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Tuesday, December 22, 2009

Link Roundup Returns - Dec 16-22

I've been busy with my thesis project for the past couple weeks, which I think is understandable, but all work and no play kinda doesn't sit well for me. So, over the weekend, I learned go, google's new programming languages, and wrote myself a simple application for keeping track of links - and dumping them out in a pretty html format that I can just cut and paste into my blog.

While I'm not quite ready to release the code for my little go application, I am ready to test it out. I went back through the last 200 twitter posts I have (about 8 days worth), and grabbed the ones that looked interesting to me. I may have missed a few, or grabbed a few less than thrilling ones. It's simply a consequence of me skimming some of the articles less well than others. I promise the quality of my links will be better in the future.

Anyhow, this experiment gave me a few insights into the process of "reprocessing" tweets. The first is that my app only records the person from whom I got the tweet - not the people from who they got it. I'll try to address that in the future. The second is that it's a very simple interface - and a lot of things I wanted to say just didn't fit. (Maybe that's for the better.. who knows.)

Regardless (or irregardless, for those of you in the U.S.) here are my picks for the week.

  • Bringing back Blast (Blast+) (PDF) - Link (via @BioInfo)
  • Incredibly vague advice on how to become a bioinformatician - Link (via @KatherineMejia)
  • Cleaning up the Human Genome - Link (via @dgmacarthur)
  • Neat article on "4th paradigm of computing: exaflod of observational data" - Link (via @genomicslawyer)

  • Gene/Protein Annotation is worse than you thought - Link (via @BioInfo)
  • Why are europeans white? - Link (via @lukejostins)

Future Technology:
  • D-Wave Surfaces again in discussions about bioinformatics - Link (via @biotechbase)
  • Changing the way we give credit in science - Link (via @genomicslawyer)

Off topic:
  • On scientists getting quote-mined by the press - Link (via @Etche_homo)
  • Give away of the best science cookie cutters ever - Link (via @apfejes)
  • Neat early history of the electric car - Link (via @biotechbase)
  • Wild (innacurate and funny) conspiracy theories about the Wellcome Trust Sanger Institute - Link (via @dgmacarthur)
  • The Eureka Moment: An Interview with Sir Alec Jeffreys (Inventor of the DNA Fingerprint) - Link (via @dgmacarthur)
  • Six types of twitter user (based on The Tipping Point) - Link (via @ritajlg)

Personal Medicine:
  • Discussion on mutations in cancer (in the press) - Link (via @CompleteGenomic)
  • Upcoming Conference: Personalized Medicine World Conference (Jan 19-20, 2010) - Link (via @CompleteGenomic)
  • deCODEme offers free analysis for 23andMe customers - Link (via @dgmacarthur)
  • UK government waking up to the impact of personalized medicine - Link (via @dgmacarthur)
  • Doctors not adopting genomic based tests for drug suitabiity - Link (via @dgmacarthur)
  • Quick and dirty biomarker detection - Link (via @genomicslawyer)
  • Personal Genomics article for the masses - Link (via @genomicslawyer)

  • Paper doing the rounds: Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data - Link (via @BioInfo)
  • Archiving Next Generation Sequencing Data - Link (via @BioInfo)
  • Epigenetics takes aim at cancer and other illnesses - Link (via @BioInfo)
  • (Haven't yet read) Changing ecconomics of DNA Synthesis - Link (via @biotechbase)
  • Genomic players for investors. (Very light overview) - Link (via @genomicslawyer)
  • Haven't read yet: Recommended review of 2nd and 3rd generation seq. technologies - Link (via @nanopore)
  • De novo assembly of Giant Panda Genome - Link (via @nanopore)
  • Welcome Trust summary of 2nd Gen sequencing technologies - Link (via @ritajlg)

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Monday, November 30, 2009

Link Roundup - November 30th, 2009

Here are my picks from the last two weeks, while I've been busy with other things. I've skimmed all of the articles below, and will probably have to return to read a few more closely, but each of them seemed interesting.

I've filtered out more than usual, simply because of the sheer number of links that collected in my in-box. (194 tweets, to be exact.) However, that also gave me an interesting opportunity to gather some statistics. For each link, I've given the twitter name of the person from whom I first saw the content. Since most of the tweets pop up in my box 2-3 times from different people, the list below is pretty much the list of people generating original content, or who are fastest at getting the content into twitter. Thus, it's kinda neat to see who's shaping the twitter conversations I follow.

Personal Genomics:
  • Reply to why Personal Genomics are worthwhile - Link (via @dgmacarthur)
  • DNA testing is changing fatherhood - Link (via @genomicslawyer)
  • Why paternity testing should be mandatory - Link (via @dgmacarthur)
  • Another DTC scam? Athleticode - Link (via @dgmacarthur)
Bioinformatics & Sequencing:
  • Benchmarking the cloud for genomics - Link (via @dgmacarthur)
  • The cost/benefit figures calculated for cloud genomics - Link (via @lukejostins)
  • Hacking Admixed 23andMe Ancestry Paintings - Link (via @dgmacarthur)
  • Amazon's usage plans for web service research grant - Link (via @BioInfo)
  • Great chart comparing 2nd gen sequencing platforms - Link (via @CLCbio)
  • Data processing for GWAS data (abstract) - Link (via (@KatherineMejia)
  • 2nd Gen sequence analysis tools in BioLinux? - Link (via @BioInfo)
  • 2nd Gen command line tools - Link (via @BioInfo)
  • Luke Jostins comments on bad (possibly wrong) media coverage of GWAS - Link (via @lukejostins)
  • Bioinformatics are too good to be true? - Link (via @Katherine Mejia)
  • Sign up for new de novo assembler coming soon from CLC Bio- Link (via @CLCBio - kinda spamish?)
Computers & Math:
  • Chrome OS starts to appear for testing - Link (via @BioInfo)
  • Give everyone the chance to use science derived data - Link (via @BioInfo)
  • How heavy is the internet - Link (via @lukejostins)
  • Arthur Benjamin on teaching the right math - Link (via @apfejes)
Odds & Ends:
  • Growing meat without animals - Link (via @KatherineMejia)
  • Seeding science in the developing world - Link (via @ritajlg)


Monday, November 16, 2009

Link Roundup - November 13-16

  • Open Office Hours with Hank Greely (Bioscience and ethics) - Link
Blogging/Popular Culture/Funny:
  • Blogger and Biologist by day, prostitute by night - Link
  • Genomics assisted dating? - Link
  • New (to me) site: - Link
  • A LOT of videos of molecular events - Link
  • 35 Amazing Science Fair Projects - Link
Stuff I haven't read/categorized:
  • Genetic links to Parkinsons - Link and Link


Friday, November 13, 2009

News Roundup - Nov 11-13, 2009

Take two at an article Roundup. Doing this project doesn't take a lot of work, but the tools I'm using for it are somewhat inconvenient, which makes it an interesting (challenging?) project. Categorization isn't difficult, but I can see how it'll be time consuming in the end. I think the only way to really do this is to use a micro-database with a small gui to do the work and generate the HTML at the end of the day.... but hey, I'm a programmer, so you'd think I could write one if I wanted. (And yes, I could try to use Go to do it...) Unfortunately, it'll have to wait a few more days. (Yes, I have a committee meeting on tuesday, and I'm still blogging - what's wrong with this picture?)

You'll notice some overlap in the days covered, mainly because I'm posting midway through the day. I could even go a step further and automate this, but somehow, I think I should take it one step at a time.

What I really wonder is if I'm casting my net wide enough, as in "what fraction of the cool genomics/bioinformatics/personalized medicine articles am I actually reading?" At least, based on the theory that I'm subscribed to the best of the cool twitterers who do a lot of the pre-filtering for me, if you believe in community filtering, maybe this really is the best of the best. (-:

Well, without any more delay, here's the best of the past 48 hours.


  • Cheap DIY Microfluidics using Shrinking Plastic - Link
Popular Health:
  • To immunize or not immunize - Link
  • Imagining Personalized Medicine - Link
  • Larry David finds out he's not who he thinks he is - Video
Sequencing Technology:
  • Nanopores with single base resolution - Link
  • Amazon offers various forms of computing resource, enumerated here - Link
  • Opening up the courts to allow anyone to challenge a patent - Link


Tuesday, November 10, 2009

Article Roundup - November 9-11, 2009

I've decided to start a new resource for myself, and for anyone who might find this useful. Each week, an incredible number of neat articles and posts do the rounds on twitter - but I often find myself skimming them and then forgetting where I saw it. Going back through twitter feeds is such a hassle that I figured I should start collecting them into a single resource.

I'm not quite sure what the right format it, but I'm sure it'll fall into place quickly. The only criteria I have for this list is that it must be 1. insightful, 2. science related, preferable genomics or genetics related and 3. well written. I'll probably end up settling for any two of the above, but hey, for the first post, I'll try to keep my standards high.

Originally, when I started this, I had assumed I could do this one week at a time, although it's rapidly becoming difficult to process the significant number of links. Instead, I'll start off with 2-3 days, which should make it manageable. Additionally, having looked at this over the past couple days, I can see that some serious categorization will be necessary in the future. So, for a first try, here are the links I've collected since Monday.

Articles & Blogs
  • Commentary on Next Gen technology and the gap to sequence analysis - Link
  • On why breakthroughs really aren't... (the curse of multiple testing and statistics) - Link
  • Differences between DTC genotyping - Link
  • Commentary on differences between DTC genotyping risks - Link
  • The difference between Genetic and Genealogical family trees - Link
  • Helicos no longer selling itself - Link
  • ResearchMatch: an NIH resource to link volunteers with studies - Link
  • Update on Bilski (Patent-ability of non-machine inventions) and biotech - Link
  • Why sequencing non-Homo sapiens genomes is important (Horse genome) - Link
  • How related are you to your relations? - Link
  • Career Development for Life Scientists: An Ongoing and Disturbing Trend - Link
Off Topic posts:
  • DRM and Apple - a business model - Link
Unusual Tweets:
  • "RT @lindaavey : Looks like my husband's 4th cousin is my dad's 10th cousin (my 11th cousin?)." - From dgmacarthur, Nov 11th, 2009