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Daniel Jurczak › Likes
Episode 02 – Systems Biology with Pedro Beltrao - http://nodalpoint.org/2011...
Piotr Byzia, Pawel Szczesny, Simon Cockell and 4 other people liked this
its so weird to hear my own voice :)
- Pedro Beltrao
Wow, I didn't realize nodalpoint was revived (and in podcast form). Love!
- Chris Lasher
Coloring a black and white drawing with the GIMP: my notebook - http://plindenbaum.blogspot.com/2010...
Pedro Beltrao, joergkurtwegner, Daniel Jurczak and Daniel Swan liked this
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
ECCB10 talk - Next-generation sequencing and structural variation - http://www.slideshare.net/jandot...
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Dave Lunt, Daniel Jurczak, Cass Johnston and 2 other people liked this
ECCB10 talk - Nextgen sequencing and SNPs - http://www.slideshare.net/jandot...
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Daniel Jurczak, Cass Johnston, Egon Willighagen and Pierre Lindenbaum liked this
Utopia Documents: Are PDFs Inevitable? - http://www.abhishek-tiwari.com/2010...
Daniel Jurczak liked this
RT @Myrmecos: Count me as a big fan of the "graphical abstract", as per here http://www.sciencedirect.com/science...
Daniel Jurczak, Abhishek Tiwari, Jan Aerts and 2 other people liked this
Gamers beat algorithms at finding protein structures - http://arstechnica.com/science...
Sally Church, Ruchira S. Datta, Jason Bobe and 4 other people liked this
Dave Haussler at HITSeq #ISMB2010
Mitsuteru N, Daniel Jurczak and Deepak Singh liked this
talking about how to handle 3rd generation data. A sequencer transuces a string of dna bases into numbers
- Iddo Friedberg
from Android
Of course, said stateless transduction is not error-free
- Iddo Friedberg
from Android
so we basically have an hmm reading the dna sequence. But as we are reading each base multiple times, the outputted sequence in a Maximum Likelihood
- Iddo Friedberg
from Android
Suggesting a BAM table. A table of events. Th.e output code strings of the machine are the way to store information. The way we do it now with quality scores is not good.
- Iddo Friedberg
from Android
Debunking the 100X GPU vs. CPU myth: An evaluation of throughput computing on CPU and GPU - http://gpgpu.org/2010...
Mike Chelen, Khader Shameer, Jason Stajich and Daniel Jurczak liked this
The truth comes out: In South Korean Soap Operas, Love is like... Starcraft? (via @anuraagagrawal) - http://kotaku.com/5549991...
Daniel Jurczak, Pedro Beltrao and Deepak Singh liked this
galaxy / galaxy-central / wiki / AddToolTutorial — bitbucket.org - http://bitbucket.org/galaxy...
Daniel Jurczak and Deepak Singh liked this
adding a tool to galaxy
- Pierre Lindenbaum
Replace yourself with a shell script - http://mndoci.com/2010...
Daniel Jurczak, Greg Tyrelle, Brad Chapman and 2 other people liked this
:-)
- Ruchira S. Datta
Wolfram|Alpha can not only calculate the roots of an equation, but it can show you step-by-step how to do it! - http://blog.wolframalpha.com/2010...
Daniel Jurczak, Ashish and Deepak Singh liked this
LOL: "We originally wrote this article in Word, but then we converted it to LaTex to make it look more like science" http://www.stat.columbia.edu/~gelman...
Daniel Jurczak and Pierre Lindenbaum liked this
Estimating genome scaffold order using reference genomes - http://www.michaelbarton.me.uk/2010...
Rob Syme and Daniel Jurczak liked this
Using Twitter to learn economy of words - try to summarize your research paper in 140 characters or less! - http://scienceblogs.com/clock...
Mickey Kosloff and Daniel Jurczak liked this
Querying pubmed on the command line - http://www.michaelbarton.me.uk/2010...
Piotr Byzia, Chris Miller, Daniel Jurczak and 7 other people liked this
Can I use it to get BibTeX starting from a DOI?
- Egon Willighagen
All it really does is allow you to search pubmed from the command line then open up the records you want in the browser. Boson is quite easy to get started with so you could adapt my function into your own to fetch bibtex records.
- Michael Barton
When I try "boson query -t genome --mail="YOUR_EMAIL" ... I get ... "Error: wrong number of arguments (3 for 1)" ... Any tips? I am working on a Mac, too.
- joergkurtwegner
Could you post the error message? Maybe as a gist?
- Michael Barton
LOL, sorry, now for dummies like me, whats a gist?
- joergkurtwegner
It's code paste site on github. Good for sharing code unrelated to anything in particular - http://gist.github.com/
- Michael Barton
Got it, actually "Error: wrong number of arguments (3 for 1)" is all error I get or is there a way getting more error logging? ... gotta go now ...
- joergkurtwegner
I can recreate these errors by doing a clean install of boson on a virtual machine. I'll see if I can fix this.
- Michael Barton
Thanks for the feedback guys I think I found the problem - http://github.com/michael...
- Michael Barton
If you still fancy trying it, hopefully it will work this time.
- Michael Barton
scrape.py - http://zesty.ca/scrape/
Konrad Förstner, Josef Scheiber and Daniel Jurczak liked this
"scrape.py is a Python module for scraping content from webpages."
- Michael Kuhn
Ah, cool. I usually use Beautiful Soup (http://www.crummy.com/softwar...) for such jobs. Do you have experiences with that and can compare both of them?
- Konrad Förstner
no, I also usually use Beautiful Soup for scraping downloaded HTML, and just bookmarked this for future reference. Looks like this one can be used to navigate links.
- Michael Kuhn
I thought Lynx is already cool, but this might be actually really useful.
- joergkurtwegner
Nature paper: Complete Khoisan and Bantu genomes from southern Africa: data available preloaded into Galaxy for immediate analysis- http://main.g2.bx.psu.edu/bushman
Mitsuteru N, Attila Csordas, Jean-Claude Bradley and 8 other people liked this
As a Galaxy fan, I love this: "It is challenging to provide convenient access to the large and complex data sets resulting from the sequencing and analysis of a human genome. In addition to submitting data to standard repositories, we provide all data sets in an immediately useful form through the Galaxy bioinformatics platform (http://usegalaxy.org), a web application designed to integrate data with analysis tools. In addition to downloading, data sets can be transformed in a variety of ways and compared with existing annotations (see ‘Data and analysis user’s guide’ at http://galaxycast.org). The positions of the SNPs for each Bushman and ABT can be viewed in a customized installation of the UCSC Genome Browser (http://main.genome-browser.bx.psu.edu/), along with supporting evidence (number of reads for each allele and hyperlinks to the actual reads) and computationally predicted phenotypic consequences for SNPs in coding regions."
- 'Mummi' Thorisson
(Supplement to Schuster et al. Complete Khoisan and Bantu genomes from southern Africa. Nature 463, 943-947 (18 February 2010) | http://dx.doi.org/10...)
- 'Mummi' Thorisson
So is this going to be a test for Galaxy's servers? Is psu going to be slashdotted? I'll be having a rummage, so how many others...
- Richard Badge
from Nambu
Neil, please clarify: from reading this it seems to me that they *are* providing the data in a useful form, and so rising to the challenge. But you're saying that they aren't? I'm not following...
- 'Mummi' Thorisson
The one search company most likely to get purchased by Microsoft to crush Google that I saw in Cambridge UK? PrismaStar.
David Brown, Daniel Rowley, Jelly Roll Morton and 24 other people liked this
Reasons for saying that?
- Ahmed
Why?
- Jim Connolly
why ?
- Kashif Khan
"crush google", wow sounds interesting.
- Rich Lazzara
I hope this is the same PrimaStar Robert is talking about
- Ashish
Rich: Google crush sounds more interesting - like the name of a drink.
- Jim Connolly
Why? You'll have to see our Building43 video to see why. :-) But let's just say they did the search technology for several camera stores and the conversion rate went WAY up. Why is that? Because they offer a new way of searching things that really rocks. I can't explain it in text. Gotta show it to you.
- Robert Scoble
looking fwd to it
- Rich Lazzara
Primestar's AnswerOil UIX is a good fit for #Bing's decision support platform, combined with shopping cart & checkout optimization products from www.allurent.com would yield further eCommerce results.
- Alexander Ainslie
Robert: direct link to the building43 video?
- James Kuypers
Several people asked which product categories we support -- here's a site that uses over 1000: http://translate.google.com/transla...
- jzt
(on the right-hand side of that translated page are some samples...)
- jzt
Also, Mark Essel: YES, we do support dynamic search/ads via keywords/tags. :)
- jzt
Most likely to get purchased by Microsoft with the intent to crush Google, perhaps. But Microsoft intends a lot of things. Maybe they'll buy PrismaStar, then rebrand MSN, er, Live Search, er Bing, and the market will be less confused.
- Andy Bakun
But Jessops the camera retailer is losing money: http://www.dailymail.co.uk/money...
- Jelly Roll Morton
Jessops has been losing money as long as anyone can remember, which is hardly Prismastar's fault. The point is though that Jessops has a very good search tool with Prismastar's AnswerOil and has seen a substantial increase in its conversion rates since adopting Prismastar's technology. It could be Answeroil which has kept them going this long (nobody would have expected them to still be around in late 2009 eighteen months ago)
- John S Cameron
John, did Jessops really see a substantial increase in conversion rates? I respectfully suggest that this is not a fact. Can anyone actually verify this claim? It is on record that Jessops are still around because HSBC Bank saved them, rather than because of their business performance.
- Jelly Roll Morton
Posting from another feed: here is the prior art that someone was looking for on Interconnected Sliders : they existed back in 2004 in the public domain - download this FLA file for free and build your own interconnected sliders: http://www.senocular.com/flash...
- Jelly Roll Morton
Microsoft hooking up with Prismastar was a good idea. Time inc. felt the same way and purchased Stylefeeder a shopping selector.
- Paul Baldovin
Hello again Mark, Comparing the Prismastar Product Selector to Jemms iBlick Finder would most depend on what the clients business requirements are. This is the way to determine which might be the best to use. Those that I've worked with would look at price, flexibility, timeline to full deployment and analytics. I would suggest any client in need of this kind of solution look at both...
more...
- Paul Baldovin
Why don’t any of these Prismastar affiliates work? - collectinstore.co.uk - offeroftheday.co.uk - prophotoinsights.net - digitalphotographyprojects.com - turkeyherald.com - vouchers-and-deals.com
- mike townsend
Uh oh - it's true that Prismastar have failed to raise funding and have now closed their Cambridge, UK office, better luck predicting big things next time, Robert!
- Jelly Roll Morton
Scoble's reputation as a prophet continues! ("crush Google" LOLing)
- The Real sofarsoShawn
whoops! LoL
- Jelly Roll Morton
RT @martiell: Useful. :) http://pleaserobme.com/
Daniel Jurczak, Egon Willighagen, Pierre Lindenbaum and Peter Miller liked this
is there a program that tries to extend a contig sequence in either direction using small overlaps and a large pool of short reads?
Daniel Jurczak liked this
so to be clear I am looking for something greedy and only concerned with growing one seed contig, not creating an assembly
- Jeremy Leipzig
ok Rene Warren says SSAKE has a seed feature - will try
- Jeremy Leipzig
Maybe this: GapCloser for SOAPdenovo http://soap.genomics.org.cn/
- Darek Kedra
LaTeX Search - http://www.latexsearch.com/LatexTo...
Dan Gezelter, novoseek, Daniel Jurczak and 2 other people liked this
"The Springer LaTeX search lets you search through over 1,342,002 LaTeX code snippets to find the equation you need."
- Abhishek Tiwari
from Bookmarklet
It's now official. I'll be speaking on open science over at #TEDxWarsaw on 5th of March.
Benjamin Tseng, Piotr Byzia, Steve Koch and 4 other people liked this
The title of the talk will be "Science Open. Science Connected." Guess who was the inspiration ;). My focus will be human face of open science. The event will be livestreamed (hopefully) and many of the talks (including mine) will be held in english.
- Pawel Szczesny
Saints' Sean Peyton should be the MVP. superior coaching and play calling
Daniel Jurczak and Deepak Singh liked this
I think bioinformaticians who use OSX would benefit from a homebrew type system for bioinformatics tools.
Daniel Jurczak liked this
You know things are bad when you've scheduled your day for the wrong timezone...
Michael Nielsen, Christina Pikas, Daniel Jurczak and 4 other people liked this
I trust you did at least arrive back ok ...
- Anna Croft
Homebrew: OS X’s Missing Package Manager | Engine Yard Blog - http://www.engineyard.com/blog...
Micah, Meryn Stol and Daniel Jurczak liked this
Homebrew is a compelling alternative to MacPorts and Fink. The Homebrew core and all the formulae are written in Ruby, so it’s easy to add new packages or even new features. If you’re looking for more control over the Unix software you have installed on your Mac, or you’ve been frustrated by other package managers in the past, check it out. I think you’ll be happily surprised.
- Deepak Singh
what would be a bioinformatics killer app for the IPhone?
Yaroslav Nikolaev, Piotr Byzia, Deepak Singh and 6 other people liked this
any comments?
- pn
I thought about doing a colony counter for the G1 ... point it a plate , click and get a the number of colonies. This could be handy :)
- Pedro Beltrao
a ncbi, pubmed search?
- pn
Pedro's idea++. However, I don't really see a reasonable workflow with mobile versions of NCBI or BLAST on the iPhone.
- Daniel Jurczak
Neil, Paulo, Daniel, have you seen this: http://www.ncbi.nlm.nih.gov/pubmed... ? It's from 2001 :)
- Pawel Szczesny
Would there have to be one? (Or am I just narrow-minded here? Hope not...) The colony counter makes sense, but there's no real added value in blast or ncbi on a mobile phone, is there? It'd really have to be an app that leverages the fact that it can be carried around. So maybe as an input portal for your labjournal (notes, photos).
- Jan Aerts
I don't know about bioinformatics, but biology could sure benefit from a killer lab timer. :-)
- Danielle Fong
Would any aspect of bioinformatics benefit from being made mobile at all? Maybe a service that could check in on the progress of molecular dynamics calculations or something?
- Mr. Gunn
@Pawel nice link. I will check it out.
- pn
@Neil: may I guess where you have lunch?
- pn
the monitoring visualization bits are relatively east ESP with a full featured browser. I love the colony idea. In a lab finding a sample by taking a picture of the bar code (for the g1) or using the phone as some sort of controller
- Deepak Singh
@Paulo What? You don't eat your lunch at the computer?
- Marcos de Carvalho
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