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 'What You're Doing Is Rather Desperate' source. Thu, 08 Jan 2009 11:40:10 +0100 http://nsaunders.wordpress.com/2009/01/08/conversation-takes-unexpected-and-welcome-direction/ This is just brilliant. The PSB 2009 panel session on “molecular bioinformatics for disease” has veered in a far more interesting direction. I’m reading it as the establishment versus the enlightened, but don’t let me influence you - go and look at the thread yourself. I so wish I was there. Posted in bioinformatics, meetings   Tagged: friendfeed, psb2009    (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2086873 Thu, 08 Jan 2009 03:09:56 +0100 2086873 http://nsaunders.wordpress.com/2009/01/07/text-to-fasta-and-other-delights-of-the-shell/ One thing I’ve learned in my current job is that some familiarity with Linux tools for processing text files: awk, sed, grep, head/tail, cut/paste and so on, often provides a speedier solution than writing a script in (insert scripting language of choice here). I know this stuff is trivial to shell gurus, but I still get a little buzz out of it. A couple of real-life examples. Delimited text to fasta Your collaborator has developed “peptides on a chip” and sends you a text file describing said chip where column 1 = spot number, column 2 = peptide sequence: 1 ELDQGSLATSF 2 VDLAATPTDVR 3 TTNEEYLDLSQ 4 SSLDVYDGRFL 5 ALVHSYMTGRR Your analysis requires that the peptide sequences be in fasta format. Easy, using awk: awk '{print ">peptide" $1 "\n&qu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2083948 Wed, 07 Jan 2009 03:02:42 +0100 2083948 http://nsaunders.wordpress.com/2009/01/06/uninspired-attend-psb-2009-virtually/ Christmas break too short? More tired after the holiday than you were before? Perhaps you’d like to be on a Pacific atoll; Hawaii, for example. Cheer up - attend the 2009 Pacific Symposium on Biocomputing via the magic of FriendFeed. They’ve already had an excellent session on open science (more details here) and the fun continues through to January 9. Thanks to Shirley, Cameron et al. for the virtual proceedings. Oh, and a belated happy New Year. Posted in bioinformatics, meetings, open science, web resources   Tagged: friendfeed, hawaii, psb2009    (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2081028 Tue, 06 Jan 2009 00:46:24 +0100 2081028 http://nsaunders.wordpress.com/2008/12/10/thesis-reflections/ All these people finishing their theses takes me back to my own Ph.D. thesis writing experience. Not that I recall much about it at all; rather like giving birth, the memory erases the excruciating pain and substitutes a kinder, gentler version. I took way too long to write up, for a variety of reasons, but a major factor can be summarised in one word: Microsoft. In those days I was running Windows 3.1 and Word 6 (I think), on 433 MHz PC with 8 MB - yes, megabytes, of memory. It crashed. A lot. In fact I could not save documents that contained embedded images, so my solution was to insert the image, draw lines around it to indicate its position, remove the image and save. Before printing I added each image back, removed the lines, printed the page then removed the image again. Insane! Eve... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2026879 Wed, 10 Dec 2008 06:03:51 +0100 2026879 http://nsaunders.wordpress.com/2008/12/07/what-i-learned-from-clay-shirky-about-science-online/ The “science online” community has somehow compiled a required reading list (thanks John!), from which many ideas and quotes are mined. I recently finished reading an entry on the list: Here Comes Everybody, by Clay Shirky. I enjoyed the book - much of it was familiar to me, but it makes good use of specific examples to convey general principles. Of more interest to me is the application of these ideas to science online. Here’s what I think we can extrapolate from the book - and this is purely my personal interpretation. Most online science communities will fail Why? Answer: almost everything on the Web fails. However, there is so much activity that a few ideas succeed. Shirky uses the notion of “failure for free”; if you have an idea, it costs little or not... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2017501 Sun, 07 Dec 2008 09:26:08 +0100 2017501 http://nsaunders.wordpress.com/2008/11/27/openid-dont-provide-if-you-wont-accept/ Once again, an interesting FriendFeed discussion has morphed into a thread on a wider issue: OpenID. OpenID is one of those brilliantly simple ideas that you’d imagine most people would applaud. A single “digital identity”, used for any website that requires a login, rather than creating multiple accounts, usernames and passwords for each site. Here’s the problem: many services allow you to use your account details as an OpenID at other sites, but they won’t accept credentials other than their own. For example, both my WordPress and GMail accounts are OpenIDs, but I can’t login to Google using nsaunders.wordpress.com. You might ask - why? Is it some sort of “brand loyalty” issue? When I sign up to Service X, is there a contract between us suc... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1990651 Thu, 27 Nov 2008 07:23:26 +0100 1990651 http://nsaunders.wordpress.com/2008/11/27/spreading-the-message-a-few-minds-at-a-time/ Given my passion for online science networking, it’s surprising that I’ve never given a talk on the subject [1]. So a big thank you to William who invited me over to his institute for an informal chat about the topic with a small group of staff. I learned that: A good quote from an internet guru goes down well Everyone loves an xkcd cartoon Many biologists still don’t know what an RSS feed is My slides are embedded, below or visit Slideshare - best viewed full screen. 1. Oh wait, I work in a university Posted in education, networking   Tagged: communication, science 2.0, social, web 2.0    (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1990652 Thu, 27 Nov 2008 04:50:48 +0100 1990652 http://nsaunders.wordpress.com/2008/11/19/reproducibility-understandable-if-not-desirable/ Greg Wilson once told me a statistic concerning the mean lifetime of research software reproducibility. That is, the time that elapses on average after which you cannot reproduce your own results using your own code, never mind anyone else’s. I forget the exact number but it was not high - a few months at best. Why does this happen, aside from obvious bad practices? Well, here’s a typical exchange in an academic research setting: Doctor X: Oh! I should have included the PDB header and diffraction resolution in my database table. Guess I’ll have to modify my parser. Doctor Y: No, don’t do that. I have those columns in one of my tables. I’ll just dump them out and you can import them in. Doctor X: Great, thanks! Six months later… Doctor X: Hey, I’m ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1968719 Wed, 19 Nov 2008 07:50:38 +0100 1968719 http://nsaunders.wordpress.com/2008/11/13/silly-script-for-the-day/ So, you’d like to submit a URL to Open Laboratory 2008, you want to know if it’s already in Bora’s list and your machine runs Ruby? I thought so! Save the following code as “bora.rb”, make it executable and run: ./bora.rb http://your.url.goes.here #!/usr/bin/ruby require 'rubygems' require 'hpricot' require 'open-uri' def check_url(url) d = Hpricot(open("http://scienceblogs.com/clock/2008/11/the_open_laboratory_2008_only.php")) d.search('a[@href]').each {|a| if url == a['href'] return "Already submitted: #{a.inner_text}" end } return "No exact match found" end puts check_url(ARGV[0]) It will only match identical URLs and is missing all kinds of checks and tests. Pos... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1955190 Thu, 13 Nov 2008 07:16:23 +0100 1955190 http://nsaunders.wordpress.com/2008/11/13/good-software-data-and-your-brain/ I recently asked the FriendFeed community about wiki usage and was struck by a comment from Allyson: I think we’re on our third incarnation of various bits of wiki software, and we’ve finally hit on the right software for both our wet lab and bioinformaticians By “the right software”, she means software that makes sense to the people who use it. When faced with several software alternatives, we often find there is one which for some reason, “makes sense” - it meshes naturally with the way our brains work. When you find a program that you like, it’s not only a joy to use but can enable understanding of data and processes that previously eluded you. In other words, good software doesn’t shield you from the fundamentals - it illuminates them. ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1955191 Thu, 13 Nov 2008 03:23:08 +0100 1955191 http://nsaunders.wordpress.com/2008/11/06/dokuwiki-pubmed-and-ruby/ I recently built a wiki for a research group using DokuWiki, one of my favourite wiki packages. As with many other wikis, developers have extended its functionality by writing plugins. Some of these are excellent, allowing users to generate lots of content with a minimum of syntax. For example, using the PubMed plugin, you type this: {{pubmed>long:15595725}} and the result is this: Which got me thinking. Assuming that you’ve searched PubMed and retrieved a bunch of references in XML format, how might you generate text in DokuWiki syntax, to paste into your wiki? Here’s the small parser that I wrote in ruby: #!/usr/bin/ruby require 'rubygems' require 'hpricot' h = {} d = Hpricot.XML(open('pubmed_result.xml')) (d/:PubmedArticle).each do |a|... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1938982 Thu, 06 Nov 2008 08:54:13 +0100 1938982 http://nsaunders.wordpress.com/2008/10/30/bar-tailed-godwit/ Bar-tailed godwitThis is a little odd - the tale of the publication that isn’t. You may recall a recent story that appeared at most media outlets concerning “E7″, a bar-tailed godwit (Limosa lapponica) that flew 11 680 km non-stop, Alaska to New Zealand. Here are some of the reports: Bird, Uninterrupted Bar-tailed Godwit Becomes a New Bird Record-Holder: “According to Proceedings of the Royal Society B…” Bird flaps wings for 9 days non-stop: “The study, reported in the Proceedings of the Royal Society B…” Extreme Endurance Flights By Landbirds Crossing The Pacific Ocean: “Proceedings B is the Royal Society’s flagship biological research journal…” Amazing Marathon Bird: “According to the U.S. Geological Sur... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1917903 Thu, 30 Oct 2008 07:17:42 +0100 1917903 http://nsaunders.wordpress.com/2008/10/21/reasons-to-love-the-web-999/ Every day, I’m amazed by the information ecosystem that we call the WWW and how it has changed forever the way we educate ourselves. Today’s illustration. I spent part of last weekend strolling through the beautiful rainforest of Brisbane Forest Park, a mere hour’s drive from the city. On the track at Maiala I heard a very bizarre noise, high in the misty canopy. The sound was a blend of fighting cats and crying children, yet strangely musical. It was a new sound to me but the cat-like aspect was a give-away, since I was aware of a species called the green catbird. Back at home, I consulted the trusty Simpson and Day’s Birds of Australia. It described a sound similar to what I had heard but of course, bird sounds don’t translate to written English very well. S... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1891929 Tue, 21 Oct 2008 06:22:42 +0100 1891929 http://nsaunders.wordpress.com/2008/10/17/the-three-phases-of-mysql-usage/ As Mike keeps reminding me, getting your data into database tables is A Good Thing. Like many people, my database of choice is MySQL - largely because it was the first one that I tried and it works for me. However, I’m far from being an expert MySQL user. In fact, I’ve identified 3 stages in my use of MySQL over the years; see if you recognise yourself in any of them. The single table database Early in your MySQL career, you discover either “LOAD DATA INFILE” or the command-line tool “mysqlimport”. You realise that this is a quick and easy way to get all of those delimited text files straight into a database. Off you go, merrily importing everything on your hard drive into tables. At some stage, you begin to wonder whether listing the same identifier (... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1883278 Fri, 17 Oct 2008 04:55:33 +0100 1883278 http://nsaunders.wordpress.com/2008/10/17/giant-panda-genome-mapped-or-sequenced/ I’m with Ogden Nash who said: I love the baby giant panda, I’d welcome one to my veranda This week, I learned via Keith that Chinese scientists announced the completion of the giant panda genome. An impressive achievement, given that the project was announced in March this year, but what exactly has been completed? Has the genome been sequenced - that is, there are strings of A, C, G and T covering most chromosomes, or mapped - that is, the approximate chromosomal location of most genes determined? The media seem unsure. The Australian: Scientists in China have mapped the genome of the giant panda… Window of China (the official source, it seems): Chinese scientists have completed sequencing the genome of giant pandas… The China Post: The Chinese-led genome-mappin... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1883279 Fri, 17 Oct 2008 01:16:14 +0100 1883279 http://nsaunders.wordpress.com/2008/10/14/open-access-day/ It’s Open Access Day. Mission: to broaden awareness and understanding of Open Access. Their approach: “synchro-blogging” - an attempt to get as many folks as possible to blog on the given topic at the same time. So, to answer their questions: Why does Open Access matter to you? OA is important for many reasons: go and read this by Jonathan Eisen instead of my rambling. One that stands out for me: it signals a fundamental change in the way that information is conveyed from writers to readers and an admission that the traditional publishing process is obsolete in the internet age. We live in a world where people expect instant, relevant information in the top 20 hits from a Google search and that expectation is transferring to science too. I don’t care how prestigiou... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1873012 Mon, 13 Oct 2008 23:29:23 +0100 1873012 http://nsaunders.wordpress.com/2008/10/04/ignobels-2008/ I mark the passing of the years in a couple of ways. One is natural events: the coral tree flowers in mid-winter, the jacaranda flowers in spring, the comings and goings of Queensland’s bird species. The other is the annual IgNobel award ceremony. 2008 is a vintage year: List of winners BBC News story The Guardian story It’s hard to choose a favourite this year. Armadillos and archaeology would have to be up there, but based on the idea that how much you laugh correlates with how much you relate, I’m going with: “You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations”, from the journal Organization Studies. Posted in humour, publications, science news   Tagged: 2008, ignobel    (Source: What Y... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1850944 Sat, 04 Oct 2008 01:49:17 +0100 1850944 http://nsaunders.wordpress.com/2008/09/27/it-would-be-too-easy-to-rant-and-rave-about-this/ Zotero is a marvellous, active open-source project, providing a Firefox extension that captures and formats bibliographic information from web pages. Thomson Reuters describe themselves as “the world’s leading source of intelligent information for businesses and professionals.” Whatever. They specialise in closed-source, proprietary solutions which to my simple mind is at odds with a role as an information source. Via FriendFeed from Rafael Sidi’s blog, I learn that Thomson Reuters are suing George Mason University, developers of Zotero, for “violating its license agreement and destroying the EndNote customer base”. Here’s my simple, black-and-white view of the world. The greatest achievement of the internet is the potential to set information free... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1833127 Sat, 27 Sep 2008 02:15:58 +0100 1833127 http://nsaunders.wordpress.com/2008/09/25/genomic-analysis-of-pseudoalteromonas-tunicata/ Some years ago, I provided advice and a little analysis for a group at UNSW studying marine bacteria. It’s nice to see that they remembered me: Thomas, T., Evans, F.F., Schleheck, D., Mai-Prochnow, A., Burke, C., Penesyan, A., Dalisay, D.S., Stelzer-Braid, S., Saunders, N., Johnson, J., Ferriera, S., Kjelleberg, S. and Egan, S. (2008). Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment. PLoS ONE 3:e3252. If correlating genomic features with microbial physiology is your thing, go and check it out. The article is open access, for your pleasure - as are five of my last six efforts, I just noticed. Posted in bioinformatics, genomics, publications, research diary   Tagged: plos one, pseudoalter... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1825493 Thu, 25 Sep 2008 06:31:41 +0100 1825493 http://nsaunders.wordpress.com/2008/09/23/theme-change/ Blog post about the blog - yawn! I’m trying a new, cleaner theme - The Journalist. It has one flaw - not at all obvious where to leave a comment. Answer: click on “with XX comments” (or “without comments”), above the post. Posted in this blog   Tagged: design, themes    (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1815225 Tue, 23 Sep 2008 06:02:29 +0100 1815225 http://nsaunders.wordpress.com/2008/09/18/not-as-many-structures-as-you-might-think/ In the midst of preparing a talk for next Monday. It occurred to me that perhaps we don’t see more protein structure-based prediction in bioinformatics because - there aren’t enough structures.pdbstatsSure, the PDB has grown a lot in the past 5 years or so and 53 103 structures (as of now) looks impressive. However, if you’re interested in protein-protein interaction, you want at least 2 chains: which more or less halves the dataset. If you want two different protein chains, you lose almost another 75%. Let’s specify a reasonable minimum resolution for X-ray diffraction data and there go ~ 3 000 entries. We probably don’t want multiple, similar proteins so let’s remove sequence identity at a redundancy of 90%. We’re left with about 2% of the origin... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1802641 Thu, 18 Sep 2008 05:14:26 +0100 1802641 http://nsaunders.wordpress.com/2008/09/08/on-parsing/ Parsing - the act of ripping through a file, pulling out the relevant parts and doing something useful with them, is an integral part of bioinformatics. It can be a dull procedure. It can also be challenging, requiring creativity and imagination. Frequently as a bioinformatician, you will generate output from an unfamiliar program, or a colleague will bring you a file that you haven’t encountered. Your task is to figure out how the file is structured, which regular expressions are required to parse it, what kind of output to produce and most importantly, how to handle those rogue files which don’t obey the rules. Here’s my top ten (language-agnostic) parsing tips, focusing only on unstructured (non-XML) text files. Search for an existing parser… Most of us don&#82... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1773166 Mon, 08 Sep 2008 06:09:44 +0100 1773166 http://nsaunders.wordpress.com/2008/09/04/blogroll/ Couple of new blogs in my Google Reader that you may want to investigate: Bioinformatics on Rails Few posts, updated infrequently - going to follow for a while and see where it goes. Bench Press “We’re four science and tech geeks who decided that the world needs yet another science blog.” A good recent post on electronic lab notebooks. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1759820 Thu, 04 Sep 2008 06:14:44 +0100 1759820 http://nsaunders.wordpress.com/2008/09/04/science-in-the-petabyte-era/ Just a brief note: the title of this post is taken from the cover of today’s Nature. It contains several very good feature articles on the challenges of dealing with peta- (and more) byte size datasets, grouped under the heading “Big data”. Nature contents Sep 4 2008. Nature News Big Data special. By far the best of the articles is The future of biocuration: it offers practical recommendations, as opposed to the “gee whizz, what a lot of data” approach. Not least of which: “curators, researchers, academic institutions and funding agencies should, in the next ten years, increase the visibility and support of scientific curation as a professional career.” Almost as good are Wikiomics, which tackles the lack of participation issue and Welcome to the p... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1759821 Thu, 04 Sep 2008 04:36:38 +0100 1759821 http://nsaunders.wordpress.com/2008/09/02/snippets-4/ Bioinformatics career survey - data released Read the blog post, join the FriendFeed discussion, edit the wiki page. Don’t like the analyses? Download the data, do your own. A new job for everyone’s favourite French bioinformatician - congratulations Pierre (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1750047 Tue, 02 Sep 2008 02:47:20 +0100 1750047 http://nsaunders.wordpress.com/2008/09/02/data-capture-versus-data-archiving/ The commonest complaint that I hear whenever electronic lab notebooks (ELNs) or laboratory information management systems (LIMS) are discussed is that it doubles the workload. People who work in labs enjoy the convenience of their paper notebooks. They perform an action or a process occurs - they write a note. A machine generates a photo - they tear it off and paste it in. Transferring that information to a digital archive is a pain: they have to sit down at a computer with their lab book, scan and upload images, enter text into form fields and so on. I sympathise, absolutely. At present, data capture and data archiving are for most people, disconnected processes. Their only comfort is that smart people are working on these problems. One day, laboratory equipment will emit data in machine-... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1750048 Tue, 02 Sep 2008 02:31:24 +0100 1750048 http://nsaunders.wordpress.com/2008/08/27/a-brief-ecological-interlude-inaturalist/ Recently, I was toying with ideas for fun side projects involving web applications. “Here’s a good one”, I thought, “a place for amateur naturalists to record their observations.” They could upload photos, place items on a Google Map, tag items and all manner of web 2.0 stuff. Over time, with enough users, such a site might even become a valuable conservation resource, allowing data miners to see interesting changes over time. Today, via FriendFeed, I discovered that someone else also likes the idea. I’m delighted, since I’ve long since abandoned all hope of even starting a fun side project; I lack both the requisite skills and the time to learn them. If these ideas appeal to you, please visit iNaturalist. Better still, post some feedback at their ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1733805 Wed, 27 Aug 2008 05:32:35 +0100 1733805 http://nsaunders.wordpress.com/2008/08/23/what-if-journal-current-contents-were-tag-clouds/ In conclusion The best RSS summaries from journals contain abstracts Cluttering up your feed with section headers (often longer than the article titles) reduces readability and information content; I’m looking at you JBC and Science Pretty pictures in feeds contribute nothing (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1726316 Sat, 23 Aug 2008 10:11:17 +0100 1726316 http://nsaunders.wordpress.com/2008/08/18/mysteries-of-ccp4/ Since moving to a structural biology group, I’ve had to become somewhat familiar with CCP4, a suite of programs that do all manner of things using structural data, typically PDB files. Being a bioinformatician, I tend to ignore the GUI in favour of the input -> script -> output approach, as I’m mostly interested in batch processing. Documentation describing this operation for CCP4 programs is strangely lacking on the web. The best that I can find is the CCP4 wiki; if you know the package well, please contribute to it. I eventually dug up what I was looking for in: /opt/ccp4/ccp4-6.0.2/examples/unix/runnable/ or the equivalent on your system. Here, you’ll find a collection of shell scripts, confusingly named with the suffix “.exam”. As an example, here&... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1711726 Mon, 18 Aug 2008 07:30:45 +0100 1711726 http://nsaunders.wordpress.com/2008/08/17/vindication-for-video/ Announced first via FriendFeed (of course), Moshe from JoVE is circulating an email with exciting news. I can’t do better than to quote it here: JoVE, the video-publication for biological research, was accepted for indexing in PubMed and MEDLINE. JoVE is the first and only video-publication to be included in these databases maintained by the National Library of Medicine (NLM). The decision was made by the NLM advisory committee, Literature Selection Technical Review Committee, which is composed of the authorities in the field of biomedicine, such as researchers, physicians, editors, health science librarians and historians. This committee evaluates the scientific quality of publications and typically approves only 20-25% of the applications. Inclusion in PubMed/MEDLINE is a big mile... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1708966 Sun, 17 Aug 2008 08:08:24 +0100 1708966 http://nsaunders.wordpress.com/2008/08/08/biobarcamp-wrap-up/ The latest “unconference”, BioBarCamp, wrapped up today. Once again a FriendFeed room was used to great effect in providing coverage. I think it’s worth stressing that in addition to the “as it happens” aspect, FriendFeed provides a permanent, searchable archive that you can revisit to revise your notes and refresh your memory. Further information is at the BioBarCamp wiki and Deepak has a nice summary of the back-channels and other, similar events. Congratulations to all involved - sounded like an excellent event. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1688952 Fri, 08 Aug 2008 05:04:07 +0100 1688952 http://nsaunders.wordpress.com/2008/08/08/why-you-young-scientist-should-have-a-web-presence/ Three good reasons why you should be writing something, somewhere on the Web: Egalitarianism I hadn’t thought much about this aspect until a conversation with Roland at ISMB. Put simply, the Web democratises the science career ladder. It doesn’t matter if you’re an Honours student or a tenured professor; if you have good ideas and can articulate them, you can bring them to the attention of others and build a community around them. Previously, you would have had to wait until the stage of your career where you’re invited to give keynote addresses - and who has the time for that, these days? Connecting with the right people Ideally, we would all work in dynamic, stimulating environments, surrounded by talented, like-minded individuals keen to bounce ideas off each ot... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1688953 Fri, 08 Aug 2008 03:03:49 +0100 1688953 http://nsaunders.wordpress.com/2008/08/04/anniversary-2/ Managed to fly through my blog anniversary. August 2 marks two years here at wordpress.com. Stats as of now: 677 posts, 10 pages, 49 categories, 255 tags, 1,128 approved comments and 67,184 spam comments (!). Blogging has really dropped off in the past few months, but I have some ideas about that. Stay tuned, thanks for reading and commenting. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1676946 Sun, 03 Aug 2008 14:52:47 +0100 1676946 http://nsaunders.wordpress.com/2008/07/25/ismb-2008-its-a-wrap/ ISMB 2008 wrapped up yesterday. I enjoyed it immensely and will have much more to say in the coming weeks. Right now I just wanted to say: - It was great to meet so many of my online friends for the first time. I’ve “known” some of you for years, others for a few months and really enjoyed catching up with you all in person. - Thanks to all who contributed to the coverage in the ISMB 2008 FriendFeed room. It was quite an experiment and I think we were all pleasantly surprised by how well it worked out. Looks like this could lead to some form of semi-official live blogging next year too, which would be excellent. Tomorrow takes me through Chicago to Manchester, UK, then north to a little place called Carlisle - which happens to be where I was born. It’s not the most w... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1652269 Fri, 25 Jul 2008 03:07:00 +0100 1652269 http://nsaunders.wordpress.com/2008/07/15/off-to-ismb-2008/ ISMB 2008 posterThe last major international conference that I attended was ISMB 2003. It was - right here in Brisbane, although I was living in Sydney at the time. I have to admit that I haven’t always been proactive when it comes to seeking funds to attend meetings. I’ll admit too that I have mixed feelings about conferences. Many of my best friends are scientists, but there’s something about being in a confined space with several hundred intense, academic types that unsettles me. There’s also the prospect (for Australians) of travelling for 24 hours to reach N. America or Europe. Tomorrow, I’m jetting off to ISMB 2008 in Toronto. I’m sure that I’ll have a fine time once I get there and look forward to putting faces to those names that I’ve... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1622074 Tue, 15 Jul 2008 00:09:10 +0100 1622074 http://nsaunders.wordpress.com/2008/07/08/more-wikis-in-biology/ Hot on the heels of WikiProteins comes: Huss, J.W. III et al. ( 2008 ) A Gene Wiki for Community Annotation of Gene Function PLoS Biol 6(7): e175 | Open Access Which anyone can read, because it’s open access. It’s a realistic assessment of community annotation, focusing on the creation of gene stubs for editing within Wikipedia. Early reaction at the OpenHelix blog and a thread at FriendFeed. Thanks to Andrew Su, who was kind enough to send me a preprint. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1593769 Tue, 08 Jul 2008 08:34:38 +0100 1593769 http://nsaunders.wordpress.com/2008/07/08/thoughts-on-other-programming-languages/ With respect to their potential for bioinformatics web applications: Feature Python Ruby Modern, clean syntax, object-oriented Yes Yes Web framework Django Rails Bio library BioPython BioRuby Extensive Bio graphics library Not really - any more than this? Kind of - Bio::Graphics Use with App Engine Yes Not yet Well-regarded by scientific programmers Yes ?? To the novice, it looks like “much of a muchness”. Thoughts? (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1593770 Tue, 08 Jul 2008 01:53:38 +0100 1593770 http://nsaunders.wordpress.com/2008/07/02/bioinformatics-career-survey/ Just in case you haven’t seen the post at multiple other locations: Mike is running a bioinformatics career survey over at his blog. It won’t take more than 5 minutes to answer and should provide an interesting picture, so help him out when you have a moment. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1560765 Wed, 02 Jul 2008 01:37:49 +0100 1560765 http://nsaunders.wordpress.com/2008/06/19/well-everyone-else-was-doing-it/ Everyone seems to be having fun with Wordle. Except for me, until I realised that all my machines were cursed with something named “icedtea-gcjwebplugin”, as opposed to the Sun java plugin. Problem solved. So there it is. But for the prominent “bioinformatics”, you’d never guess I was a biologist, would you. I do believe that this is telling me something. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1526041 Wed, 18 Jun 2008 14:14:58 +0100 1526041 http://nsaunders.wordpress.com/2008/06/17/linux-tip-forward-email-from-m-exchange-server-to-gmail/ My work email has migrated to M$ Exchange Server, with M$ Outlook Web Access. Eurgh. No more POP3 retrieval to my GMail account. I restored sanity using an Ubuntu server as follows. Needless to say, this requires that (a) the exchange server allows IMAP access and (b) the SMTP server for your machine will relay mail outside of your domain. Updated: to do it all via procmailrc, without .forward Install fetchmail and edit /etc/fetchmailrc: sudo apt-get install fetchmail sudo nano -w /etc/fetchmailrc Make /etc/fetchmailrc look something like this: set daemon 300 poll your.exchange.server protocol imap username “user” password “pass” smtpname “user@gmail.com” ssl replacing your.exchange.server, user (exchange), pass (exchange) and user@gmail.com (your ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1526042 Tue, 17 Jun 2008 07:50:25 +0100 1526042 http://nsaunders.wordpress.com/2008/06/17/friendfeed-best-of-the-week/ The new best of FriendFeed feature is proving to be a hit. It also provides material for people who are too busy to write real blog posts. Here’s my top 10, according to FriendFeed, from the past 7 days: We’re all looking forward to having an insider at Amazon Web Services Cameron explains FriendFeed for scientists A variety of (non-serious) explanations for the falling number of Google searches for bioinformatics-related keywords Our thoughts on certifying online research Get to know Prochlorococcus - you’re probably breathing the by-product of its metabolism right now Pierre on sorting articles by journal impact factor Could XMPP be the new MPI? Welcoming new members to the Life Scientists room Who’s off to ISMB 2008? Paris area employers: call this talented man ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1521987 Tue, 17 Jun 2008 00:28:48 +0100 1521987 http://nsaunders.wordpress.com/2008/06/06/automatic-content-for-the-people/ Anyone who has ever built a website knows that maintaining it is a lot of work. There’s just making sure it hasn’t gone offline because the httpd daemon died. Constant monitoring for script kiddies and their SQL injections. Not to mention continually feeding it with fresh content, lest your audience become bored and desert. I’ve always thought it would be cool to build a site that could more or less look after itself. There’s a myriad of content management systems to choose from, most of which are somewhat hackable in whatever language they happen to be coded in. One of the more mature in this respect is Drupal - which is the engine behind Eureka! Science News. It’s a fully-automated science news portal, using a bunch of customised Drupal modules to aggregate,... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1497390 Fri, 06 Jun 2008 11:53:22 +0100 1497390 http://nsaunders.wordpress.com/2008/06/03/notes-from-the-day-job-published-3-4-2008/ This year, I’ve experienced what bloggers call - um, not blogging very much. One reason is that much of our conversation has moved to other services - notably FriendFeed. However, the main reason is that I have a day job: develop bioinformatics applications, perform research, publish articles, present talks and keep the boss happy. Read on for some “notes from the day job” - especially if protein kinases and their substrates are your thing. When I arrived at UQ a couple of years ago, I inherited a project named Predikin. The goal of Predikin is to predict substrates for protein kinases, using structural features in the kinase catalytic domain. It’s a simple but effective idea: you look at the available structures of protein kinase-substrate peptide complexes and lo... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1488130 Tue, 03 Jun 2008 04:49:43 +0100 1488130 http://nsaunders.wordpress.com/2008/05/30/too-beta-to-be-live/ Yes, I’m referring to you, SciLink. I create an account On trying to add contacts from my address book, 7 alert windows pop up with the message “the page at scilink says error” - fixed The page then hangs with a spinning icon Some time later, the site spews errors including “Exception org.springframework.web.util.NestedServletException” Not to be deterred I try to edit my profile The “extensive database” finds 6 13 of my 23 publications and provides no easy way (e.g. PubMed ID) to add the rest The dates of my education are saved incorrectly (1988-92 not 1989-93, 1992-96 not 1993-97) - fixed Apparently I will be in my current post until the year 9998 - fixed The final insult - no link to delete my account and escape Can you tell that I’m ann... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1477854 Fri, 30 May 2008 07:34:32 +0100 1477854 http://nsaunders.wordpress.com/2008/05/29/wikiproteins/ It’s not every day that a publication in an academic journal devoted to genomics receives wide attention all over the Web. I’m referring of course to: Mons, B. et al. 2008 Calling on a million minds for community annotation in WikiProteins Genome Biology 9:R89. Nor is it every day that one of the “et al.” is a WWW pioneer; in this case a certain J. Wales. I’m looking forward to seeing S. Brin and L. Page in PubMed any day now. This is important. The early adopters and web technology enthusiasts can evangelise for years about concepts such as community annotation of scientific data using wikis. However, the sad fact is that the majority of researchers in academia will pay no attention whatsoever until the work appears in what they consider a reputable source:... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1475107 Thu, 29 May 2008 06:38:26 +0100 1475107 http://nsaunders.wordpress.com/2008/05/27/life-on-mars/ Late one evening back in July 1997, I was alone in the lab writing my Ph.D. thesis, several months behind schedule. I fired up the web browser (probably Mosaic in those days) on our single computer and discovered that a tiny rover was about to land on Mars. Live, on the web! When people use the phrase “web design circa 1996″, this is what they mean. It was all very exciting back then. Up came the first image, in near-real-time. Wow! I’ve been a Mars geek ever since. Yesterday morning there I was again, except this time I was watching live streaming video of the Phoenix lander. After a near-perfect landing, the science is set to begin and it could be pretty exciting. Phoenix is the first lander since the Viking program to dig into and analyse the Martian surface. If there ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1469585 Tue, 27 May 2008 03:50:34 +0100 1469585 http://nsaunders.wordpress.com/2008/05/20/google-health-live/ The much-vaunted Google Health is online. There’s a good early review at TechCrunch. Expect further coverage from bloggers who cover personalised medicine issues; you know who they are. Questions that occur to me are: (1) how much personal information do you need to enter for the service to be useful; (2) how much will users be willing to enter? This will be a real test of the degree to which people trust Google with personal information. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1454304 Tue, 20 May 2008 01:12:41 +0100 1454304 http://nsaunders.wordpress.com/2008/05/12/proteomics-discussion-from-the-science-streamosphere/ We find ourselves wondering why codon adaptation index (CAI) is used as a measure of protein expression level in this article. One answer is that CAI does correlate well with protein expression in many proteomics studies; but surely these same studies contain raw data with protein expression level? On reflection, I bet the answer is that it’s too difficult and laborious to access this type of data. There are plenty of papers that describe large-scale analysis of protein expression using proteomics, but the data are locked up in the articles or as inappropriate supplementary files. Note to self: look into open-source software and standard data formats for proteomic data. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1436793 Mon, 12 May 2008 01:27:45 +0100 1436793 http://nsaunders.wordpress.com/2008/05/09/published-2-2008/ It’s turned out to be a pretty good week. This one has been in press for ever, but finally hit the web: Frith, M.C., Saunders, N.F.W., Kobe, B. and Bailey, T.L. (2008). Discovering Sequence Motifs with Arbitrary Insertions and Deletions. PLoS Computational Biology 4(4):e1000071. [Open Access] | [PubMed] This paper describes GLAM2, a Gibbs sampler that finds and refines variable-width motifs, allowing insertion and deletion, in related but dissimilar sets of sequences. The work is very much Martin’s baby; my minor contribution was to try it out on some test datasets. It’s open-access, so you can all go and enjoy it. Two more (unrelated) in press to tell you about soon. See, I do have a day job outside of this blog. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1432379 Fri, 09 May 2008 13:42:36 +0100 1432379 http://nsaunders.wordpress.com/2008/05/08/a-brief-history-of-the-platypus-in-5-parts/ Who isn’t fascinated by the strangest of mammals, the platypus? It has fur and lactates, like a mammal. It has a bill and webbed feet, like a bird. It lays eggs and produces venom, like a reptile. It finds prey using electroreception, like sharks. The platypus is so weird that when first described, many scientists assumed that it was a hoax. To celebrate the publication of the draft platypus genome, here’s a brief guide to this wondrous creature. Part 1. The Dreamtime Story We scientists think that we’re very smart when it comes to explaining the natural history of Australia. However, the original inhabitants of this country have a rather different and quite compelling explanation, which goes by many names, but is most often known as the Dreaming. During the Dreaming, an... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1428947 Thu, 08 May 2008 07:20:14 +0100 1428947