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Merck Seeks Medical Informatics Dud On The Cheap @ $30/hrEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
P { MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px } BODY { SCROLLBAR-ARROW-COLOR: #3f52b8; SCROLLBAR-DARKSHADOW-COLOR: #fafafa; SCROLLBAR-BASE-COLOR: #f7f7f7; SCROLLBAR-HIGHLIGHT-COLOR: #cecfce; SCROLLBAR-TRACK-COLOR: #fffbff } At the post "Medical Informatics, Pharma, Health IT, and Golden Advice That Sits Sadly Unused" and other posts I lamented the fact that the pharma sector (in deep decline due to scientific mediocrity, ill-qualified leadership, public image tarnished by scandal, and other reasons), as well as the Healthcare IT industry (now also racked by similar issues and undergoing a Senate investigation while its products ...
Source: Health Care Renewal - November 17, 2009 Category: Health Medicine and Bioethics Commentators Tags: Moffatt Cancer Center medical informatics bioinformatics Merck pharmaceuticals Source Type: blogs

Merck Seeks Medical Informatics Loser @ $30/hrEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
P { MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px } BODY { SCROLLBAR-ARROW-COLOR: #3f52b8; SCROLLBAR-DARKSHADOW-COLOR: #fafafa; SCROLLBAR-BASE-COLOR: #f7f7f7; SCROLLBAR-HIGHLIGHT-COLOR: #cecfce; SCROLLBAR-TRACK-COLOR: #fffbff } At the post "Medical Informatics, Pharma, Health IT, and Golden Advice That Sits Sadly Unused" and other posts I lamented the fact that the pharma sector (in deep decline due to scientific mediocrity, ill-qualified leadership, public image tarnished by scandal, and other reasons), as well as the Healthcare IT industry (now also racked by similar issues and undergoing a Senate investigation while its products ...
Source: Health Care Renewal - November 17, 2009 Category: Health Medicine and Bioethics Commentators Tags: Moffatt Cancer Center medical informatics bioinformatics Merck pharmaceuticals Source Type: blogs

Duncan Hull's blog has movedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
If you're here looking for Duncan Hull's blog, it has moved to O'Really?. Nodalpoint lives on at nodalpoint.org. (Source: nodalpoint.org - A bioinformatics weblog)
Source: nodalpoint.org - A bioinformatics weblog - November 6, 2009 Category: Bioinformaticians Authors: Duncan Tags: Bioinformatics blog oreally Source Type: blogs

Google Wave invite: who wants one?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I have two Google Wave invites to go. If you want one send me an email (paulo.nuin on Gmail) or leave a comment here. The best “offer” takes it. Offer means anything: a poem, a sticker, another invite to another service, a scientific collaboration, anything. Be creative and you will have it. Update: I will send both invites later tonight, Canada’s ET. Google says it might take a while for the invite to reach the recipient. Some people are selling invites on Ebay, some for 100 dollars. Again the best “offer” wins. And remember, I’m not checking Twitter or Friendfeed. (Source: Blind.Scientist)
Source: Blind.Scientist - October 1, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

Detecting Cancer Through MusicEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Music and cancer do not go together, and I mean that in the context of this new technology: A project at Harvard Medical School created a program to translate the signals from cells into musical notes. Normal signals will sound harmonious, abnormal signals like those coming from cancer cells will sound awful. Listen to this –     Using date from a pre-existing colon cancer study, bioinformatician Gil Alterovitz and his team created a program that transforms complex genomic information into musical notes, so that abnormal data will sound discordant. “When things go awry, such as in the case of p53...
Source: Genetics and Health - September 30, 2009 Category: Geneticists and Genetics Commentators Authors: Grace Ibay Tags: Cancers Genetic Diseases and Conditions Genetic Future bioinformatics Colon Cancer gene expression genetic technology gil alterovitz harvard medical school Source Type: blogs

Mendeley’s PR machine and moreEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There has been a somewhat heated debate in Roderic Page’s blog about Mendeley’s hype in the current reference management scenario. Also, I was forwarded to this blog post, which praises the right horse in the ref-management race, Zotero. The comments in that post are pure gold, showing how PR in science is pernicious to science itself. I will give two examples. For those who don’t know, I’m one of the poster-boys of the anti-Mendeley movement. Not because I want to be a poster-boy, but because I’m not afraid to confront their PR machine, even more after the censorship attempt. One of the wors...
Source: Blind.Scientist - September 30, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

This is when I say farewell …Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
to “social websites”. Yes, this is a farewell to my two readers and the handful of people that read my tweets/friendfeed posts. I’m not going away, everything is still going to be channeled through FriendFeed, and posted on Twitter, but I won’t comment anymore or actually write them. It will be automatic, and personal to the level where it’s generated by my selections, not meaning they are good or bad, right or wrong, just that whatever caught my eye. I will still write here, have my Facebook account and the other “social” things, but myself, I’ll be gone. There’s a fe...
Source: Blind.Scientist - September 28, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

MetaproteomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microbial ecology is currently experiencing a renaissance spurred by the rapid development of molecular techniques and "omics" technologies in particular. As never before, these tools have allowed researchers in the field to produce a massive amount of information through in situ measurements and analysis of natural microbial communities, both vital approaches to the goal of unraveling the interactions of microbes with their environment and with one another. While genomics can provide information regarding the genetic potential of microbes, proteomics characterizes the primary end-stage product, proteins, thus conveying fu...
Source: Microbiology Blog: The weblog for microbiologists. - September 23, 2009 Category: Microbiology Tags: Microbial community Proteomics Metaproteomics microbial communities Proteome microbial ecology genomics Omics technologies Mass spectrometry Bioinformatics Source Type: blogs

Wikis as Tools in GeneticsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I’ve been planning to write about these wikis that can be very useful tools in the hands of researchers for a long time. The first one is WikiPathway which is an open platform dedicated to the curation of biological pathways by and for the scientific community. The second is the WikiGenes which aims to build the database of evolutionary knowledge on Nature.com. The reason why I mention the third one now is there is a new publication focusing on the pros and cons of using a wiki in genetics research. In Wikipedia, Andrew and his friends created the Gene Portal a year ago and later analyzed the usability and the resu...
Source: ScienceRoll - September 17, 2009 Category: Geneticists and Genetics Commentators Authors: Bertalan Meskó Tags: Bioinformatics Gene Web 2.0 genetics science Source Type: blogs

WolframAlpha Community: Medicine and HealthEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I use WolframAlpha because sometimes (if I know exactly what I want to find) it saves me plenty of time and clicks. If I want to calculate BMI, Google lists me several calculators. WolframAlpha calculates it itself. If I want to find information very fast about a clinical marker, Google gives me resources, WA gives me the best answer in one click. I also use it for ICD classification, as it’s more easily accessible than Wikipedia; for epidemiological data and other calculations. To sum it up, I think WolframAlpha is for those who perfectly know what they want to find and want to save time and clicks. For other search que...
Source: ScienceRoll - September 4, 2009 Category: Geneticists and Genetics Commentators Authors: Bertalan Meskó Tags: Bioinformatics Biotechnology Community Site Medical Search Medicine Medicine 2.0 Web 2.0 WolframAlpha Source Type: blogs

FriendFeed Life Scientists: 14-day summaryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Since I haven’t posted for 14 days, what better (and lazier) way to post something than to surf over to a 14-day summary from the Life Scientists Group and link to the top ten items! Review process files in the EMBO Journal – but why only for “the majority of papers”? How XML threatens Big Data. Or not. How JSON might be an alternative – or not. Solve any computer problem – with this classic XKCD flowchart. Science reviews the revolution in ’strategic scientific reading’ – are they way behind the curve, or providing a useful summary for the uninitiated? Best practice i...
Source: What You're Doing Is Rather Desperate - August 28, 2009 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics web resources friendfeed life-scientists summary Source Type: blogs

Wave testEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Let’s see if it works. function initialize() { var wavePanel = new WavePanel("http://wave.google.com/a/wavesandbox.com/"); wavePanel.loadWave("wavesandbox.com!w+RqxqUECK%B"); wavePanel.init(document.getElementById('waveframe')); } (Source: Blind.Scientist)
Source: Blind.Scientist - August 21, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

What we learned last week: August 10th editionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(this will be a weekly post on the most important news of the week, things that caught our eyes here at Blind.Scientist headquarters) - Apparently there is a rich guy on the internet that likes to show off how many computers he has, but doesn’t know a lot about technology and stuff. Anyway, how not to write a post. Never used his website. - Skulpt is a nice project that I really like to see come to fruition. Check it out. - Universal health care, or whatever it will be, in US won’t be approved, because both parties are in the pocket of the (un)health industry. It’s like the joke where the father doctor le...
Source: Blind.Scientist - August 10, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion weekly news Source Type: blogs

Paper of the week: INDELible: A Flexible Simulator of Biological Sequence EvolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The paper of this week touches a subject that I have been involved in the past: sequence simulation. INDELible, by Fletcher and Yang, is a program that is capable of simulating both DNA and amino acid sequences, and it seems to be the complete package to do so. It contains several substitution models and it can even simulate codon substitutions. As the article mentions, the closest comparison to INDELible is DAWG, developed by Reed Cartwright, that seems to be faster. DAWG is a nice program and generates good simulations and has a very well designed code with strong models and quite reliable results. And that’s what ...
Source: Blind.Scientist - August 10, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Science bioinformatics Computer simulation Source Type: blogs

RSRuby in the IRB consoleEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
R is terrific, of course, for all your statistical needs. But those data structures! “Everything is a list.” Leading to such wondrous ways to access variables as “p <- Meta(gds)$platform", or "last <- mylist[[1]][length(mylist[[1]])]". Sometimes, you want something more familiar. An array, a hash, a hash of arrays. Or, you may need to access R data in the language of your choice – e.g. as part of a Rails project. In Ruby, IRB is your friend. On the right, an IRB session in which we invoke RSRuby, load the GEOquery library from Bioconductor, fetch a dataset from the GEO database ...
Source: What You're Doing Is Rather Desperate - August 6, 2009 Category: Bioinformaticians Authors: nsaunders Tags: R bioinformatics computing ruby statistics Source Type: blogs

A proposal for encouraging user contributed annotations to UniprotEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussion” tab, ala Wikipedia (not pictured). • Each field, or block of related fields, would have an Add/edit button at the top right of the block. (I’ve chosen the Universal Edit Button as an example) Aftertought: Maybe putting these features under tabs isn’t quite the best place, since the existing tabs are ‘actions’ that can be taken rather than ‘extra info’ to be viewed. This UI detail could certainly be refined. This proposal has many wiki-like features (history, attribution, open editing, curation by trusted users and potentially page/section locking) but doesn’t ...
Source: Your bones got a little machine. - August 3, 2009 Category: Bioinformaticians Authors: perry Tags: bioinformatics science uniprot Source Type: blogs

How-to: combinations of covariates using RubyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I work with people who generate a lot of microarray data. One question that they often ask is: can we find those genes with a two-fold or more change in median expression under two or more different conditions? For example, let’s say that we have 3 conditions: “normal”, “adenoma” and “cancer”. That gives us 3 pairwise comparisons: normal-adenoma, normal-cancer and adenoma-cancer. Here’s a Ruby solution to the problem. First, I installed StatArray, a Ruby gem that provides statistical methods for array objects. It’s not been updated for 3 years, but seems to work. req...
Source: What You're Doing Is Rather Desperate - July 30, 2009 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics computing ruby statistics Source Type: blogs

RSRuby and Rails revisitedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A couple of months ago, I wrote a brief guide to displaying R plots in a Rails application using RSRuby. It worked at the time – really it did – but since then, I’ve encountered problems. One is that despite sending the plot output to a PNG file, R X11 windows started to pop up on loading the web page containing the plot. Another is the appearance of long error messages related to “stack smashing” on terminating Mongrel server. Fortunately, I read an excellent guide by Ana Nelson, R on Rails with RSRuby, which convinced me that I was doing things all wrong. So here is an amended version of my ...
Source: What You're Doing Is Rather Desperate - July 24, 2009 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics computing rails ruby plotting rsruby Source Type: blogs

It’s when I struggle to stay alive, or another Mendeley reviewEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I usually don’t get personal with software reviews. I even praised TNT in the past for being extremely fast, even though it mainly does maximum parsimony. But Mendeley’s case is outstanding and their attempt to censor me, makes things personal. I’m the closest you can get to be a “no one” in the scientific realm, I have this blog, a site needing updates and a couple of applications that no one uses. I still have a voice, maybe a smallish one, but I have. And I don’t like hype. And I’m a masochist. So, after reading several hype-like entries on the internet about how hyper-super-dup...
Source: Blind.Scientist - July 13, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion software review Source Type: blogs

Attribution vs Citation: Do you know the difference?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article outlines the differences between attribution and citation, and suggests that what most scientists are interested in is not attribution, which can be ensured via licensing restrictions, but instead citation, which is a much tougher nut to crack. At ISMB last week, there were a number of conversations about the difference between attribution and citation. This topic was brought up again yesterday in a conversation between the two authors of this post, Frank and Allyson. It is an important distinction which is explored in this post. First, some definitions for attribution and citation. These are not the only def...
Source: peanutbutter - July 10, 2009 Category: Bioinformaticians Authors: peanutbutter Tags: Journals Publishing bioinformatics data standards life-science ontology open data open science attribution Creative Commons licenses Knowledge Management Knowledge Representation Metadata OBO Foundry Wikipedia Source Type: blogs

Great work, ISMB microblogging teamEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Another year, another ISMB/ECCB meeting and – another great blogging effort. It’s all at the FriendFeed group: ISMB/ECCB Stockholm 2009, with outgoing links to individual blogs too. Thanks and congratulations to all involved for a great effort. Looking forward to the official write-up. Posted in bioinformatics, computing, meetings, web resources Tagged: friendfeed, iscb, ismb, microblogging (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - July 3, 2009 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics computing meetings web resources friendfeed iscb microblogging ismb Source Type: blogs

Educating students for a career in the workforce or a place in society: why do not both?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
For those of you who may have been wondering where I've been, these past few weeks have seen me grading final projects, writing a chapter on analyzing Next Gen DNA sequencing data for the Current Protocols series, and flying back and forth between Seattle and various meetings elsewhere in the U.S. It will probably take years of bike commuting to make up for my carbon credits, but most meetings I attend don't have viable alternatives in venues like Second Life or World of Warcraft. Anyway, as I sit writing on an airplane, I think I could revise the title for Dr. Seuss' famous book to "Oh the places I've been." Inside the ...
Source: Discovering Biology in a Digital World - June 20, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

One In Three Billion Found: Single Mutation In FOXL2 Gene May Cause Granulosa Cell Ovarian CancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
“… Vancouver scientists from the Ovarian Cancer Research (OvCaRe) Program at BC Cancer Agency and Vancouver Coastal Health Research Institute have discovered that there appears to be a single spelling mistake in the genetic code of granulosa cell tumours, a rare and often untreatable form of ovarian cancer. This means that out of the three [...] (Source: Libby's H*O*P*E*)
Source: Libby's H*O*P*E* - June 11, 2009 Category: Cancer Authors: Paul Cacciatore Tags: Causes Discoveries Genetic Testing Genetics Medical Study Results BC Cancer Agency BC Cancer Foundation bioinformatics David Huntsman M.D. Dr. Dianne Miller Dr. Marco Marra Dr. Michael Birrer FOXL2 gene Genome BC Genome Science Source Type: blogs

The OBO foundry principlesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This week, is a week long ontology building week, consisting of two days at the OBO Foundry workshop followed by 4 days at the OBI workshop, all hosted at the EBI. In advance of the meeting (even though I am writing this during the meeting) Duncan asked “how can the ontology development principles be improved“. Ally and Melanie responded commenting on each principle, and I would pretty much agree with every issue the ontology ladies raise. These principles should be used to guide ontology developers to build a consistent resource and which are used to “peer-review” the ontology. However, my concern ...
Source: peanutbutter - June 7, 2009 Category: Bioinformaticians Authors: peanutbutter Tags: bioinformatics conference data standards ontology open data open science semantic web bio-ontology Creative Commons licenses Knowledge Management Knowledge Representation Metadata OBI OBO Foundry Ontologies Peer review Source Type: blogs

So you want to cover the next conferece via social media?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Yes, you do. I know because you’re hip, right? No. Do you want to publish a paper about it? Yes. But that’s so 2008. Shouldn’t you wait for Google Wave? Maybe. Now, seriously. There’s a current discussion on the subject after CSHL threatened to forbid anyone to liveblog/tweet/friendfeed presentations at their conferences if they don’t follow the usual rules for media coverage. That’s outrageous! No, it’s not. That’s what they want to do, let them do it. They have the right to forbid anyone to broadcast whatever is going on during presentations at the conferences they organize...
Source: Blind.Scientist - June 3, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

New HIV Microbicide Can Be Produced in Transgenic PlantsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
© Sully PixelScientists have developed a new anti-HIV drug as well as a possible means of producing the drug in large quantities using transgenic plants. In the research paper, Ma and colleagues desc... (Source: The Biotech Weblog)
Source: The Biotech Weblog - May 29, 2009 Category: Medical Scientists Tags: Drugs, Vaccines and Therapeutics , Genomics, Proteomics and Bioinformatics Source Type: blogs

Querying NCBI Entrez database fields using RubyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Here’s a problem. You’d like to construct a complex query at NCBI Entrez using various fields. Example: “9606″[Taxonomy ID] to limit your search to Homo sapiens. Except – you don’t know which fields are available for the database that you want to query. EInfo can return an XML file with this information. Ruby + Hpricot eats XML for breakfast. Here’s an example using the GEO Datasets (gds) database. #!/usr/bin/ruby require 'rubygems' require 'hpricot' require 'open-uri' doc = Hpricot(open("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcg...
Source: What You're Doing Is Rather Desperate - May 27, 2009 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics computing ruby entrez eutils hpricot ncbi Source Type: blogs

P[acman]-Generated Gene Libraries for Drosophila melanogasterEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Using a tool called P[acman], group of researchers has established a library of clones covering most of the genome of Drosophila melanogaster (fruit fly), an organism widely used in genetics research.... (Source: The Biotech Weblog)
Source: The Biotech Weblog - May 25, 2009 Category: Medical Scientists Tags: Diagnostics, Methodologies and Instrumentation , Genomics, Proteomics and Bioinformatics Source Type: blogs

Internet “democracy”Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Since I last criticized Mendeley for being an horrible software and received an email from one of the lads there, threatening and censoring (attempting) me, I have this unnerving feeling. Apparently Mendeley website (or whatever they use there) got a facelift and my comment on FriendFeed was “still sucks”. Not the facelift, the software, but this is a side note to the story. Another user there said that I need to “self-censor” my comment because they are “unfair, aggressive and insulting”. A two-word comment … So, what should I do? Cave in to the power of the mass and put my head d...
Source: Blind.Scientist - May 21, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

Golden Rice is an Effective Source of Vitamin AEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Golden Rice is a genetically modified plant developed to contain more beta-carotene in the grains, seen as a viable method of alleviating vitamin-A deficiency particularly in developing countries. In ... (Source: The Biotech Weblog)
Source: The Biotech Weblog - May 15, 2009 Category: Medical Scientists Tags: Food and Agriculture , Genomics, Proteomics and Bioinformatics Source Type: blogs

Where next for this blog?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It’s apparent that my activity at this blog has been on a downward-slope for some time. I currently post about once a month and when I do, it’s more likely to be a rant about some social network/web2.0 application than about bioinformatics. So the question is what to do about it. Update: thanks for the many, rapid and helpful responses. The unanimous view was – stay here, keep blogging. So that’s what it will be! Options include: Nothing; just let it slide, don’t worry and post when I have something to say Declare this blog closed and focus on other activities Declare this blog closed and st...
Source: What You're Doing Is Rather Desperate - May 12, 2009 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics this blog web resources Source Type: blogs

Developing ontologies in decentralised settingsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I have placed a e-prints of a manuscript, on Nature preceedings, that I have been working on, in collaboration with the authors listed on the manuscript. It presents a review of the available published ontology engineering methodologies, and then assess their suitability when applied to community ontology development (the decentralised setting). It is a lengthy document. Here is the abstract: This paper addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be de...
Source: peanutbutter - May 8, 2009 Category: Bioinformaticians Authors: peanutbutter Tags: bioinformatics ontology ontology engineering ontology methodology ontology review Source Type: blogs

Content, Syntax and SemanticsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
These are the slides I gave at a DCC workshop entitled, “Digital curation 101″ which aimed to give and overview of what to consider regarding data curation and management in the context of applying for research funding. The presentation starts with definitions of content syntax and semantics, and example of how these concepts are being applied in the life-sciences, specifically proteomics. (Source: peanutbutter)
Source: peanutbutter - May 2, 2009 Category: Bioinformaticians Authors: peanutbutter Tags: MIBBI bioinformatics computer science conference data curation Research Research funding Digital curation Slideshare Business Education Digital Curation Centre content syntax semantics Source Type: blogs

Open science, peer review and the fluEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences. If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want to mention before getting down to work and posting my BLAST results. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - May 1, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

More flu follies: comparing sequences and making trees, activity 4Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu? If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer. Activity 4. Picking influenza sequences and comparing them with phylogenetic trees Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - April 29, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

Did the California H1N1 swine flu come from Ohio?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. UPDATE: I'm not so certain anymore that the strains are the same. I'm doing some work with nucleic acid sequences to look further at similarity. Here's the data. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - April 29, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

Finding influenza: the data are out there, let's get them, activity 3Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I was pretty impressed to find the swine flu genome sequences, from the cases in California and Texas, already for viewing at the NCBI. You can get them and work them, too. It's pretty easy. Tomorrow, we'll align sequences and make trees. Activity 3: Getting the swine flu sequence data Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - April 28, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

Further fun with the flu: digital biology activity 2Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I'm a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases. In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I'm a little skeptical about the blowfly, but... Now, you might wonder, what kinds of flu do these different creatures get? Are they all getting H1N1, or do they get different variations? What are H and N anyway? We can discuss all of these, but for now, lets see what kinds of flu strains infect different kinds of creatures. Activity 2. What flu infects who? Read the rest of this post......
Source: Discovering Biology in a Digital World - April 28, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

Having fun with the flu: digital biology activity IEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let's do a bit of digital biology and see what we can learn. Activity 1. What kinds of animals get the flu? Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - April 28, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

It’s not just me, Victor.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
“Mendeley seems to be choking while importing my 1039 pdfs from ~/Documents/Papers/. Beachballing, can’t tell what it is doing.” mja on Twitter. And in reply: “@mja Mendeley did exactly the same to me. Hangs on every start up now.” sjcockell on Twitter. So, I guess it’s not something personal to the nice chaps that work at Mendeley. The software is pretty bad, and that’s the only reality here. And I’m not criticizing, I’m just stating. Related articles by Zemanta Community Liaison @ Mendeley (my.biotechlife.net) I haven’t joined Mendeley as community liaison (bli...
Source: Blind.Scientist - April 25, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion mendeley On the Web twitter Source Type: blogs

The Semantic Web of Life ScienceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This summary was born out of a question  on Twitter and percolated to FriendFeed, which was “Who is using RDF and integrating other resources at the minute and what are those resources? From this question, several resources were highlighted. UniProt. The comprehensive resource of protein information is available as an RDF distribution and each Protein record has a corresponding RDF download option. Phil pointed out Semantic Systems Biology, As systems biology is largely concerned with representing networks and interactions at a systems level, a language like RDF would seem an obvious choice to represent this type of kno...
Source: peanutbutter - April 25, 2009 Category: Bioinformaticians Authors: peanutbutter Tags: bioinformatics life-science semantic web Biology Resource Description Framework RDF Twitter FriendFeed systems biology open data Linked Open Data Source Type: blogs

Under MAFFT's hoodEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Hello I am trying to learn what exactly MAFFT does to align sequences, but i am currently having a hard time to understand it. I have read its papers and references. Anyone knows of some kind of tutorial or review for it? I am researching the FFT-NS-i and E-INS-i algorithms. Currently, i am trying to understand what are the 6-tuples parameters. I guess the 6-tuples are the weight, volume and charge, compared in pairs of sequences. Is that right? Thanks in advance EDIT: Just in case someone is interested: read more (Source: nodalpoint.org - A bioinformatics weblog)
Source: nodalpoint.org - A bioinformatics weblog - April 24, 2009 Category: Bioinformaticians Authors: p_lucio2000 Tags: Bioinformatics MAFFT sequence alignment Source Type: blogs

Under MAFFT's hoodEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Hello I am trying to learn what exactly MAFFT does to align sequences, but i am currently having a hard time to understand it. I have read its papers and references. Anyone knows of some kind of tutorial or review for it? I am researching the FFT-NS-i and E-INS-i algorithms. Currently, i am trying to understand what are the 6-tuples parameters. I guess the 6-tuples are the weight, volume and charge, compared in pairs of sequences. Is that right? Thanks in advance (Source: nodalpoint.org - A bioinformatics weblog)
Source: nodalpoint.org - A bioinformatics weblog - April 24, 2009 Category: Bioinformaticians Authors: p_lucio2000 Tags: Bioinformatics MAFFT sequence alignment Source Type: blogs

The cost of DNA sequencing revisitedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A couple of years ago, I answered a reader's question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and the reported coverage to estimate the cost of sequencing Craig Venter's genome. As you can imagine, the cost of sequencing has dropped quite a bit since then. Read the rest of this post... | Read the comments on this post... (Source: Discovering Biology in a Digital World)
Source: Discovering Biology in a Digital World - April 23, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs

Thanks, Jim!Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia It was a great ride. It all started (for me) with a Crash and it will never end. Thanks for all the metaphors and for the books, they will be sorely missed. (Source: Blind.Scientist)
Source: Blind.Scientist - April 20, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

This should not be here … or Notes to a bioinformatician – two years laterEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via CrunchBase I was contacted a couple of months (maybe more) to write a guest entry for their blog. I did that and on March 11th I sent the text you see below. It’s not my best creation (and not the worst, believe me), but as they’re taking so long to publish it and I don’t want it to go to waste, I’m publishing it. — Exactly two years ago (or almost exactly), I posted a follow-up blog entry to Notes to a young computational biologist. I still believe that 97% of all advice is worthless, but I also believe that it’s worth sharing your experiences as it might be useful to some...
Source: Blind.Scientist - April 17, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Biology Computer programming FriendFeed twitter Source Type: blogs

A Catalog of Published Genome-Wide Association StudiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We desperately need a database of genome-wide association studies and now here it is (organized by Genome.gov). The genome-wide association study (GWAS) publications listed here include only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies focusing only on candidate genes are excluded from this catalog. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasiona...
Source: ScienceRoll - April 8, 2009 Category: Geneticists and Genetics Commentators Authors: Bertalan Meskó Tags: Bioinformatics Genome Source Type: blogs

What Books Would Be Good For Self-Study in Bioinformatics?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite my lack of commitment to this site, it seems that I’m still getting comments every now and again. And I appreciate the interest. It really helps me realize the potential interest in the kind of things I’ve written about here. Most recently, I got a comment from Sudhang requesting books for the computer programmer who wants to self-study in the field of Bioinformatics. The following is my list. It may seem like its a bit everywhere but that’s kind of what you get with the field of Bioinformatics. Molecular Cell Biology. One would get glossy eyed trying to read through this book, but you need to ha...
Source: biowhat.com - April 4, 2009 Category: Bioinformaticians Authors: Ryan Castillo Tags: Statistics Computer Science Bioinformatics Biology Source Type: blogs

Mendeley: an extremely short review (sort of)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia I decided to test Mendeley again (Yes, I have some kind of a masochist behaviour for software), and as the last time I tried, I can say I’m not impressed. I tested on a directory containing mixed bag of PDFs, books, book chapters, articles and misc stuff. Most of the time the data was extracted but I ended with a wrong reference or garbage information about the file. Not mentoning that it took almost one full hour to analyse a little bit more than 500 files. I think I need to buy an eight-core machine now. The CPU peaked at 25-30% (one full core for it) on Vista, and the memory got up to 300 M...
Source: Blind.Scientist - April 3, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion mendeley Portable Document Format Source Type: blogs

Phasing out scientific softwareEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia There’s always the right time for everything. And for some scientific software it’s time for retirement. I will give here a one examples, but I bet if you’re a bioinformatician you will have others, and if you’re something else you will scratch your head and think “This guy is right!”. So let’s see the case of ClustalW. ClustalW was the first massively used alignment program and it’s a great program. But in my opinion it was a great program and has to be remembered as such, a great tool that introduced the mysteries of sequence alignment to so many peop...
Source: Blind.Scientist - March 31, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Clustal ProbCons Source Type: blogs