Daniel Swan › Likes

Andrew Su
RT @pathogenomenick: How many hours have been wasted on formatting documents for journal submission!!! arrrrrrggggggggggggggggggghhhhhhhhhhhhhhhhhhhh
Richard Akerman
AOL still exists?
Michael Kuhn
Hacking HTTP Status Codes - http://www.schneier.com/blog...
"When you visit my website, I can automatically and silently determine if you're logged into Facebook, Twitter, GMail and Digg. There are almost certainly thousands of other sites with this issue too, but I picked a few vulnerable well known ones to get your attention. You may not care that I can tell you're logged into GMail, but would you care if I could tell you're logged into one or more porn or warez sites? Perhaps http://oppressive-regime.example.org/ would like to collect a list of their users who are logged into http://controversial-website.example.com/?" - Michael Kuhn
Jan Aerts
RT @suncoolsu: been updating my gist to install #bioinformatics / NGS tools everyone should have https://gist.github.com/407882 (via @brent_p)
Piotr Byzia
RT @sjcockell: Announcing KCite - "easy" citations in Wordpress. http://blog.fuzzierlogic.com/archive... #kcite #kblog #jiscmrd
Simon Cockell
KCite – easy citations in WordPress - http://blog.fuzzierlogic.com/archive...
I’m excited about this one. For a couple of months now, I’ve been working on a referencing plugin for Knowledgeblog. The idea is to make it easy for authors to add citations to their posts, and have a bibliography produced automatically. Key to this approach (as with everything we’re doing on Knowledgeblog) is enabling authors [...] - Simon Cockell
Darren Wilkinson
Pawel Szczesny
Recent Neil's comment on BioStar goes to my book of "How to deal with difficult questions on my bioinformatics seminar". Neil said: "Still, the query in principle is a good approach, even if the database annotation leaves something to be desired". Classic.
Michael Meadon
The unsuccessful self-treatment of a case of “writer's block” - http://www.ncbi.nlm.nih.gov/pmc...
Best paper, EVER. - Michael Meadon
Pierre Lindenbaum
Something is rotten in the UCSC Genome Browser http://twitpic.com/384w8y
Something is rotten in the UCSC Genome Browser http://twitpic.com/384w8y
Ricardo Vidal
What's with these folks that wear pajamas in public? Has North America become THAT lazy? O_o
Not at all uncommon in the UK either, certainly not where I live. Split between the girls in their 20's who marry PJ's with Ugg boots and the people who seem to wander around my local area in dressing gowns and slippers at all times of the day. - Daniel Swan
I wore my pyjamas to a university exam once. Couldn't be arsed to get dressed when I'd been up all night studying and was going to bed right after the exam! :-) - Bill Hooker
Over here (US), I think people walking around in duvets are usually homeless. I see one or two most days as I pass through downtown Pdx on the train. Never seen one in a post office though. - Bill Hooker
Yann Abraham
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis - http://www.citeulike.org/user...
Bioinformatics, Vol. 22, No. 22. (15 November 2006), pp. 2825-2827. Summary: While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004)FEBS Lett., 573, 83â92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A... - Yann Abraham
I get so much use out of this package.. - Daniel Swan
@Daniel do you have any tip to the new/future user? - Yann Abraham
@Neil thanks for the tip, will look it up tomorrow - Yann Abraham
@Neil thanks again! - Yann Abraham
Conor Lawless
Statistical Computing in R by Colin Gillespie - Conor Lawless
You can also use "<<-" to assign global variables. It's a code smell but useful from time to time. - Michael Barton
Heather Piwowar
RT @silent_d: RT @marinakastan: To be honest, learning that Dublin Core is from Dublin, Ohio rather than Ireland killed some of the magic for me.
Todd Hoff
Halting State by Charles Stross. 4/5. Another fascinating and well done technothriller by Stross. I love his books because he's really thoughtful. He considers deep ideas and makes them real enough to be scary. His characters, not so deep, but they get the job done. This book is about crime and espionage in the virtual world. ** spoilers**
One of the ideas I love is the takeover of virtual reality gaming to use game players as unwitting and unpaid spies in a game called SPOOKS. It's called a virtual HUMINT operation. The idea is pervasive game play. It's hard to "rollup" a spy network whey don't they are really spies. This is a bit Enders Gameish, but people playing spooks are actually being controlled by actual spooks who use the game to run ops on a grand scale. This part of the book is wonderfully explored and makes a great deal of practical sense. Why not crowdsource and train your own amazon turk army of spies? If only we were that creative... - Todd Hoff
Another idea that is explored is what happens if the "bad guys" own the network and can use quantum cryptography to break all the security protocols in real-time. They can control all automated processes like smart cars. They can ease drop on all bank account numbers and other sensitive information. The fault was put on the original designers of the internet and TCP/IP, which isn't... more... - Todd Hoff
One the more interesting and depressing parts of the book was his depiction of the future political landscape. Modern war-fare is capital intensive and hasn't been profitable for decades. It was already a marginal proposition in 1939 when Hitler embarked oon his pan-European asset-stripping spree-- his government would have been bankrupt in 1940 if he hadn't invaded Poland and France.... more... - Todd Hoff
His blog at http://www.antipope.org/charlie... is also a great read - Daniel Swan
Thanks Daniel - Todd Hoff
Simon Cockell
I’m giving a lecture next week to the Bioinformatics Masters students here about protein structure prediction. As part of the introduction to this topic, I have a traditional ‘data explosion’ slide, to illustrate the gap between the quantity of protein sequence data available versus the number of solved protein structures in the PDB (hence the [...] - Simon Cockell
Nice work! - joergkurtwegner
Conor Lawless
Work from the IAH in Newcastle featured in the Guardian today, with video: http://www.guardian.co.uk/science...
Conor Lawless
Ageing geordies chase the secret of eternal youth | James Kingsland | Science | guardian.co.uk - http://www.guardian.co.uk/science...
Pierre Lindenbaum
Coloring a black and white drawing with the GIMP: my notebook - http://plindenbaum.blogspot.com/2010...
Single window mode is in the latest release. It's made me enjoy using GIMP a whole lot more. - Chris Miller
BTW: The image looks great, Pierre! - Konrad Förstner
Your drawings always make me want to draw as well, Pierre. But after 3-4 strokes I give up because it looks as bad as chicken scratchings... How long did it take you to make the black/white drawing? - Jan Aerts
:-) The B&W took ~45min/1hour, coloring 3 hours - Pierre Lindenbaum
Amazing work Pierre.. - Daniel Jurczak
Agreed, amazing work. - joergkurtwegner
Thank you all, I'm crossing my fingers that my doodle will be accepted as the cover of a coming issue. - Pierre Lindenbaum
@Joerg, I just saw the comment you left on my blog. My problem with gimp is that is is not intuitive with respect to another tool like 'inkscape'. - Pierre Lindenbaum
Stefan Hayden
Simon Cockell
Yesterday I wrote to my MP, which is something I’ve not done before. The axe is about to fall on public spending in the UK, and science is at grave threat. My letter was based on the template that the ‘Science is Vital‘ campaign provide, but I embellished it with some personal experiences that I [...] - Simon Cockell
I too have now done this. - Daniel Swan
Simon Cockell
Welcome to DataCite UK - https://datacite.org.uk/
This is the local DataCite service for the UK. DataCite is an international consortium which aims to enable data citation and facilitate easier access to scientific research data on the Internet. - Simon Cockell
Cesar Sanchez
How (not) to write a news website article about a scientific finding, by @mjrobbins - #scicomm #science #journalism - http://www.guardian.co.uk/science...
How (not) to write a news website article about a scientific finding, by @mjrobbins - #scicomm #science #journalism
Dear Friend, We are writing to ask you to complete the European Bioinformatics Institute (EBI) Survey at: http://www.surveymonkey.com/s... - It should take 10-15 minutes. - There are no compulsory questions. - You can be entered into a prize draw where you could win an iPad. This survey is collecting input from users and potential users of... - http://www.surveymonkey.com/s...
10-15 minutes of your time - EMBL-EBI Services Survey - Chris from Bookmarklet
Done. And Suprised to see my usage of EBI resources. - Pawel Szczesny from iPhone
it is quick and painless .. no option for postdoc .. that was weird. - Pedro Beltrao
I'll pass back the postdoc comment... Otherwise, thanks loads guys. Feedback is vital for a place like ours to do its service job properly. - Chris from twhirl
Done. Hope it helps. - Greg Tyrelle
Thanks Greg, much appreciated. - Chris from twhirl
Conor Lawless
Cameron Neylon
Warning: Misusing the journal impact factor can damage your science! - http://cameronneylon.net/blog...
I had a bit of a rant at a Science Online London panel session on Saturday.As usual when discussing scientific publishing the dreaded issue of the Journal Impact Factor came up. While everyone complains about metrics I've found that people in general seem remarkably passive when it comes to challenging their use. Channeling Björn Brembs more than anything else I said something approximately like the following. - Cameron Neylon
"...as professional measurers and analysts of the world we should be embarrassed to use JIFs to measure people and papers. It is quite simply bad science." Hear, hear! - Bill Hooker
Ironically enough, just yesterday I filled in a form required for an application for a professorship, where they wanted to know how many papers I had in which IF journals. Should I be interviewed, this particular position would be so important for me, that for the first time ever, I would probably not say anything about this embarrassing use of the IF, which would normally disqualify them as employers immediately. - Björn Brembs
Björn, was that Göteborg? I was trying to find the details, but they are apparently using that as part of the officiel job application process... did not find those details yet, though... - Egon Willighagen
Now, and that makes it even more embarrassing, it was here in Berlin. When I interviewed in Uppsala I did not see any of this nonsense. If I get the professorship, you can be sure there'll be a lecture or two about IFs. And there will be figures with forms from certain universities... - Björn Brembs
This whole sad discussion reminds me: why isn't there a tool available, that allows people to construct their own citation list??? I've been doing this by hand for years now: http://bjoern.brembs.net/citatio... - Björn Brembs
Bjoern, have you tried PoP http://www.harzing.com/pop.htm? - Bill Hooker
Yes, I use it, but it only pulls from GS which is neither as user friendly nor as 'accurate' as WoS/Scopus. So I use all three, de-duplicate by hand, copy and paste into an HTML editor and format (also by hand). I don't know of any other way to do this. To stay on topic: I think this is currently the best way to replace IF counts when evaluating people: use actual citations. - Björn Brembs
In Poland JIF is used every single time scientists are evaluated (whether it's a grant or a new position). Also, quite often a lecturer on a science seminar is introduced with mentioning her/his "total IF points". We have also "ministry points" (from Ministry of Science). These are awarded in the same manner as IF - per publication (points are also awarded for writing a syllabus for a... more... - Pawel Szczesny
@Björn We're working on something with the intention of delivering this and PM-R has been arguing a lot recently for open citations and open metrics. - Cameron Neylon
I would have thought that using JIF in a job application process would open an organization up to being sued... - Cameron Neylon
@Pawel - that was kind of the basis of the prestige vs outcomes riff that I most recently wrote about in the interview with Michael. It's a perfectly reasonable decision for a country, particularly a small country to go for prestige as a way of making a mark. But they shouldn't expect that to lead to either a viable, stable, or particularly valuable research community. If you want those things then you need to optimise for them (which is harder to measure obviously, but most important things are) - Cameron Neylon
I was thinking the other day about changing my cv and instead of listing 'my publications' start listing the papers that cite my papers (first order) and those that cite those first order papers (second order)) (or some quantification of that sort based on 'order'). A visualization of it could be fun to do too. Then I start wondering whether I should wait until I am out of my continuation period .... - Kubke
@Kubke... agreed... if your research published in a low ranking journal but used significantly in Nature X publications, what JIF should you fairly take... should we perhaps make a black list of universities where JIFs are used? it seems that SHOUTING is the only way to get things changed these days... :( - Egon Willighagen
@Egon :) I am on the advisory board for creative commons Aotearoa New Zealand, and one thing that came up is that 'opening up' requires a serious change in assessment policies. One example: Lets say someone gets 1000 citations on nature preceedings (not peer reviewed) shouldn't that count more than zero or 1 citation on a 'peer reviewed' nature? Should we move from 'peer reviewed' to 'peer accepted'? - Kubke
@Graham or 'peer uptake' - Kubke
And depending on who your peers are, we could have top peer, instead of top tier. - Noel O'Boyle
What if the citing papers all cite the paper to dismiss it, or because it was shown to be fraudulent? You'd need either a citation typology or he possibility to retract papers from the record, the latter being difficult in non-peer-reviewed archives. - Björn Brembs
@Cameron: Looking forward to that tool! - Björn Brembs
@Björn It's not so much the tool. That's pretty trivial. It's getting hold of the data that is the problem.... but that's what the project is about. - Cameron Neylon
Similar issue here as what Bjorn mentioned in the beginning: about to start a tenure-track, and one of the items on my checklist to be eligible for tenure in 5 yrs is "x papers/yr in a journal with IF >= y". Which obviously completely bypasses my open-source work... But at this point in my career there is nothing much that I can do. - Jan Aerts
I think there are two things I would say to that. One is don't assume that tenure process in 5yrs will look like tenure today. Things are shifting, slowly admittedly, and perhaps too slowly but they are shifting. "Impact" and demonstrated income potential will be very important, both of which your prominence in the Open Source community will help with. Secondly, yes you need some good... more... - Cameron Neylon
@Björn wrt. citation typology: here's a recent paper on this very topic: Shotton. CiTO, the Citation Typing Ontology. Journal of Biomedical Semantics 2010, 1(Suppl 1):S6 http://dx.doi.org/10... "..ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web information resources, and for publishing these descriptions on the Semantic Web. .." - 'Mummi' Thorisson
@Mummi: nice! This sort of technology needs to be developed and incorporated in citation analyses are to progress. - Björn Brembs
A Roy
08/25/10 PHD comic: 'Lab coat rationale' - http://www.phdcomics.com/comics...
Cameron Neylon
Three Rules for Supervising Student Programming Projects - http://third-bit.com/blog...
Lars Juhl Jensen
Analysis: Half of published URLs are dysfunctional a decade later - http://larsjuhljensen.wordpress.com/2010...
As a small aside when setting up a local mirror of Medline, I extracted 15,915 URLs that were mentioned in the abstracts. Checking them revealed that 12,354 of them (78%) were functional, which may not seem that bad. However, plotting the percentage of dysfunctional URLs as a function of publication year reveals a less pleasant [...] - Lars Juhl Jensen
Interesting analysis--and needs to be compared to the old estimate that the half-life of a URL, in general, is 90 days. Ten years is first-rate by comparison. - walt crawford
Oh neat - thanks Andrew, I'll add a reference to it. - Lars Juhl Jensen
I've never been too worried about this. If the content were disappearing it would be a different matter. New pages get written with the new links to the important content. I know from an archival POV this is troubling, but not from a researcher POV. - Mr. Gunn from Android
@Mr. Gunn - I did a small subsequent check in response to a comment on the blog, and for 4 of 10 randomly chosen cases I was not able to locate the content elsewhere. So it is also content disappearing. I agree that the URL moving without a proper redirection is more of a nuisance than an actual problem. - Lars Juhl Jensen
@Duncan, thanks I hadn't seen that one before but it reminded me of the original paper by Jonathan Wren from 2004 on the topic :-) - Lars Juhl Jensen
It can just strengthened my opinion about why we should abolish the supplementary material sections of papers... - Julien Colomb
To me it rather shows that we need the publishers (or university libraries) to take responsibility for the supplementary information. If it just lives on the authors' website, it will eventually disappear. - Lars Juhl Jensen
Extract the email address from each abstract with nonfunctional url-s and send them a note. At least you can compare the # of bad url-s with the # of bad email addresses. - Hedi Hegyi
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