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 'friendfeed'. Sat, 03 Sep 2011 02:05:05 +0100 http://www.medworm.com/index.php?rid=5077941&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F07%2F28%2Fanalysis-of-ismb-coverage-at-friendfeed-2008-2011%2F ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting. Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB at FriendFeed now – why not look at all of them? So I did. Read on for the details. 1. First – an apology In my post from last year, I included some R code which will grab a FriendFeed feed in JSON format using the API and convert it to an R list. I would have used it again this year, except that the ISMB 2008 feed is no longer a complete archive of the 2008 meeting. This is, unfortunately, my fault – but all is not lost. I decided to leave FriendFeed earlier this year and began by deleting the se... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=5077941 Thu, 28 Jul 2011 02:40:17 +0100 5077941 http://www.medworm.com/index.php?rid=4419352&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F31%2Ffarewell-friendfeed-its-been-fun%2F I’ve been a strong proponent of FriendFeed since its launch. Its technology, clean interface and “data first, then conversations” approach have made it a highly-successful experiment in social networking for scientists (and other groups). So you may be surprised to hear that from today, I will no longer be importing items into FriendFeed, or participating in the conversations at other feeds. Here’s a brief explanation and some thoughts on my online activity in the coming months. The value of FriendFeed FriendFeed is simply an aggregator, displaying items from other online services. There’s nothing special about that: other sites do the same thing (although many have fallen by the wayside) and were FriendFeed to disappear, those items would still exist at thei... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4419352 Mon, 31 Jan 2011 13:34:07 +0100 4419352 http://www.medworm.com/index.php?rid=4405960&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fapis-have-let-me-down-part-22-friendfeed%2F In part 1, I described some frustrations arising out of a work project, using the Array Express API. I find that one way to deal mentally with these situations is to spend some time on a fun project, using similar programming techniques. A potential downside of this approach is that if your fun project goes bad, you’re really frustrated. That’s when it’s time to abandon the digital world, go outside and enjoy nature. Here then, is why I decided to build another small project around FriendFeed, how its failure has led me to question the value of FriendFeed for the first time and why my time as a FriendFeed user might be up. At the beginning of each year, I frequently experience a period of angst with respect to my social network and other web activity. Specifically, I ask... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405960 Thu, 27 Jan 2011 09:06:30 +0100 4405960 http://www.medworm.com/index.php?rid=4405961&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fapis-have-let-me-down-part-12-arrayexpress%2F The API – Application Programming Interface – is, in principle, a wonderful thing. You make a request to a server using a URL and back come lovely, structured data, ready to parse and analyse. We’ve begun to demand that all online data sources offer an API and lament the fact that so few online biological databases do so. Better though, to have no API at all than one which is poorly implemented and leads to frustration? I’m beginning to think so, after recent experiences on both a work project and one of my “fun side projects”. Let’s start with the work project, an attempt to mine a subset of the ArrayExpress microarray database. 1. Introduction ArrayExpress is an online database of microarray experiments, organised by both gene (the expression at... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405961 Thu, 27 Jan 2011 09:04:11 +0100 4405961 http://www.medworm.com/index.php?rid=4117879&cid=t_173036_139_f&fid=38879&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FVirologyBlog%2F%7E3%2FTuRVxRrSPD8%2F Readers of this blog know that I embrace social media for teaching virology. My experience with two types of social media, blogging and podcasting, has been published as an Opinions piece by PLoS Pathogens (read the full text or download the pdf file). In this article I discuss how social media is becoming an increasingly integral component of both research and education in the world of science. My experience has convinced me that scientists must embrace these applications to not only better communicate their work to the public, but to facilitate the progress of research. Blogging and podcasting are not the only forms of social media that I have found useful for teaching and research. I use Twitter to locate or disseminate information about virology. I often tweet when I write a new blog ... virology blog blogs http://www.medworm.com/rss/comments.php?id=4117879 Fri, 29 Oct 2010 13:28:24 +0100 4117879 http://www.medworm.com/index.php?rid=3903081&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F26%2Fbrief-words-on-cliqset%2F Since I seem to be at least partially-responsible for a burst of new users at Cliqset, I thought I’d clarify my own ideas about our future use of so-called “lifestream” applications. In my opinion, FriendFeed is by far the best approach that I’ve seen, so far, to creating discussions and communities around items of information. Unfortunately, it is unlikely to survive much longer. Yes, its creators tell us that their intention is to keep it running “indefinitely”, but the cracks are beginning to show. Search no longer works, feeds do not import reliably, outages are becoming more frequent and lasting longer. It’s natural, then, to ask if anything similar exists. Search Google for “lifestream application” and you’ll find many alter... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3903081 Thu, 26 Aug 2010 06:01:20 +0100 3903081 http://www.medworm.com/index.php?rid=3798733&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F29%2Flazy-post-a-life-scientists-best-of%2F When stuck for ideas or pressed for time, a blogger can always fall back on a round-up of activity from elsewhere on the web. Yes, it’s time for a “best of the past 14 days” from the FriendFeed Life Scientists group. Just a slight twist to make it more exciting (?) – we’ll automate the process using the API and a little Ruby. #/usr/bin/ruby require "rubygems" require "json/pure" require "open-uri" bestof = JSON.parse(open("http://friendfeed-api.com/v2/feed/the-life-scientists/summary/14").read) 0.upto(9) {|entry| url = bestof['entries'][entry]['url'] body = bestof['entries'][entry]['body'] puts "<li><a href='#{url}'>ff#{entry+1}</a> - #{body}</li>" } Run, copy output and paste to ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3798733 Thu, 29 Jul 2010 07:10:20 +0100 3798733 http://www.medworm.com/index.php?rid=3795022&cid=t_173036_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2010%2F07%2F28%2Fsmile-open-your-eyes-love-and-go-on%2F Today marks the 2nd anniversary of Libby’s death from ovarian cancer at the age of 26. Although the family healing process continues, we celebrate Libby’s life formally on this day to honor her memory, and remind ourselves that life is precious and should not be taken for granted. Today marks the 2nd anniversary of Libby’s [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=3795022 Wed, 28 Jul 2010 08:00:47 +0100 3795022 http://www.medworm.com/index.php?rid=3767238&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F20%2Fanalysing-the-ismb-2010-meeting-using-r%2F The colossus of bioinformatics meetings, ISMB, convened in Boston this year from July 9 – 13. As in recent years, the meeting was covered online at its website, FriendFeed and Twitter. I thought it would be fun to run a quick analysis of activity at the FriendFeed room using R. 1. Fetch the data We can use the FriendFeed API to fetch data in JSON format. R provides two useful packages: RCurl, for making the HTTP request and rjson (or RJSONIO), to parse the results into a list. Since we don’t know in advance how many entries to expect, we set some arbitrarily large maximum number of entries, loop towards it and break when no more entries are returned. library(RCurl) library(rjson) ismb.url <- "http://friendfeed-api.com/v2/feed/ismb2010" ismb.data <- list() fo... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3767238 Tue, 20 Jul 2010 07:24:19 +0100 3767238 http://www.medworm.com/index.php?rid=3570009&cid=t_173036_132_f&fid=35021&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FYourBonesGotALittleMachine%2F%7E3%2FO4btHltj2IM%2F Recently I’ve noticed the emergence of several Stack Overflow-style sites for science-related questions and answers. For those unfamiliar with Stack Overflow – it’s a question and answer ‘forum’ for computer programmers that keeps the signal-to-noise ratio very high through a carefully refined reputation system. Late last year the creators of Stack Overflow launched a hosted service called Stack Exchange, which allows anyone to start their own “Stack Overflow” based around any topic. http://www.flickr.com/photos/alicebartlett/ / CC BY-NC 2.0 The service is was a little pricey ($129+/month), and I suspect this is one reason why a few open source clones inspired by Stack Overflow also exist. Since then, Stack Exchange sites (or clones) have prolifer... Your bones got a little machine. blogs http://www.medworm.com/rss/comments.php?id=3570009 Wed, 12 May 2010 05:33:48 +0100 3570009 http://www.medworm.com/index.php?rid=3556283&cid=t_173036_132_f&fid=35021&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FYourBonesGotALittleMachine%2F%7E3%2FO4btHltj2IM%2F Recently I’ve noticed the emergence of several Stack Overflow-style sites for science-related questions and answers. For those unfamiliar with Stack Overflow – it’s a question and answer ‘forum’ for computer programmers that keeps the signal-to-noise ratio very high through a carefully refined reputation system. Late last year the creators of Stack Overflow launched a hosted service called Stack Exchange, which allows anyone to start their own “Stack Overflow” based around any topic. http://www.flickr.com/photos/alicebartlett/ / CC BY-NC 2.0 The service is was a little pricey ($129+/month), and I suspect this is one reason why a few open source clones inspired by Stack Overflow also exist. Since then, Stack Exchange sites (or clones) have prolifer... Your bones got a little machine. blogs http://www.medworm.com/rss/comments.php?id=3556283 Wed, 12 May 2010 05:33:48 +0100 3556283 http://www.medworm.com/index.php?rid=3456828&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F04%2F10%2Fthis-is-friendfeed%2F …at its very best. Scientists Embrace Openness – discuss. Filed under: open science, web resources Tagged: discussion, friendfeed, social (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3456828 Sat, 10 Apr 2010 03:19:49 +0100 3456828 http://www.medworm.com/index.php?rid=3223442&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F30%2Fismb-2009-reports%2F Great to see more reports describing the use of online tools to cover scientific meetings. Here are the publications, from PLoS Computational Biology: Live Coverage of Scientific Conferences Using Web Technologies. doi:10.1371/journal.pcbi.1000563 Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009. doi:10.1371/journal.pcbi.1000640 And here’s Ally a.k.a the robo-blogger on Social Networking and Guidelines for Life Science Conferences. Looks like we’ve started a trend, long may it continue at future meetings. Filed under: bioinformatics, meetings, publications Tagged: 2009, eccb, friendfeed, ismb, report (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3223442 Sat, 30 Jan 2010 04:22:12 +0100 3223442 http://www.medworm.com/index.php?rid=3149253&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F07%2Fhow-to-archive-data-via-an-api-using-ruby-and-mongodb%2F I was going to title this post “How to: archive a FriendFeed feed in MongoDB”. The example code does just that but (a) I fear that this blog suggests a near-obsession with FriendFeed (see tag cloud, right sidebar) and (b) the principles apply to any API that returns JSON. There are rare examples of biological data with JSON output in the wild, e.g. the ArrayExpress Gene Expression Atlas. So I’m still writing a bioinformatics blog ;-) Let’s go straight to the code: #!/usr/bin/ruby require "rubygems" require "mongo" require "json/pure" require "open-uri" # db config db = Mongo::Connection.new.db('friendfeed') col = db.collection('lifesci') # fetch json 0.step(9900, 100) {|n| f = open("http://friendfeed-api.com/v2/feed/... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3149253 Thu, 07 Jan 2010 00:17:46 +0100 3149253 http://www.medworm.com/index.php?rid=3115235&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F12%2F23%2Fthe-life-scientists-at-friendfeed-2009-summary%2F The Life Scientists 2009 It’s Christmas Eve tomorrow and so I declare the year over. My Christmas gift to you is a summary of activity in 2009 at the FriendFeed Life Scientists group. It’s crafted using R + Ruby, with raw data and some code snippets available. If you want to see the most popular items from the group this year, head down to the bottom of this post. (Note: this post is a work in progress) The contributors First of all, take a look at yourselves. There are, allegedly, 1250 subscribers to the group, but I can only retrieve profiles for 1053 of them. 248 of you are rather shy, opting for the default avatar and one or two of you look rather like porn stars. If nothing else, this illustrates the difficulty of compiling reliable user statistics. Here’s how this ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3115235 Wed, 23 Dec 2009 08:15:40 +0100 3115235 http://www.medworm.com/index.php?rid=3079512&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F12%2F11%2Fapis-i-wish-the-life-sciences-would-learn-from-social-networks%2F I was prompted by a thread on the apparent decline of FriendFeed to look for evidence of declining participation in my networks. First, a quick and dirty Ruby script, tls.rb to grab the Life Scientists feed and count the likes and comments: #!/usr/bin/ruby require 'rubygems' require 'json/pure' require 'net/http' require 'open-uri' def format_date(d) if d =~ /(\d{4}-\d{2}-\d{2})T(\d{2}:\d{2}:\d{2})Z/ return "#{$1},#{$2}" else return d end end def count_items(i) if i.nil? return 0 else return i.count end end n = ARGV[0] u = "http://friendfeed-api.com/v2/feed/the-life-scientists?start=#{n}" f = open(u).read j = JSON.parse(f) j.each_pair do |k,v| if k == "entries" v.each do |entry| date = format_date(entry['date']) likes = count_it... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3079512 Fri, 11 Dec 2009 02:50:49 +0100 3079512 http://www.medworm.com/index.php?rid=2751832&cid=t_173036_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2009%2F09%2F01%2Fbeware-of-top-50-great-tools-to-double-check-your-doctor-or-whatever-lists%2F Just the other week I wrote a post “Vanity is the Quicksand of Reasoning: Beware of Top 100 and 50 lists!” In short this post describes that (some) Top 100 etc lists may not be as useful or innocent as they seem. Some of these lists are created by real scam-sites, who’s only goal is to [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=2751832 Tue, 01 Sep 2009 01:33:45 +0100 2751832 http://www.medworm.com/index.php?rid=2741537&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F08%2F28%2Ffriendfeed-life-scientists-14-day-summary%2F Since I haven’t posted for 14 days, what better (and lazier) way to post something than to surf over to a 14-day summary from the Life Scientists Group and link to the top ten items! Review process files in the EMBO Journal – but why only for “the majority of papers”? How XML threatens Big Data. Or not. How JSON might be an alternative – or not. Solve any computer problem – with this classic XKCD flowchart. Science reviews the revolution in ’strategic scientific reading’ – are they way behind the curve, or providing a useful summary for the uninitiated? Best practice in microbial genome annotation – spirited discussion on the nature of best bioinformatics practice. FriendFeed Life Scientists user survey – no further word on... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2741537 Fri, 28 Aug 2009 07:03:56 +0100 2741537 http://www.medworm.com/index.php?rid=2691710&cid=t_173036_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2Fvj5BIAQ6hN8%2F I don’t like Facebook, the same way I don’t like Orkut. The only reason for me to use Facebook is contact people I don’t see in years, and that facet of it I appreciate. On the other hand I really liked FriendFeed, which is (was) a great service, but didn’t have a commercialization plan, hence it was sold. Anyway, the best analogy I can make of this purchase is: It’s like when that indie, miniscule band that you love and cherish goes mainstream. In a matter of seconds, the whole world knows that band and you don’t like it anymore, because you “discovered” it, because they were “connected” only to you, not the whole world. Now, FriendFeed is Facebook, and Facebook is mainstream, and we scientists need to stay indie, or at least ke... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2691710 Tue, 11 Aug 2009 23:53:15 +0100 2691710 http://www.medworm.com/index.php?rid=2571048&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F03%2Fgreat-work-ismb-microblogging-team%2F Another year, another ISMB/ECCB meeting and – another great blogging effort. It’s all at the FriendFeed group: ISMB/ECCB Stockholm 2009, with outgoing links to individual blogs too. Thanks and congratulations to all involved for a great effort. Looking forward to the official write-up. Posted in bioinformatics, computing, meetings, web resources Tagged: friendfeed, iscb, ismb, microblogging (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2571048 Fri, 03 Jul 2009 00:42:35 +0100 2571048 http://www.medworm.com/index.php?rid=4098296&cid=t_173036_132_f&fid=35016&url=http%3A%2F%2Ffgibson.com%2F2009%2F04%2F25%2Fthe-semantic-web-of-life-science%2F This summary was born out of a question  on Twitter and percolated to FriendFeed, which was “Who is using RDF and integrating other resources at the minute and what are those resources? From this question, several resources were highlighted. UniProt. The comprehensive resource of protein information is available as an RDF distribution and each Protein record has a corresponding RDF download option. Phil pointed out Semantic Systems Biology, As systems biology is largely concerned with representing networks and interactions at a systems level, a language like RDF would seem an obvious choice to represent this type of knowledge, to aid semantic description and data integration. Melanie pointed out the following resources such as Bio2RDF. This project aims to RDF-ize numerous public life-s... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=4098296 Sat, 25 Apr 2009 08:45:02 +0100 4098296 http://www.medworm.com/index.php?rid=2367524&cid=t_173036_109_f&fid=35044&url=http%3A%2F%2Fadultaddstrengths.com%2F2009%2F04%2F25%2F12-ways-to-fight-mental-health-stigma-with-social-media%2F Post from: Adult ADD Strengths 12 Ways to Fight Mental Health Stigma With Social Media This is for a presentation I’m doing at Mental Health Camp Vancouver (a conference combining social media with mental health) called ADHD - Busting the myths, breaking the stigma, showing reality, one post and tweet at a time. While ADHD is especially stigmatized as the orphan of mental health conditions, especially Adult ADHD, it’s not the only one that suffers stigma. 12 Ways to Fight Mental Health Stigma With Social Media Arranged from more anonymous to more personal, and less effort to more effort. There’s a choice for everyone. 1. Click on a factually correct, non stigmatizing mental health article, or personal story via a blog post, tweet, podcast, YouTube video, Facebook update, ... Adult ADD Strengths blogs http://www.medworm.com/rss/comments.php?id=2367524 Sat, 25 Apr 2009 06:31:07 +0100 2367524 http://www.medworm.com/index.php?rid=2349281&cid=t_173036_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FJqd895EuEzA%2F Image via CrunchBase I was contacted a couple of months (maybe more) to write a guest entry for their blog. I did that and on March 11th I sent the text you see below. It’s not my best creation (and not the worst, believe me), but as they’re taking so long to publish it and I don’t want it to go to waste, I’m publishing it. — Exactly two years ago (or almost exactly), I posted a follow-up blog entry to Notes to a young computational biologist. I still believe that 97% of all advice is worthless, but I also believe that it’s worth sharing your experiences as it might be useful to someone in the future. In this guest blogging, I will examine those two-year old posts, mixing, matching, remixing, adding and deleting thins. Consider this my four cents on ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2349281 Fri, 17 Apr 2009 16:07:25 +0100 2349281 http://www.medworm.com/index.php?rid=2323829&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F04%2F07%2Fbrief-words-on-the-friendfeed-beta%2F The best place for discussion about the latest FriendFeed beta is at FriendFeed, of course. However, it would be amiss of me not to record a couple of thoughts. On the whole, there’s little about which I feel strongly for better or worse - which rather suggests that the current design is just fine. With three major exceptions: The service favicons and service filtering Someone has decided that the source of information is less important than the content - in fact, that the source is irrelevant. I and many others disagree strongly. It seems that many people use the small icons that identify the item source as a subconscious visual cue, in ways that the designers have not anticipated. Richard describes this concisely. Retain source icon and ability to filter by source. Merging of roo... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2323829 Tue, 07 Apr 2009 09:06:37 +0100 2323829 http://www.medworm.com/index.php?rid=2296199&cid=t_173036_132_f&fid=35016&url=http%3A%2F%2Fpeanutbutter.wordpress.com%2F2009%2F03%2F26%2Fthe-biosysbio-conference-2009%2F Image via Wikipedia The premise of the BioSysBio conference is to bring together the best young researchers working in Synthetic Biology, Systems Biology and Bioinformatics, providing a platform to hear and discuss the most recent and scientific advances and applications in these fascinating fields. This years BioSysBio 09 has just taken place in Cambridge, UK. The program was more slanted towards synthetic biology rather than more traditional systems biology, which I think reflects the growing momentum that synthetic biology has gained in the past year. I think this is a good progress and  I was secretley glad as I did not want to spend 3 days looking at massive network diagrams squashed onto power point slides. This was the first conference I had been to that the organisers actually ... peanutbutter blogs http://www.medworm.com/rss/comments.php?id=2296199 Thu, 26 Mar 2009 12:00:41 +0100 2296199 http://www.medworm.com/index.php?rid=2260167&cid=t_173036_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fchoosing-a-license-for-your-ontology.html%3F_c%3Dfeed-rss Over on Friendfeed this week, I started a discussion (both in The Life Scientists room and in the Science 2.0 room) about ontologies and licensing them. I am creating a couple, and was trying to determine whether I should use some flavor of CC lic... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2260167 Fri, 13 Mar 2009 08:29:42 +0100 2260167 http://www.medworm.com/index.php?rid=2163540&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F02%2F06%2Fadd-friendfeed-comments-and-likes-to-wordpresscom-posts-using-ruby%2F The problem FriendFeed aggregates your blog posts from WordPress.com. Naturally, people prefer to comment on your post at FriendFeed - it’s quicker, easier and more fun. However, you would like to see an indication of this activity back at the original blog post. The solutions You could self-host your blog using software from WordPress.org. This allows you to install plugins such as FriendFeed comments. But you’re at WordPress.com because you don’t want to self-host, right? So you just have to live with the absence of useful plugins. My advice: don’t try discussing issues like this one in the WordPress.com forums unless you’re the kind of person who enjoys comment threads at YouTube. For intelligent, mature and constructive discussion go to FriendFeed of cours... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2163540 Fri, 06 Feb 2009 07:50:43 +0100 2163540 http://www.medworm.com/index.php?rid=2150752&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F02%2F02%2Fbrief-notes-on-export-from-friendfeed%2F During discussion of the ISMB 2008 room, Thomas asks: “Does FF really provide long-term archival?” Lars points out that it’s as permanent as anything else on the Web, Dorothea points out that FriendFeed offer no guarantees and Deepak discusses the FriendFeed API. Question: how useful is the FriendFeed API as a tool to, for example, archive a FriendFeed room? We can access the ISMB 2008 room via the API using a URL like this: curl “http://friendfeed.com/api/feed/room/ismb-2008?format=xml” > ismb.xml We can also retrieve items in other formats by substituting “xml” in the URL with one of: json, atom, rss. Note that where a FriendFeed post contains a “N more comments” link, those comments are actually present on the page and revealed... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2150752 Mon, 02 Feb 2009 02:01:45 +0100 2150752 http://www.medworm.com/index.php?rid=2125284&cid=t_173036_132_f&fid=35024&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FBlindscientist%2F%7E3%2FRuLoNou1lAk%2F So, we’re back! And to the old-new story of why the Open Science movement will fail, at least for now. I was planning to post something on a different note, but a recent discussion thread on FriendFeed called me to post about it. This thread was started by a blog entry the poster-boy of the Open Science/Research/Buzz-Word-of-the-moment Movement, Cameron Neylon. As most of the “literature” you find in his blog, very well written, he uses a metaphor of some mundane human social behaviour/activity trying to captivate the reader and bring him to his “open” universe. Sometimes it’s related to a train commute, sometimes a music or a scientific article. When the the reader is inside his web, BANG! comes the open science mantra, that we have to be open, that w... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=2125284 Thu, 22 Jan 2009 22:46:07 +0100 2125284 http://www.medworm.com/index.php?rid=2112880&cid=t_173036_88_f&fid=38129&url=http%3A%2F%2Fsandnsurf.medbrains.net%2F2009%2F01%2Ftwitter-essential-blog-nutrient%2F Prompted by a series of conversational musings and twitterings the concept of a ‘blogging ecosystem‘ became apparent. With the ‘blogging host‘ as the primary producer and ‘blog posts’ as distribution seeds - I went in search of the other energy sources necessary to create a fit, helathy and viable blog. Additional correlates within the blog life cycle include [...] (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=2112880 Sun, 18 Jan 2009 11:12:36 +0100 2112880 http://www.medworm.com/index.php?rid=2086873&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F08%2Fconversation-takes-unexpected-and-welcome-direction%2F 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://www.medworm.com/index.php?rid=2081028&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F06%2Funinspired-attend-psb-2009-virtually%2F 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://www.medworm.com/index.php?rid=2078783&cid=t_173036_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2009%2F01%2F04%2F10-tips-how-to-filter-discussions-on-twitter%2F I follow more than 570 users on Twitter that leads to more than 100 new tweets an hour and I don’t have hours a day to check all the messages. Co-bloggers frequently ask me how I can follow all of them efficiently. Well, I have a few tips on this and feel free to share yours with us: Tweetdeck: The best tool to organize your tweets. I created a Health 2.0 group to filter the tweets of the users who are writing about medicine or health 2.0. Twitter Search:  I always do a search for a few keywords to find new people twitting about my field of interest. Twilert.com: It works like Google Alerts which means it lets you receive regular e-mail updates of tweets containing your keywords. Filter by replies: It’s easy to discover ongoing discussions as people reply to each oth... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=2078783 Sun, 04 Jan 2009 15:31:00 +0100 2078783 http://www.medworm.com/index.php?rid=2027020&cid=t_173036_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fthis-site-now-listed-in-nature-blogs-and-the-reason-behind-my-keyword-choices.html%3F_c%3Dfeed-rss Last week when scanning through Friendfeed, someone mentioned Nature Blogs. A number of my friends and fellow friendfeeders (1,2,3,4,5,6,etc.) already have their blogs registered there. I took the plunge and submitted my request last week, and thi... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2027020 Thu, 11 Dec 2008 08:03:23 +0100 2027020 http://www.medworm.com/index.php?rid=2011110&cid=t_173036_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fciteulike-friendfeed-and-me-bff.html%3F_c%3Dfeed-rss I'll start off by saying that I'm new to the whole Friendfeed thing, and I've also only recently started using Citeulike in a more comprehensive way. I started out on the former through the recommendation of Frank over at peanutbutter, and it's on... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2011110 Thu, 04 Dec 2008 13:46:08 +0100 2011110 http://www.medworm.com/index.php?rid=1750047&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F02%2Fsnippets-4%2F 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://www.medworm.com/index.php?rid=1521987&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F06%2F17%2Ffriendfeed-best-of-the-week%2F 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://www.medworm.com/index.php?rid=1436793&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F05%2F12%2Fproteomics-discussion-from-the-science-streamosphere%2F 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://www.medworm.com/index.php?rid=1392480&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F04%2F23%2Fnow-officially-living-in-my-browser%2F Firefox screenshot, from left to right: Vertical tabs, courtesy of Vertigo - because you can never have too many tabs Main window: the feeds roll into GReader On the right, almost all the functionality of FriendFeed (except search) in fantastic new extension MySocial 24×7 On the right? Yes, because sidebars look better on the right IMHO, made possible by MultiSidebar Tenuous bioinformatics connection: well, you work more effectively if you’re happy with your browser setup (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1392480 Wed, 23 Apr 2008 07:28:52 +0100 1392480 http://www.medworm.com/index.php?rid=1371904&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F04%2F15%2Ftwo-great-open-science-resources%2F The Twitter + FriendFeed combination is proving to be a very useful information stream; not just from other people but as a reminder of what I thought was worth sharing. Two links from there that I think deserve wider attention: One Big Lab proposes that we become, well, one big lab - and has some ideas as to how that might work. From the OWW wiki, an excellent article on python in computational biology. This has been presented at Pycon 2008 and is also a companion article to a paper in PLoS Computational Biology. Imagine if everyone described their methods in this detail. Deepak has some commentary on what we’re now calling the “bio-twitterverse”. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1371904 Mon, 14 Apr 2008 23:56:50 +0100 1371904 http://www.medworm.com/index.php?rid=1358513&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F04%2F09%2Faggregating-the-aggregators%2F Cameron has a good discussion of lifestream aggregators in a research context. I have a non-research problem: two apps (FriendFeed and Profilactic), doing essentially the same job, each with features that make both worthwhile. I like Profilactic for these reasons: Design and appearance (YMMV) Ability to fetch content from my friends if they use the same services that I do, without having to get them to subscribe to Profilactic (killer feature IMHO - FriendFeed has the “imaginary friend” to do a similar job, but way less convenient) Huge number of services that can be aggregated Ability to aggregate any feed without giving it a misleading label (FriendFeed will aggregate any feed too, but insists on titling items as “blog post”) On the other hand, FriendFeed has th... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1358513 Wed, 09 Apr 2008 04:40:42 +0100 1358513 http://www.medworm.com/index.php?rid=1316735&cid=t_173036_93_f&fid=36200&url=http%3A%2F%2Fblog.jammedph.com%2Ffriendfeed-what-are-your-friends-into%2F I was reading a CNET article a while ago and found out about FriendFeed thought to be as the new Twitter. I will disagree however. Although it has similar feature like Twitter where you are able to know what’s your friends been up to (in fact, Twitter is one of the shared sites), it has a lot better functionality than the latter. FriendFeed lets you share your favorite website, whereabouts through Twitter, YouTube video uploads and favorites, del.icio.us bookmarks, Stumble Upon reviews, etc to your friends. So it is basically social media and web 2.0 sites rolled into one. Similar sites include Plaxo and Iminta. (Source: Jammed: Full into Capacity) Jammed: Full into Capacity blogs http://www.medworm.com/rss/comments.php?id=1316735 Thu, 20 Mar 2008 12:42:28 +0100 1316735 http://www.medworm.com/index.php?rid=1289733&cid=t_173036_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F03%2F10%2Flifestreaming%2F In yet another moment of BBGM synchronicity, I started to think about lifestreaming and its applications as Deepak wrote about it. My inspiration was the recent article 35 ways to stream your life. I’ve tried (and you can find me at): Mugshot - aggregates a limited number of sources, doesn’t seem to update properly from del.icio.us, has conversation features (quips, comments) FriendFeed - nice look and feel, a limited number of sources, has conversation features (comments, ratings) Profilactic - by far my favourite in terms of look/feel and sources (you can add anything that has a feed) but no conversations as yet Lifestreams are fun. I don’t expect anyone to care about what I just played on last.fm (and likewise), but these are all ways of broadcasting yourself and mak... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1289733 Mon, 10 Mar 2008 02:47:45 +0100 1289733