Gamers, get your folding on
discuss this article
Technology Review was the first place I saw it, then someone put it up on Friendfeed and now Andrew Perry has a great post on Foldit. Foldit comes out of the lab of a bbgm favorite, David Baker, right here at the University of Washington.
Foldit combines gaming with protein structure prediction. It’s an interesting approach to spreading scientific problems. Folding@home built upon the success of Seti@home and the geek cred of running on gaming consoles and has built quite a following. Will Foldit, which presents a simple, fun interface to get people interested in protein structure (and the existence of Folding@home m...
Source: business|bytes|genes|molecules - May 9, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Computing Geek Life Science Modeling & Simulation David Baker Folding@Home Foldit Microsoft Protein Structure Prediction University of Washington newtag Source Type: blogs
Published #2 (2008)
discuss this article
It’s turned out to be a pretty good week. This one has been in press for ever, but finally hit the web:
Frith, M.C., Saunders, N.F.W., Kobe, B. and Bailey, T.L. (2008).
Discovering Sequence Motifs with Arbitrary Insertions and Deletions.
PLoS Computational Biology 4(4):e1000071. [Open Access] | [PubMed]
This paper describes GLAM2, a Gibbs sampler that finds and refines variable-width motifs, allowing insertion and deletion, in related but dissimilar sets of sequences. The work is very much Martin’s baby; my minor contribution was to try it out on some test datasets. It’s open-access, so you can all go a...
Source: What You're Doing Is Rather Desperate - May 9, 2008 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics publications research diary glam2 motifs Source Type: blogs
I still haven't found what i'm googling for
discuss this article
Twenty one years ago this month, in May 1987, Irish rockers U2 released their classic Joshua Tree single, I Still Haven't Found What I'm Looking For. Those twenty one years have seen incredible technological change: the adoption of desktop computers, mobile phones, the birth of the Web and the widespread use of search engines like Google. So with sincere apologies to Bono, The Edge, Adam and Larry, it's time we updated the lyrics for the 21st century. So, I give you "I Still Haven't Found What I'm Googling For" (21st anniversary, 2008 webby edition)...
read more (Source: nodalpoint.org - A bioinformatics weblog)
Source: nodalpoint.org - A bioinformatics weblog - May 9, 2008 Category: Bioinformaticians Authors: Duncan Tags: Bono Data management Google googling Ireland joshua tree lyrical search technology u2 web Source Type: blogs
Foldit - crowdsourcing to solve the protein folding problem
discuss this article
David Baker’s lab and friends, have recently released a new ‘experiment’ in protein folding called FoldIt. Essentially, individuals or teams can compete online to manually fold protein structures, guided by the internal energy function within the game (it very likely uses code from the impressive ab initio folding software Rosetta under the hood). The interface is designed as a game to make it accessible to everyone, not just experts in protein folding. While it’s pretty simplified compared with your average molecular structure editing software, I think designers of scientific software (often scient...
Source: Your bones got a little machine. - May 8, 2008 Category: Bioinformaticians Authors: perry Tags: science software structural biology folding protein structure wine Source Type: blogs
A brief history of the platypus, in 5 parts
discuss this article
Who isn’t fascinated by the strangest of mammals, the platypus? It has fur and lactates, like a mammal. It has a bill and webbed feet, like a bird. It lays eggs and produces venom, like a reptile. It finds prey using electroreception, like sharks. The platypus is so weird that when first described, many scientists assumed that it was a hoax.
To celebrate the publication of the draft platypus genome, here’s a brief guide to this wondrous creature.
Part 1. The Dreamtime Story
We scientists think that we’re very smart when it comes to explaining the natural history of Australia. However, the original inhabi...
Source: What You're Doing Is Rather Desperate - May 8, 2008 Category: Bioinformaticians Authors: nsaunders Tags: australia bioinformatics genomics publications genome research monotremes nature platypus Source Type: blogs
For my money, one of the greatest songs ever written
discuss this article
Armed with a killer acoustic guitar sound, Ani Difranco’s “Both Hands”: (Source: Trapped in the USA)
Source: Trapped in the USA - May 7, 2008 Category: Bioinformaticians Authors: bosco Source Type: blogs
Does anyone have a clue who this could be?
discuss this article
Job Description
You don’t get to see job descriptions like this too often in the life sciences. Have to love the What you get section.
What does the job description tell us. It’s a web-based consumer focused company with a focus on healthcare and with an informatics backend. Comes out of Stanford and has a Nobel prize winner advising it, which sounds very much like Andy Fire (based on the Stanford angle).
Let’s start the speculation.
Guess where I found this position; by tracking ‘bioinformatics’ on Twitter
Technorati Tags: Andy Fire, Healthcare, Stealth Startup, Stanford, Xooglers
ShareThis (...
Source: business|bytes|genes|molecules - May 7, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Healthcare Software & Internet newtag Source Type: blogs
Drug-drug interactions and network connectivity
discuss this article
How does the effect of drug-drug combinations relate to the cellular interactions of their targets ? Last year, Joseph Lehár and colleagues published a paper in MSB looking into this question.One way to study the effect of drug combinations on growth of a bacteria for example is to measure the inhibition of growth of all possible combinations of serially diluted doses of two combined drugs and plotting dose-matrices like the ones shown in figure 1 of the paper and shown here adapted from the paper. In fig1A the authors show how the combined effect of increasing doses of two drugs inhibit the growth of a methicillin-resist...
Source: Public Rambling - May 7, 2008 Category: Bioinformaticians Tags: network reconstruction systems biology Source Type: blogs
Harvard law faculty votes for ‘open access’ to scholarly articles
discuss this article
From an email I received earlier today. Would normally not pay this much attention, but this is the Berkman Center and Open Access is always a good thing
Good afternoon,
The Berkman Center for Internet & Society is pleased to announce that the faculty of Harvard Law School has unanimously approved a motion for open access: articles will be made freely available in an online repository. With the success of this motion, Harvard Law becomes the first law school to make an institutional commitment to open access to its faculty’s scholarly publications.
In February, Harvard University’s Faculty of Arts and Scie...
Source: business|bytes|genes|molecules - May 7, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Open Science Berkman Center for Internet & Society newtag Source Type: blogs
Discussion on business models around open data is building up
discuss this article
This post got deleted during a blog snafu. Reposting
Many months ago, I started talking about the monetization of biological data, a theme that’s been present throughout the history of bbgm. In general, I have maintained that for the most part, the value lies not in the raw data, but in what we can do with the data. It looks like there is an interesting discussion brewing on the web around some of these ideas. Here are three a couple of posts, I think in chronological order
Peter Murray-Rust. The comment from Rich Apodaca is a must read. There is a follow up post from Antony Williams as well.
I will just re-iterate a...
Source: business|bytes|genes|molecules - May 7, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Business Open Science Software & Internet newtag Source Type: blogs
Loss of posts and various wordpress issues
discuss this article
I have lost some recent posts. Will try and resurrect them from Google Reader. Once again I apologize for all these Wordpress issues.
Please email me if you continue seeing problems … mndoci AT mndoci — DOT — com
ShareThis (Source: business|bytes|genes|molecules)
Source: business|bytes|genes|molecules - May 7, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Admin Source Type: blogs
Hpc and structure-based drug design
discuss this article
Here is the abstract of a paper in Hypertension entitled Structure-based identification of small-molecule angiotensin-converting enzyme 2 activators as novel antihypertensive agents.
Angiotensin-converting enzyme 2 (ACE2) is a key renin-angiotensin system enzyme involved in balancing the adverse effects of angiotensin II on the cardiovascular system, and its overexpression by gene transfer is beneficial in cardiovascular disease. Therefore, our objectives were 2-fold: to identify compounds that enhance ACE2 activity using a novel conformation-based rational drug discovery strategy and to evaluate whether such compounds re...
Source: business|bytes|genes|molecules - May 6, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Computing Drug Development Modeling & Simulation Blood pressure British Heart Foundation Cardiovascular Disorders Conditions and Diseases Drug Design drug discovery Health Hypertension newtag Source Type: blogs
Sun and amazon jump into the pool together
discuss this article
At JavaOne, one of the big announcements was a hookup between Amazon, specifically EC2, and OpenSolaris (finally generally released as a full open source OS). The collaboration between Amazon and OpenSolaris will give customers access to OpenSolaris (for feree) and MySQL premium technical support, and more. The key selling points are ZFS and D-Trace. Now, I am a big Linux guy, but options are always good and enterprise relationships/partnerships are just a sign of the maturing and relevance of cloud computing.
Related articles
Amazon Now Serving OpenSolaris on EC2 [via Zemanta]
Sun debuts OpenSolaris; OS to be served...
Source: business|bytes|genes|molecules - May 5, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Business Open Science Physical Science Software & Internet Amazon Amazon Web Services cloud computing JavaOne Linux MySQL Open Source OpenSolaris Sun Microsystems ZFS newtag Source Type: blogs
Around the web - may 4, 2008
discuss this article
Discussion forum for next gen sequencing (was down when I was writing this)
In perpetual pursuit of context
Open Metabolomics Data
EquityEdit is an interesting organization. They edit and translate biomedical manuscripts and the compensation funds small, innovating, global health organizations (with a focus on the developing world, e.g. Nyaya Health). Don’t know too much about them, but the financial model is definitely interesting.
WIkiPatents
Interview with Paul Graham
Subversion & Git
Stagerat - a site for live music fans
Data stores and BI
Multimedia & Presentations
Bio2RDF do SPARQL
Nodalities become...
Source: business|bytes|genes|molecules - May 5, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Weekly Roundup Dell EquityEdit Gnomedex Metabolomics Paul Graham SPARQL Web 2.0 Expo Source Type: blogs
Workshop: brew 2008
discuss this article
I was in Bielefeld, Germany for BREW2008 workshop. I was quite suspicious of this place as people (http://www.cebitec.uni-bielefeld.de/index.php?option=com_cudbhome&task=show&cudbname=sniemeie , http://www.cebitec.uni-bielefeld.de/index.php?option=com_cudbhome&task=show&cudbname=twittkop ) informed me that Bielefeld does not exist ( http://en.wikipedia.org/wiki/Bielefeld_Conspiracy )! So I went out and took loads of snaps ( http://picasaweb.google.com/sharma.animesh/BREW2008?authkey=ranwczoE2-Q ) to prove its existence ... well on second thought map is not the territory ( http://en.wikipedia.org/wiki/Thomas...
Source: Bioinformatics Latest News - May 4, 2008 Category: Bioinformaticians Source Type: blogs
Andrew releases the final golem beta and other cool stuff
discuss this article
The announcement
The protagonist. What is it?
Golem is a set of tools, and ontology language, for processing data written in the CML, the Chemical Markup Language. The Golem language is XML, and the tools and libraries are written in Python.
A shout out to the MaterialsGrid, which my former employer, Accelrys, is involved with. I’ve talked about some of the cool stuff he does before. That’s only the tip of the iceberg. He writes and records cool electronica and does creates mashups like the one below (using RDF)
Crystallography, 2000-2007 from Andrew Walkingshaw on Vimeo.
Video via Andrew under a Creativ...
Source: business|bytes|genes|molecules - May 4, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Geek Open Science Semantic Web Software & Internet Accelrys Andrew Walkingshaw Chemical Markup Language Python RDF XML newtag Source Type: blogs
Tons of data everywhere. do we need life science cdns?
discuss this article
This weeks Bio-IT World meeting was all about data storage. Driven by the needs of integrating complex, heterogenous data and most of all by next gen sequencing, it’s amazing how much data the life sciences are generating and how poorly prepared we are. I won’t necessarily mention names, but there are places which have data hitting the petabytes AFTER throwing away most of it. How do you access this data? How do you back it up? What kind of data centers do you need? What kind of power do you need? When people are worried about the city being able to handle their power needs then there is cause for concern.
It i...
Source: business|bytes|genes|molecules - May 3, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: BioIT Informatics Life Science Technology BigTable Chris Dwan Google Open Data Yahoo newtag Source Type: blogs
Introducing the eyelims project
discuss this article
Scientists usually share information with collaborators from all around the world. For that purpose, eyeOS (www.eyeos.org) provides an unvaluable system to access and share documents, create and save data files or store crucial personal and professional information.
To see eyeOS widely used by scientists all around the world, we initiated the eyeLIMS project ! eyeLIMS is a community-driven project which aims at providing a Free, web-based, Open Source Laboratory Information Management System (LIMS) powered by eyeOS.
read more (Source: nodalpoint.org - A bioinformatics weblog)
Source: nodalpoint.org - A bioinformatics weblog - May 3, 2008 Category: Bioinformaticians Authors: amejat Tags: Bioinformatics Data management Free LIMS Open Bioinformatics Open Source Open source software Science 2.0 web-based XML Source Type: blogs
Tranche in the news: more wins for open data
discuss this article
Proteome Commons Tranche is one of the cooler resources on the web. Ever since I met Jayson Falkner, I have liked their approach to open data, and their early support for CC0. Looks like Tranche has hit the big time with the announcement that the resource has been chosen to host all mouse model proteomics data collected by the National Cancer Insititute. From the press release (which you can read in its entirety here).
The innovative scientific file sharing network and data repository, Tranche, has been chosen to host all Mouse Models proteomics data collected by the National Cancer Institute (NCI) Mouse Proteomic Technol...
Source: business|bytes|genes|molecules - May 2, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Life Science Omics Open Science Jayson Falkner National Cancer Institute NCI MPTI Philip Andrews proteomics scientific file sharing network University of Michigan newtag Source Type: blogs
Biobootcamp 2008
discuss this article
Perhaps I was premature in bemoaning the lack of a startup school for life scientists. Adam Rubenstein points to biobootcamp 2008. Not exactly what I had in mind, but knowing some of the people involved, I suspect it will be quite useful to people.
Image via Wikipedia
Technorati Tags: biobootcamp, entrepreneurship
ShareThis (Source: business|bytes|genes|molecules)
Source: business|bytes|genes|molecules - May 2, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Business Life Science Adam Rubenstein newtag Source Type: blogs
Bio-it world day 3 - linda avey keynote
discuss this article
ShareThis (Source: business|bytes|genes|molecules)
Source: business|bytes|genes|molecules - April 30, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Event Source Type: blogs
Bio-it world day 2 - iphones, virtualization, ec2 and the semantic web
discuss this article
A quick report on Day 2 of Bio-IT World.
The day started with a keynote by Josh Boger, founder and CEO of Vertex. His talk spanned several real world examples and some food for thought. Highlights
Vertex has made active use of a MedChem ELN, which has been extended to their entire MedChem community, including external partners. In his own words the goal was “enabling the virtual research organization”
Metric of success was user adoption and there were some good analytics supporting uptake
He spoke at length about the HCV program, where they have used extensive predictive modeling and simulation
Clinical data ...
Source: business|bytes|genes|molecules - April 30, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: BioIT Computing Drug Development Event Life Science Modeling & Simulation Pharma Semantic Web Software & Internet Amazon Web Services BioTeam Chris Dagdigian ELN Eric Neumann Joe Landman John Wilbanks Josh Boger Source Type: blogs
Open-ed gel electrophoresis data
discuss this article
Several months ago - about 3, I made a public commitment to make the data I have generated during my Phd open and available online. Well I have not ignored this and in the interim I have been investigating various ways I can do this. Not only do I want to make it available but I want to structure it in a standard form, namely the gelML format. In addition, I was involved in developing it the specification and therefore, I have somewhat an obligation to use it. As it is an XML transfer format I needed to be make changes and revision it, like developing code, so in that sense recording the data on a wiki or blog would not be...
Source: peanutbutter - April 30, 2008 Category: Bioinformaticians Authors: peanutbutter Tags: FuGE Google Proteomics Thesis bioinformatics data standards notebook online ontology open data open science subversion Source Type: blogs
Habs
discuss this article
New poll finds Montreal Canadiens as Canada’s team, more than Toronto Maple Leafs. Ok, next Saturday when the bandwagon suddenly stops, please try not to fall and hurt yourself.
Flyers in five. (Source: Blind.Scientist)
Source: Blind.Scientist - April 29, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: Misc longer than one line bandwagon canadiens flyers Source Type: blogs
Bio-it world day 1 - visualization, the cloud and people
discuss this article
Detailed blog posts will follow when I have some additional cycles, but thought I’d share some quick thoughts on day 1 of Bio-IT World. My conference started with a workshop on data visualization, which was mostly about the importance of visualization for making sense of multidimensional data sets and what kind of visualizations could be done. My take aways from the talks
There was a distinction made between statistical methods and data mining and presenting information to humans.
Life science data is inherently multiscalar and reducing dimensions without losing information or creating artifacts is not trivial
Impor...
Source: business|bytes|genes|molecules - April 29, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: BioIT Event Informatics Innovation Life Science Semantic Web Visualization Ben Fry Data Mining Information Visualization innovation networks John Reynder Michael Cariaso Pfizer newtag Source Type: blogs
Texshade: useful, and still kickin’
discuss this article
I’ve been looking at doing an analysis with some protein subfamily sequence logos, using Eric Beitz’s texshade. While it’s a little strange that it does the actual analysis part (rather than just the rendering) using LaTeX, it’s the only implementation of the method I know of, and it beats reimplementing it from the paper.
Although it was published in 2006 (and earlier in 2000), with the original URLs now dead, I noticed the latest update for the version of texshade in CTAN (v1.18) was on 15th of April, 2008 … ie texshade was updated just 14 days ago !
It happens all to often that published bi...
Source: Your bones got a little machine. - April 29, 2008 Category: Bioinformaticians Authors: perry Tags: bioinformatics software Source Type: blogs
A missed creative science opportunity?
discuss this article
Either Science or Nature (I can't find the item now) had a blurb noting that a Chilean observatory will play a prominent role in an upcoming James Bond movie -- the hideout of the villain (original press release here). A bit later in the item it is mentioned that the observatory will basically be simply compensated for its costs.Given the state of public science funding, it's too bad they didn't extort something more. This isn't somebody's production-costs-charged-to-my-personal-Visa indie film, but 007 himself. Budget never seems to matter much in those films, so why not extract a bit of cash? The movie is at least titled...
Source: Omics! Omics! - April 29, 2008 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
New business models for life science content
discuss this article
Let me start of by pointing everyone to the standard disclaimer.
Now to the good stuff. I have blogged about NextBio in the past. A couple of weeks about I was on the site and noticed that I could use the search engine without having to log in and get some pretty interesting results fast (well presented, well laid out, etc). I also registered and got an account for enhancements to the search experience. So when I got an advance copy of a press release announcing the formal public launch of the NextBio search engine. From the release
Using NextBio, any researcher or clinician can search the world’s public life scien...
Source: business|bytes|genes|molecules - April 28, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Business Industry Watching Informatics Search Software & Internet newtag Source Type: blogs
Space, the final bio-frontier?
discuss this article
In case it hasn't been obvious from the occasional post, I am a spaceflight aficionado. As a very young child I watched some of the last moon landings. Many hours of play were spent imagining riding a rocket, playing with toy rockets, and building Lego spaceships. At some point I realized I really didn't quite have the Right Stuff. Clearly I was never going to cut it as a pilot (I carry scale models of Hubble's corrective lenses on my nose daily), and in the end my scientific interests weren't really going to support traveling to space. So it became purely an observational hobby, though the dream has been rekindled a bit b...
Source: Omics! Omics! - April 28, 2008 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
Brief hardy heron notes
discuss this article
Nothing exciting - just a couple of notes on the Ubuntu upgrade experience from 7.10 to 8.04.
Machine #1: LG Express Dual T1-72C1A laptop, Intel GMA950 graphics card
Pretty much a flawless upgrade
Machine #2: Desktop cobbled together with all sorts of bits over the years; problem feature being ATI Radeon 9600XT graphics card
Garbled screen on reboot; my own fault due to multiple, conflicting fglrx + compiz modules; went for a clean install
Seems Ubuntu have packaged a working fglrx + compiz combo; X11 radeon used by default but gives you the option to switch to fglrx on first login; works fine with compiz (except for k...
Source: What You're Doing Is Rather Desperate - April 27, 2008 Category: Bioinformaticians Authors: nsaunders Tags: computing linux 8.04 hardy heron ubuntu upgrade Source Type: blogs
Twitter updates for 2008-04-26
discuss this article
@roguepuppet here in Toronto, there is a good place to find some different fruits. Supermarket bananas have a bland taste. #
@mndoci I discuss anything, anything at all. I have an incommensurable amount of useless knowledge #
@mndoci I discuss anything, anything at all. I have an incommensurable amount of useless knowledge #
going to eat some traditional japanese sushi and buy some gohan to stock #
@roguepuppet I am not fan of bananas sold in NA. Stay away from the supermarket bananas and get some apple-banana. Better taste #
@roguepuppet Magnolias are one of my favourite plants. #
@roguepuppet Magnolias are from a very ol...
Source: Blind.Scientist - April 27, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: longer than one line tweets twitter Source Type: blogs
Bizarre inanity from the financial analysis world
discuss this article
In general I try to ignore the various bleatings of stock pickers. Given the mountain of evidence in favor of the efficient market hypothesis, claims of successful stock picking should be generally lumped in with schemes for perpetual motion machines.However, sometimes something truly ludicrous crosses my eyes & keeps them crossed. I've previously http://omicsomics.blogspot.com/2007_06_01_archive.html, but now I get to pick on someone calling a stock a buy.The stock is (surprise!) Millennium, which Zacks.com is diligent to inform us is still a buy in their opinion. When I saw the headline I did a double-take, and then had ...
Source: Omics! Omics! - April 27, 2008 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs
Rethinking software access
discuss this article
So today, I tried to download MODELLER which is free for academics and $$$ for commercial via Accelrys (Full Disclosure: While i did not directly manage MODELER at Accelrys, I had indirect responsibilities). I completely understand that part. The problem is that the MODELLER license does not seem to address what I want to do: hobby science. So I had to wait for my request to be approved, which it didn’t.
There’s two thoughts that arise from this exercise, or maybe three. First, it’s clear that when the MODELLER license was written, personal research use was not considered. It harks back to the assumption...
Source: business|bytes|genes|molecules - April 26, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Business Modeling & Simulation Software & Internet CHARMM GAUSSIAN molecular modeling MOPAC programmable newtag Source Type: blogs
Twitter updates for 2008-04-25
discuss this article
@ChristianBurns what program are you using? #
why are Planet Nature and Postgenomic feeds "seasonal"? All of a sudden hundreds of entries appear … #
@rvidal Nada como conhecer os patricios. #
@rvidal indeed, and the anniversary of the Cravos. #
@michaelbarton OK, thanks a lot. #
@rvidal thanks, will see what I can do … #
@mndoci email me too, I’d take a look if you want … #
@michaelbarton sorry to ask, but what is ONS? #
@SciPhu man, that’s sad … #
Sometimes I lose faith in the humanbeing: http://www.thestar.com/article/418415 #
isn’t Neil awake today/tonight? #
@pierreyv...
Source: Blind.Scientist - April 26, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: longer than one line tweets twitter Source Type: blogs
Twitter updates for 2008-04-24
discuss this article
@attilacsordas Thanks a lot … #
@attilacsordas can you add some tag to the email subject? Something like [BioCamp] or similar … #
gas will be 2.25 $CDN in 2012. Predicted by the same bank that lost 5 blln with the house bubble. #
konqueror does not like FriendFeed … #
"molecular data from extinct organisms may have the potential for resolving relationships at critical areas of the vert. evolutionary tree" #
@pierreyves thx, added to Google Reader … #
@rvidal @freesci I would say API too. #
@neilfws 2:30 am madness, for sure #
@yokofakun @covert basically you can merge all your "social...
Source: Blind.Scientist - April 25, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: longer than one line tweets twitter Source Type: blogs
Your personal health: the personal genome
discuss this article
Last evening, I had a chance to attend an interesing panel discussion on The Personal Genome. The Symposium featured Eric Lander, George Church, Leena Peltonen and Bill Gates and was moderated by Maynard Olson.
My take away from the discussion, which was fueled by questions submitted by the audience and via the web, was that there is so much uncertainty at this time. We know so much, yet so little. At some level, we do not understand the implications of what we know, ethical and medical, at the same time, we underestimate the ability of our own genetics to withstand changes.
Perhaps one of the things that jumped out at me...
Source: business|bytes|genes|molecules - April 24, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Healthcare Life Science Your personal health Bill Gates Eric Lander Genomics George Church Leena Peltonen Maynard Olson Sandra Porter newtag Source Type: blogs
Scifoo and biobarcamp
discuss this article
(Via Attila) The invitations for the 3rd SciFoo have apparently been sent. It will be held from the 8th to the 10th of August at the Googleplex. There is also an idea floating around to organize a BarCamp at the same time as SciFoo. A BarCamp Check out the BioBarCamp wiki and discussion group. There are already several suggestions for venues to organize it and several people interested in attending.On a side note it's fun to see something like this getting thought of and set up from Twitter/FriendFeed conversations. I have been trying out FriendFeed for a while now and although I am not a big fan of micro blogging (yet?) I...
Source: Public Rambling - April 24, 2008 Category: Bioinformaticians Tags: scifoo biobarcamp Source Type: blogs
The clue initiative
discuss this article
The emergence of extremely large datasets, well beyond the capacity of almost any single computer, has challenged traditional and contemporary methods of analysis in the research world. While a simple spreadsheet or modest database remains sufficient for some research, problems in the domain of “computational science,” which explores mathematical models via computational simulation, require systems that provide huge amounts of data storage and computer processing (current research areas in computational science include climate modeling, gene sequencing, protein mapping, materials science and many more). As an a...
Source: business|bytes|genes|molecules - April 24, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Computing Science distributed computing technology Google IBM National Science Foundation utility computing newtag Source Type: blogs
Twitter updates for 2008-04-23
discuss this article
@rvidal Thnx, because she refused to add my blog sometime ago. #
@rvidal what is the requisite to have a blog added to the network? #
@rvidal question: you are one of the organizers of the DNA network, right? #
@attilacsordas I am fully engaged on the BioBarCamp. The only problem is getting there … #
@attilacsordas I don’t even have an AppEngine account … #
@mza Damn, it beats my cassette player … #
early leave … #
@mza I think the repository is a major issue. The release policy is also non-existent, and regarding the busy I will blog about it … #
@mndoci Yes, I should have put inside qu...
Source: Blind.Scientist - April 24, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: longer than one line tweets twitter Source Type: blogs
How to improve scientific software?
discuss this article
Do you know the answer to the above question? No? Me neither, but I can offer some suggestions. On a daily basis, a bioinformatician is exposed to hundreds of applications, computer languages, websites, you name it. Some of them are commercial, some of them free and open source. Some of the academia-developed software are open-source, some of them are not.
A good portion of the academia-developed software are published in scientific journals, as an 2-page application note in Bioinformatics , or on a longer paper on BMC Bioinformatics, just to name two of the journals of the field.
I cannot complain of non-published appli...
Source: Blind.Scientist - April 23, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion BMC Bioinformatics Computer software how-to improve Java Languages Open source Programming scientific software Source code Source Type: blogs
The “cloud” in the spotlight
discuss this article
Here are some blog headlines in my feed readermo
Live Mesh: First look at Microsoft’s new platform
A conversation with Ray Ozzie about Live Mesh
Bungee Labs evolves to compete with Salesforce, Oracle, & others
IBM’s new servers for cloud computing
Data center makeover
Earlier today, I received an email from Amazon with the subject
Amazon Web Services: Lower Data Transfer Costs
And here is a conversation that Michael Barton and I had on twitter.
If you don’t know that we’re in the middle of a significant change in how we consume and access compute cycles, either directly or indirectly, it&#...
Source: business|bytes|genes|molecules - April 23, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Admin Bungee Labs cloud computing IBM Michael Barton Microsoft Oracle Ray Ozzie Web Services newtag Source Type: blogs
New platforms = cool stuff
discuss this article
Andrew Perry joins the rank of biogeeks leveraging the various platforms in the cloud. He has announced the release of ResolveRef, which is essentially a RESTful way of querying PubMed. ResolveRef has been built on top of Google’s AppEngine
It’s good to see these kinds of projects, and I suspect this is hardly the last of what we’ll see. Technorati Tags: ResolveRef, AppEngine
ShareThis (Source: business|bytes|genes|molecules)
Source: business|bytes|genes|molecules - April 23, 2008 Category: Bioinformaticians Authors: Deepak Singh Tags: Geek Informatics Software & Internet Andrew Perry newtag Source Type: blogs
Now officially living in my browser
discuss this article
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)
Source: What You're Doing Is Rather Desperate - April 23, 2008 Category: Bioinformaticians Authors: nsaunders Tags: firefox networking web resources extensions friendfeed mysocial web2.0 Source Type: blogs
Twitter updates for 2008-04-22
discuss this article
time to go home … #
@mza I wish I could go in August, but whoever is coming to ISMB drop me a note and we can organize something … #
@attilacsordas further proof that I am out of the loop, need to catch up … #
looking for suggestions for a new SciView interview, last couple were declined … http://blindscientist.genedrift.org/category/sciview/ #
@yokofakun I remember reading your blog at the time. It was when I started to get into the "community" #
@attilacsordas @mndoci why not something around ISMB too? Are you guys coming to TO? #
@attilacsordas thanks, I am a little bit out of the loop ...
Source: Blind.Scientist - April 23, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: longer than one line tweets twitter Source Type: blogs
App engine for research #2
discuss this article
ResolveRef, a RESTful way to resolve PubMed queries by journal, year, volume and page is Andrew’s port of OpenRef to App Engine. Simple, but very effective and a nice illustration of how to get to grips with the App Engine environment.
Keep those “App Engine apps for researchers” rolling in, folks. (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - April 22, 2008 Category: Bioinformaticians Authors: nsaunders Tags: blogroll computing google web resources appengine pubmed rest Source Type: blogs
Announcing resolveref on google app engine
discuss this article
About two weeks ago, tipped off by Neil, I heard about Google App Engine. I managed to get a beta account, and I’ve finally had a chance to do something (hopefully) useful with it.
In the absence of any quickly achievable ideas for a bioinformatics app, I ported over the OpenRef application I wrote on top of TurboGears a few months back.
Just like the original, the new app, ResolveRef, is essentially a RESTful way of doing PubMed queries.
A query like:
http://resolveref.appspot.com/ref/journal/year/volume/page
or when there is no volume number, like:
http://resolveref.appspot.com/ref/journal/year/page
will query Pub...
Source: Your bones got a little machine. - April 22, 2008 Category: Bioinformaticians Authors: perry Tags: bioinformatics biopython code mashup software web2.0 app engine google openref resolveref turbogears Source Type: blogs
Essential computational biology clothing
discuss this article
I know that we, computational biologists, are sometimes jealous of ye olde white labcoat that our experimental colleagues wear, and which immediately identifies them as scientists. What can we, who sit in front of a computer all day, wear to truly show that we are master of our cpus in the service of science?
Here’s the solution, from designer Erik De Nijs:
hat tip: Petrice Gaskin (Source: Trapped in the USA)
Source: Trapped in the USA - April 22, 2008 Category: Bioinformaticians Authors: bosco Source Type: blogs
Twitter updates for 2008-04-21
discuss this article
@hyphaltip 700 ISMB registration fee for ISCB members is also pretty high #
@attilacsordas the Dude is the dude. #
@mndoci @neilfws I am averaging 80-85 Gb a month. I saw people in a discussion group that averages 300 a month. #
@neilfws 20Gb combined is "nothing". People around here complain that we have a so far non-enforced 100 Gb cap. #
@neilfws why is your internet being shaped? how much cap do you have? #
@neilfws coming from Australia, 1000 US is quite reasonable to ask. #
@neilfws Registration this year is quite expensive. 700 dollars for members #
@neilfws I got an ECCB travel fellowship in 2005. They ga...
Source: Blind.Scientist - April 22, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: longer than one line tweets twitter Source Type: blogs
Xkcd got it wrong
discuss this article
He got it wrong. Nobody is “wrong” on the internets, everyone is right. Always. (Source: Blind.Scientist)
Source: Blind.Scientist - April 21, 2008 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion right wrong xkcd Source Type: blogs
The model beetle and pest genome sequenced
discuss this article
We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell–cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. (Source: Bioinformatics Latest News)
Source: Bioinformatics Latest News - April 21, 2008 Category: Bioinformaticians Source Type: blogs
