'll be acting on your feedback, so do drop us a line.There'll be more official announcement on Nascent later. (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=676016 Tue, 12 Jun 2007 04:00:00 +0100 676016 http://www.ghastlyfop.com/blog/2007/06/if-youre-goin-to-san-francisco.html I'll be in San Francisco for a couple of days at the beginning of August (1st-3rd), before SciFoo.Anybody in the Bay Area fancy meeting up? (Source: Flags and Lollipops - Bioinformatics Blog) Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=676017 Mon, 11 Jun 2007 04:00:00 +0100 676017 http://www.ghastlyfop.com/blog/2007/05/facebook-as-platform-pt-1.html (The next couple of posts have very little to do with bioinformatics - sorry).I've been trying out a whole bunch of online social networks this year in the name of research (no, really). LinkedIn is the most boring. Bebo, which has a widget that suggested that my celebrity lookie-likie is Whoopi Goldberg, is the weirdest. MySpace is just scary.Facebook is pretty good, though. The design is grown up and so is the userbase (relatively speaking). Nature has a group there to help point young scientists towards some of the less obvious services that NPG provides (like free drinks at Nature Network meetups - if you're in London then come along). Facebook were the first big social network to release an API and now they've gone a step further and opened up Facebook as a platform.I was pretty excit... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=638196 Sat, 26 May 2007 04:00:00 +0100 638196 http://www.ghastlyfop.com/blog/2007/05/pg10k.html OK, it's cheating because the figure includes books as well as papers, but Postgenomic has now tracked more than ten thousand citations in blog posts. As the majority of blogs either (a) don't supply fulltext RSS feeds, just excerpts or (b) strip out HTML and thus the links from feeds there must be a sizeable dark figure, too - how many citations are being missed by Postgenomic and Chemical Blogspace, I wonder?Anyway, paper #10,000 was Mauro Costa-Mattioli's paper in Cell about stress induced translation regulation (conveniently the citing post from Gene Expression explains what that is and then goes into some interesting detail - an excellent advert for science blogging).I'm pleased. Scientists write blogs and put science in them. They talk about recent papers. Their numbers are growing. ... Flags and Lollipops - Bioinformatics Blog blogs http://www.medworm.com/rss/comments.php?id=612354 Thu, 17 May 2007 04:00:00 +0100 612354