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Bio Info Headlines

NodalPoint Yi Xing’s Alternative Splicing
Keat’s telescope YoungFemaleScientist
The Struggling Grad Student Andrew Dalke’s Writings
El Cau del Drac The Personal Genome
Three-Toed Sloth Crooked Timber
The Pands’s thumb

Recent Headlines

16 Jul pm07:42 Let’s Talk . The Pands’s thumb
Back in the middle of last month, I had a few things to say about Casey Luskin (DI flak) and his understanding of so-called junk DNA. It’s now the middle of the month again, and Casey is again talking…
16 Jul pm05:37 Apocrypha Now II: The Revenge of Samuel Pepys Crooked Timber
Jerome Weeks offers another tale from the crypt:
A 17th century English lit doctoral candidate has completed her dissertation on Samuel Pepys, the famous diarist. Early on in her studies (yes, the gender makes this seem sexist, but I’m…
16 Jul pm05:19 Without, they gilded are so that it dazzles/ But … Crooked Timber
Hewitt defends Vitter against charges of hypocrisy:
16 Jul am03:01 Forrest and Gross: Biochemistry by design The Pands’s thumb
Barbara Forrest and Paul Gross have a paper titled Biochemistry by design published in TRENDS in Biochemical Sciences Vol.32 No.7 , 2007. (10 pages including 1.75 pages of references) I am not surprised why the defense in the Kitzmiller…
15 Jul pm11:19 Quote mining elevated to quote mania The Pands’s thumb
After a group of ultra-Orthodox rabbis issued a “fatwa” forbidding Jews even to touch books by Rabbi Nathan Slifkin, he became kind of a celebrity. The popularity of his books jumped dramatically. A number of reviewers (and blurb writers)…
15 Jul pm10:46 Dept of Being Savaged by a Dead Sheep Crooked Timber
Someone I believe to be Megan McArdle weighs in at the Economist blog on the laughable graphic run by the WSJ the other day. Brad DeLong is not impressed, nor is Mark Thoma (in part because comments are misattributed to him in the post), and nor am I….
15 Jul am07:16 Volume 1: Challenges of the NIH system of support YoungFemaleScientist
As per my last post, the series begins.1. Challenges of NIH System of Research SupportPlease describe any specific challenges presented by NIH?s support of biomedical and behavioral research such as the current array of grant mechanisms, number of…
15 Jul am02:28 Gordy Slack interview The Pands’s thumb
Gordy Slack was on the radio in the Bay Area yesterday and the show is now online. I haven’t listened to the whole thing yet but I’m sure it was good, since Gordy is quite a thoughtful guy. Gordy…
14 Jul pm09:42 The Invasion Crooked Timber
The Invasion (UK) is, perhaps, the greatest of the Cyberman stories – prefiguring the Pertwee years on earth, establishing UNIT as a regular feature and clearly influenced by Quatermass 2. It set the stage for the earthbound adventures of the…
14 Jul am06:35 Outliers Crooked Timber

By now you’ve probably all seen this ridiculous graphic from todays’ WSJ, which purports to show that the Laffer curve is somehow related to the data points on the figure. Brad DeLong, Kevin Drum, Matt Yglesias, Mark Thoma and Max…
14 Jul am02:56 SCANDAL AT THE PANDA’S THUMB! The Pands’s thumb
Professor Steve Steve, how could you? He will be going into rehab, and promises never to do it again. (via Zeno)…
13 Jul pm10:20 Shalizi on Page on Diversity Crooked Timber
While messing around on Cosma Shalizi’s website (surely the Wunderkammer of the blogosphere) I came across this piece on Scott Page’s ideas about diversity, which sums them up rather better and more crisply than I did in my own review of…
13 Jul pm09:59 Creato-Terrorism Update The Pands’s thumb
Today’s Denver Post and Colorado Daily have articles on the threats made to the CU Boulder faculty. The perpetrator has been identified as one Michael Korn, a former Messianic Jew who has converted to Christianity. And he’s been up…
13 Jul pm08:33 More Camembert, Less Crime Crooked Timber
Via Unfogged, a key piece of empirical evidence in the gun control debate. Faced with an intruder attempting to rob them at gunpoint, the homeowners responded successfully with wine and cheese. Merely brandishing the Camembert and bottle of Chateau…
13 Jul pm08:18 Evolution of a sex ratio observed The Pands’s thumb
If you’ve been reading that fascinating graphic novel, Y: The Last Man(amzn/b&n/abe/pwll), you know the premise: a mysterious disease has swept over the planet and bloodily killed every male mammal except two, a human named Yorick and a monkey…
13 Jul pm04:36 Apocrypha Now? Crooked Timber
A friend has asked about a story that may be the academic equivalent of an urban legend. I had never heard it. I asked some journalists who cover higher education, and they also say it does not ring a bell. But the thing sounds just plausible enough…
13 Jul am09:45 Don’t say I didn’t warn you… The Pands’s thumb
And they say evolution isn’t predictable. Ever since ID went down in flames in the Kitzmiller v. Dover case, creationism watchers have predicted that creationism would evolve yet again, this time into something called “critical analysis of…
13 Jul am07:21 Discussing open research NodalPoint
What’s the best way to discuss “open research”? Let’s say that you have a research problem. You might post it on your blog and receive comments. Or you might create a wiki with questions, to which people can contribute answers. All well and good,…
13 Jul am01:44 Durkin down under Crooked Timber

Under intense pressure from the rightwing commentariat (several members of which have been appointed to its board by the Howard government) the Australian Broadcasting Corporation presented a shortened version of Martin Durkin’s The Great…
12 Jul pm11:52 Who Will Defend the Children of Priviledge? Crooked Timber
The cover story of the Washington City Paper this week is about Late Night Shots, “a very exclusive, invite-only social-networking Web site” enabling rich young white people from good prep schools to get drunk and have casual sex with…
12 Jul pm11:05 Yet another reason Paul Nelson is extremely silly The Pands’s thumb
Over on UD, Paul Nelson claims that he is representing the “Darwinian tree of life” position correctly when he asserts that the tree must trace to a single cell, not just a single species:…
12 Jul pm09:11 Nova’s “Judgment Day” Coming November 13 on PBS The Pands’s thumb
From NOVA Upcoming Summer & Fall 2007 Programming: NOVA shows on PBS on Tuesdays @ 8 pm ET/PT (check local listings): Judgment Day: Intelligent Design on Trial (w.t.) November 13, 2007 at 8 pm ET check local listings One…
10 Jul am04:06 Ooh, homework! YoungFemaleScientist
I’ve beentaggedto address the latest call for comments on thestate of the NIHRFI (that’s “request for information” for all you non-acronymites out there).So here’s the assignment, directly quoted from DrugMonkey:Post the following RFI queries1….
6 Jul am11:12 Practical BioGrids NodalPoint
If you’re the kind of bioinformatician who is interested in using Grid or Web Services, then the Practical High Throughput Computing for Bioinformatics course held at Imperial College London, on the 16th to 20th July, would probably be worth…
6 Jul am06:31 What’s worst? YoungFemaleScientist
When I make lists, I can’t help trying to put things in order. So in order of least annoying to most annoying thing that happened to me today, where would you rank these?– Got 5 Jul am00:53 What’s a holiday? YoungFemaleScientist Did you work today (July 4th)?No, are you crazy?Yes, like any other dayI only went in to do essential stuff part of the dayMy advisor was there so I had to be there too pollcode.comfree polls 3 Jul am06:04 Thanks for clicking through! YoungFemaleScientist Whoo hoo! Imagine my amazement when I got home today and found a check- looking like junkmail of course- from Google adsense!I could almost afford to quit science for…. a couple days!More likely it might pay for a new pair of shoes… or contribute… 1 Jul pm07:00 Bio::Blogs #12 – 1 year anniversary NodalPoint Welcome to the 12th edition of Bio::Blogs, a monthly blog journal covering bioinformatic related blog posts. This month officially marks 1 full year that Bio::Blogs has been running (we skipped a month along the way). In the last couple of months… 28 Jun am06:06 Freebase invitations NodalPoint I have a couple of Freebase invitations to give away. If you’re interested, send an email to greg[dot]tyrelle[at]gmail[dot]com. For more information on Freebase see Pierre’s posts. Update: they’re gone. I waited for 24hrs (timezone issues) and then… 27 Jun pm02:14 Meme-tag. YoungFemaleScientist I got tagged byanother young female scientist. It feels a bit like a chain letter, of which I’ve never been a fan, but I’ll do it partway and generally ruin the whole point of a chain letter by helping it die a slow, pathetic death.Heh heh heh.”Rules*… 25 Jun pm05:32 SciView part 3: interview with Jeremy Squire NodalPoint The SciView project is back with another interview. This time, Dr Jeremy Squire answered my questions. He is cytogeneticist from the Ontario Cancer Institute, so I tried to get his view on some bioinformatics topics as wet lab scientist. Some great… 25 Jun pm02:00 Parsing SMILES, compression, Ragel Andrew Dalke’s Writings SMILES Some classes of molecular structures can be represented using graphs from number theory, with atoms as nodes and bonds as edges. These happen to include effectively all of the molecules used to make drugs and pesticides… 25 Jun am00:44 Nice. YoungFemaleScientist This was written as a response tothis postover at Science Professor. Then I noticed that she’s apparently taken me off her blogroll.Interesting. I wonder what that’s about.Briefly, in this post she writes about what to do when someone she’s pretty…
24 Jun pm02:06 Mem catosfèric El Cau del Drac
Bé, escampo també el mem d’en Marc Roca i animo als meus lectors blocaires a fer el mateix. Si voleu informar-ho a en Marc, qui ha començat la iniciativa, envieu-li un missatge a

  1. Recomana’m un bloc en català.
    El doctor…
    23 Jun pm02:24 Canvis propers a EstatPropi.Cat El Cau del Drac
    Els promotors de la campanya per un Estat Propi per als Països Catalans vam reunir-nos ahir al Centre Cultural Cruma de Barcelona, on vam aprofitar per a donar la benvinguda al país a n’Alexis, qui ha estat un parell de mesos enmig de l’oceà.

    20 Jun pm09:53 Novetats a Ubuntu Gutsy Gibbon El Cau del Drac
    A llegeixo que Scott James ha enviat a la llista d’anuncis de desenvolupament d’Ubuntu quines seran les novetats més importants de la propera versió, la 7.10, anomenada Ubuntu Gutsy Gibbon.
    GNOME 2.20
    KDE 3.5.7 (KDE 4.0.rc2…
    17 Jun pm06:29 More long-winded responses, continued. YoungFemaleScientist
    Re: the Ben Barres comment,I?m wondering how respect and opportunity are measures, if people crediting you for revolutionizing a field and getting tenure at Stanford are on the low end of the spectrum.I think the point is, she wasn’t happy until she…
    17 Jun pm01:54 Blast is the same as google, but for sequences NodalPoint
    I was looking for the best way to explain what is blast to people with no background in biology/bioinformatics.
    I thought I could to say it’s a search engine:
  • Blast is the same as google, but for biological sequences instead of search…
    16 Jun pm11:38 dbGaP finally makes data available! NodalPoint
    Finally, NCBI’s dbGaP ( has started making available data from various genome wide association studies. This will be an awesome resource for understanding the causes of complex diseases.
    16 Jun pm09:54 Response to a variety of comments on last post- K… YoungFemaleScientist
    Anonymous 1 writes:It is interesting to note (and I dont mean this as a dig at you) that all the FEMALE scientific blogs do not really cover science at all but are generally full of moaning and bitching about people in the lab colleagues etc. Whereas…
    13 Jun pm06:06 Response to comments from two posts ago (leapfrog… YoungFemaleScientist
    Dear Noah, Bill and others,I think I’ve written about this before, but it was before I started tagging on blogger and I don’t have time to search for it. I’ll tag this one for future reference.To make a long story short, again, I applied for the K99. I…
    12 Jun pm04:45 SciView: call for participation NodalPoint
    Hi everyone
    I have posted two interviews in the Blind.Scientist blog with some very good feedback to them, The two interviews posted were more related to Phylogenetics and Bioinformatics, and the third one, which is in the works, will be more…
    8 Jun pm12:19 bioinformaticists or bioinformaticians NodalPoint
    On there is this old poll:
    Asking if bioinformatics people are supposed to be called bioinformaticist or bioinformaticians, and if they are technicians or…
    7 Jun am02:07 Una agència de l’ONU guardona Mozilla per fer ava… El Cau del Drac

La Unió Internacional de Telecomunicacions, agència de tecnologies de la informació i la comunicació de les Nacions unides, ha guardonat Mozilla per la seua contribució al desenvolupament d’Internet.
A través d’en Tristan, em faig ressò de…
6 Jun am02:00 Des dels pobles, Galícia també es mou pel program… El Cau del Drac
Si fa unes poques setmanes des de l’àmbit català va fer-se públic un manifest per a reclamar l’adopció del programari lliure i els estàndards oberts des de les administracions municipals, n’ha seguit el mateix exemple la comunitat gallega. En Manuel…
4 Jun pm05:43 NeoOffice i diccionari català El Cau del Drac

El corrector ortogràfic català que s’incorpora a l’ és una de les característiques que més usuaris m’han destacat quan he parlat d’aquesta aplicació ofimàtica.
De fa un temps, també diferents usuaris de Mac OS X m’han demanat…
2 Jun pm08:07 Sunbird/Lightning i Google Calendar El Cau del Drac

Una de les novetats segurament més populars que s’incorporaran a les imminents versions 0.5 del Lightning i el Sunbird és la integració amb el Google Calendar.
Per a fer-ho, apart del Lightning (que s’instal·la com a extensió del…
2 Jun pm02:57 Què hi ha a la meua bossa de mà? El Cau del Drac

Com ha fet en Xavi i ha seguit en Gil, llisto els continguts de la meua bossa de mà.
Una estelada
Un telèfon mòbil
Una memòria USB
Una càmera fotogràfica digital
Mocadors de paper
1 Jun pm10:05 Bio::Blogs #11 NodalPoint
Welcome to the 11th edition of Bio::Blogs, a monthly round-up of bioinformatics related blog posts (with some additional -omics and open science flavors). The PDF version for this month can be found here for offline reading. For the curious, the…
1 Jun pm02:00 LOLPython Andrew Dalke’s Writings

Combining the cuteness of LOLCODE and
the cuddliness of Python I bring you….
Example code to generate all Fibonacci numbers less than a given value
24 May pm07:42 Instal·lació d’extensions al Thunderbird El Cau del Drac
24 May am00:35 Ús dels referents de cercadors externs per a sugg… El Cau del Drac
23 May pm02:00 OE8BitImage to PNG Andrew Dalke’s Writings
23 May pm02:00 Administrative trivia Andrew Dalke’s Writings
4 May pm09:18 Feed share beyond the blogroll The Personal Genome
4 May pm07:40 Eye on DNA: Hsien’s new blog The Personal Genome
2 May pm11:58 Emerging communities in the Noob Sea The Personal Genome
24 Mar pm01:36 Blonde and brunette mammoths Keat’s telescope
6 Nov pm01:00 IterParseFilter Andrew Dalke’s Writings
24 Oct pm02:00 XML-RPC in TurboGears Andrew Dalke’s Writings
12 Oct pm02:00 NBN notes Andrew Dalke’s Writings
2 Oct pm02:00 Added examples of Python calling C Andrew Dalke’s Writings
22 Sep pm02:00 Slides for “Useful and New Modules” talk Andrew Dalke’s Writings
19 Aug am04:24 Last Post Here Yi Xing’s Alternative Splicing
24 Jul pm12:07 R/Bioconductor Yi Xing’s Alternative Splicing
11 Jul am03:10 Rafael A. Irizarry’s Stanford course on Microarra… Yi Xing’s Alternative Splicing
8 Jul am07:46 Soaked at the outsource Keat’s telescope
6 Jul am11:14 RECOMB Systems Biology 2006 Yi Xing’s Alternative Splicing
1 Jul pm01:06 Ten most difficult feats in sports Keat’s telescope
30 Jun pm03:38 Does life shape the landscape? Keat’s telescope
29 Jun pm02:22 “Who needs coffee when you have a family of sober… Keat’s telescope
27 Jun am10:22 Viruses as engines of evolution Keat’s telescope
24 Jun am11:01 Detecting exonic splicing elements using comparat… Yi Xing’s Alternative Splicing
24 Jun am06:33 Science is the seed corn Keat’s telescope
20 Jun pm07:29 Supply and demand- laser eye surgery and the mili… Keat’s telescope
20 Jun am04:32 Mosquito version of DSCAM also has many isoforms Yi Xing’s Alternative Splicing
19 Jun pm04:47 The “HIV resistance mutation” might be very old Keat’s telescope
19 Jun pm01:22 Two-tongued but not tongue-tied Keat’s telescope
8 Jun am04:16 Our new review on alternative splicing Yi Xing’s Alternative Splicing
8 Jun am04:03 more on motif findings Yi Xing’s Alternative Splicing
7 Jun am00:58 See our recent NAR paper on probabilistic isoform… Yi Xing’s Alternative Splicing
2 Jun am08:34 Copy editing symbols Yi Xing’s Alternative Splicing
Refreshing look at notebook management The Struggling Grad Student
Thoughts on First Beholding McKeesport, PA Three-Toed Sloth
Science blogs The Struggling Grad Student
So You Think You Have a Power Law — Well Is… Three-Toed Sloth
Bibliometrics The Struggling Grad Student
Books to Read While the Algae Grow in Your Fur, M… Three-Toed Sloth
More on manuscript collaboration or dissertation … The Struggling Grad Student
Reformatting in Progress Three-Toed Sloth
BLAST art? The Struggling Grad Student
Books to Read While the Algae Grow in Your Fur, A… Three-Toed Sloth
Day of fun on pentax’ bill The Struggling Grad Student
Slothful Reading Update Three-Toed Sloth
Converting LaTeX document to Word (RTF) format The Struggling Grad Student
Let Me Be Among the First to Welcome Our Six-Peda… Three-Toed Sloth
PubMed Central in UK The Struggling Grad Student
Lecture Notes on Stochastic Processes (Advanced P… Three-Toed Sloth
Linux and the HHS The Struggling Grad Student
Tao on Structure and Randomness Three-Toed Sloth
The future of bioinformatics The Struggling Grad Student
The Reason for the Season Three-Toed Sloth

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