Blog Tag: Bioinformatics
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ISMB/ECCB 2009 reports
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Great to see more reports describing the use of online tools to cover scientific meetings. Here are the publications, from PLoS Computational Biology:
Live Coverage of Scientific Conferences Using Web Technologies.
doi:10.1371/journal.pcbi.1000563
Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009.
doi:10.1371/journal.pcbi.1000640
And here’s Ally a.k.a the robo-blogger on Social Networking and Guidelines for Life Science Conferences.
Looks like we’ve started a trend, long may it continue at future meetings.
Filed under: bioinformatics, meet...
Source: What You're Doing Is Rather Desperate - January 30, 2010 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics meetings publications 2009 eccb friendfeed ismb report Source Type: blogs
PhosphoGRIDEmail this article to a colleague.
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I no longer work on protein kinases but when I did, PhosphoGRID is the kind of database that I would have wanted to see. It features:
A nice clean interface, with good use of Javascript
Useful information returned from a simple search form
Data for download in plain text format with no restrictions or requirements for registration
All it lacks is a RESTful API, but nothing is perfect :-)
Published in the little-known but often-useful journal Database:
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.
doi:10.1093/database/bap026.
Fil...
Source: What You're Doing Is Rather Desperate - January 30, 2010 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics publications web resources database phosphory protein kinases Source Type: blogs
iPad is excellent!!!Email this article to a colleague.
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Just sayin’. With all the negative reviews, ponderations, blog posts, newspaper reports, I just wanted to give so kudos to Steve and the Apple family. Is it the best product ever? No. Is it the next coming of Jesus Christ? No. So what is it? It’s just another product, and you, only you (maybe with your wife/husband/partner/household) will decide if it fits your budget, if it is useful for you and if you actually need to buy it. Apart from that, rants are always good for the people that writes them (I know it firsthand).
The icing on the cake is when I overheard two homeless guys discussing if you could multitas...
Source: Blind.Scientist - January 28, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Misc apple ipad rants Source Type: blogs
Feynman and meEmail this article to a colleague.
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I’m reading the second book on Feynman, What Do You Care What Other People Think?: Further Adventures of a Curious Character and the only thing I can he was an incredible person, one that any one can admire. I have no idols, I don’t worship anyone, but Feynman gets the closest possible to being one for me. (Source: Blind.Scientist)
Source: Blind.Scientist - January 28, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
Clustering GEO samples by title (briefly) revisitedEmail this article to a colleague.
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So, we had a brief discussion regarding my previous post and clearly the statement:
The longest key for which values exist classifies your titles
does not hold true for all cases. Not that I ever said that it did! I remind you that this blog is a place for the half-formed ideas that spill out of my head, not an instruction manual.
Let’s look, for example, at GSE19318. This GEO series comprises 2 platforms: one for dog (10 samples) and one for humans (1 sample), with these sample titles:
['Dog-tumor-81705', 'Dog-tumor-78709', 'Dog-tumor-88012', 'Dog-tumor-8888302', 'Dog-tumor-209439', 'Dog-tumor-212227', 'Dog-tumor...
Source: What You're Doing Is Rather Desperate - January 27, 2010 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics programming research diary ruby clustering geo microarray samples Source Type: blogs
“Thinking algorithmically”: clustering GEO samples by titleEmail this article to a colleague.
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Today’s challenge. Take a look at this array, which contains the “title” field for the 6 samples from GSE1323, a series in the GEO microarray database:
['SW-480-1','SW-480-2','SW-480-3','SW-620-1','SW-620-2','SW-620-3']
Humans are very good at classification. Almost instantly, you’ll see that there are 2 classes, “SW-480″ and “SW-620″, each with 3 samples. How can we write a program to do the same job?
I’m sure that for those with formal training in computer science and algorithms, this is pretty trivial. The rest of us have to figure it out from first principles. He...
Source: What You're Doing Is Rather Desperate - January 24, 2010 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics programming research diary ruby clustering geo microarray samples Source Type: blogs
Thanks Conan!Email this article to a colleague.
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Seven months of fun, barely missed one episode. (Source: Blind.Scientist)
Source: Blind.Scientist - January 23, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
Stay awayEmail this article to a colleague.
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from Toronto’s (GTA’s) streets for sometime. Twelve people died crossing the streets this year in the region. Stay away. (Source: Blind.Scientist)
Source: Blind.Scientist - January 22, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
Why I won’t watch Avatar (or at least pay for)Email this article to a colleague.
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That works for me, maybe not for you.
And that is where the mask of Canadian-style humility and niceness came off James Cameron, the engineer’s son from Kapuskasing, and the scarily arrogant, tactless King of the World (as he called himself at the 1998 Oscar show) slipped out. (Source: Blind.Scientist)
Source: Blind.Scientist - January 19, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
Genomics of SunflowerEmail this article to a colleague.
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© Esdras CalderanGenome Canada, Genome BC, US Departments of Energy and Agriculture, and France's INRA (National Institute for Agricultural Research) has undertaken a US$10.5 million research project that will create a reference genome for the sunflower family - currently the world's largest plant family, containing 24,000 species of plants, including many crops, medicinal plants, horticulture plants and noxious weeds.
Th project, titled Genomics of Sunflower, will use next-generation genotyping and sequencing technologies to sequence, assemble and annotate the sunflower genome and to locate the ... (Source: The Biotech Weblog)
Source: The Biotech Weblog - January 17, 2010 Category: Medical Scientists Tags: Genomics, Proteomics and Bioinformatics Source Type: blogs
Citizen Science and Digital Biology: ScienceOnline 2010Email this article to a colleague.
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Is there a place for citizen scientists in the world of digital biology?
Many of the citizen science projects that I've been reading about have a common structure. There's a University lab at the top, outreach educators in the middle, and a group of citizens out in the field collecting data.
After the data are collected, they end up in a database somewhere and the University researchers analyze them and write papers. At least that's my impression so far.
It seems to me, that with all kinds of databases out there, on-line, there should be plenty of opportunity for both citizens and student groups to participate in analyz...
Source: Discovering Biology in a Digital World - January 13, 2010 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs
A new twist on the identifier mapping problemEmail this article to a colleague.
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Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, but that’s apparently way too much of a challenge.
However, there are times when this situation is forced upon us. Consider this code snippet, which uses the Bioconductor package GEOquery via the RSRuby library to retrieve a sample from the GEO database:
require "rubygems"
require "rs...
Source: What You're Doing Is Rather Desperate - January 12, 2010 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics programming research diary ruby databases identifiers mapping mongodb Source Type: blogs
In the cloud, Next Gen DNA sequencing computesEmail this article to a colleague.
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These days, DNA sequencing happens in one of three ways.
In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this.
Then, in the 90's, genome centers came along. Genome centers are like giant factories that manufacture sequence data. They have buildings, dedicated staff, and professional bioinformaticians who write programs and work with other factory members to get the data entered, analyzed, and shipped out to the databases. (You can learn more about this and go on a virtual tour in this nice video from Washington ...
Source: Discovering Biology in a Digital World - January 8, 2010 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs
Samples per series/dataset in the NCBI GEO databaseEmail this article to a colleague.
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Andrew asks:
I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere?
At work, we joke that GEO is the only database where data goes in, but it won’t come out. However, there is an alternative: the GEOmetadb package, available from Bioconductor.
The R code first, then some explanation:
# install GEOmetadb
source("http://bioconductor.org/biocLite.R")
biocLite("GEOmetadb")
library(GEOmetadb)
# connect to database
getSQLiteFile()
con <- dbConnect(SQLite...
Source: What You're Doing Is Rather Desperate - January 8, 2010 Category: Bioinformaticians Authors: nsaunders Tags: R bioinformatics computing statistics database geo microarray ncbi Source Type: blogs
Phrase of the dayEmail this article to a colleague.
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Post of the day is the phrase of the day, overheard online in an interview on the Brazilian TV channel, Globo News: “(…) Brazil’s urban planning is prehistorical (…)”.
I can say that not only urban planning is prehistorical. (Source: Blind.Scientist)
Source: Blind.Scientist - January 5, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
A biologist by yet another nameEmail this article to a colleague.
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What do you call a biologist who uses bioinformatics tools to do research, but doesn't program?
You don't know?
Neither does anyone else. 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 - January 2, 2010 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs
365 in 365Email this article to a colleague.
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I plan to post 365 entries either here, here or here in 2010. I might not post everyday, but I will try to keep the mark, even if it’s only a one-liner or some link to interesting news/software/paper.
Happy New Year everyone! (Source: Blind.Scientist)
Source: Blind.Scientist - January 1, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
Best of the decadeEmail this article to a colleague.
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Friends, as the year draws to a close, I felt compelled to compile the best of the decade of 00s. The list is:
will be posted here as soon as the decade ends on Dec 31st, 2010. (Source: Blind.Scientist)
Source: Blind.Scientist - December 31, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
A useful guide for the bioinformatics tool buildersEmail this article to a colleague.
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I often get questions about bioinformatics, bioinformatics jobs and career paths. Most of the questions reflect a general sense of confusion between creating bioinformatics resources and using them. Bioinformatics is unique in this sense. No one confuses writing a package like Photoshop with being a photographer, yet for some odd reason, people seem to expect this of biologists. In the same respect, even the programmers and database administrators who work in bioinformatics, are unfairly assumed to have had graduate level training in biology.
In many ways, it's easiest to understand what bioinformatics is, and to choose...
Source: Discovering Biology in a Digital World - December 30, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs
2009 in reviewEmail this article to a colleague.
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Here’s the best and worst of 2009:
- Movie: Rockrolla, not the best one, but highly entertaining, worst: Funny People
- Book: Born Standing Up: A Comic’s Life by Steve Martin, highly entertaining too
- Website: The Secret Diary of Steve Jobs, worst: of the ones I usually read is the Daring Fireball
- Software: Textmate, worst Mendeley, by 1000 miles
- TV: Stephen Colbert and Jon Stewart, the best hour of TV, worst: Dexter’s finale
- Purchase: MacBook 13”, the best computer I ever had
- Money-grabbing-scheme: Global Warming or Climate Change
- Politician: no best in the category, but the worst is the...
Source: Blind.Scientist - December 20, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs
Peptide Identifies Tumors and Penetrates to Deliver Anti-Cancer CompoundsEmail this article to a colleague.
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© kaibara87Researchers at Burnham Institute for Medical Research have identified a new peptide called iRGD that specifically recognizes and penetrates cancer tumors but not normal tissues. The peptide was also shown to deliver diagnostic particles and medicines into the tumor.
This discovery stems from the previous discovery of "vascular zip codes," which showed that blood vessels in different tissues (including diseased tissues) have different signatures. These signatures can be detected and used to dock drugs onto vessels inside the diseased tissue. In addition to ... (Source: The Biotech Weblog)
Source: The Biotech Weblog - December 8, 2009 Category: Medical Scientists Tags: Genomics, Proteomics and Bioinformatics Source Type: blogs
Soy Peptide Lunasin Has Anti-Cancer, Anti-Inflammatory PropertiesEmail this article to a colleague.
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© Kanko*Two studies report that lunasin, a soy peptide present in effluents from soy-processing plants, may have important health benefits that include fighting leukemia and blocking the inflammation that accompanies such chronic health conditions as diabetes, heart disease, and stroke.
In the cancer study, de Mejia's group identified a key sequence of amino acids—arginine, glycine, and aspartic acid, (the RGD motif)—that triggered the death of leukemia cells by activating a protein called caspase-3.
"Other scientists have noted the cancer-preventive effects of the RGD ... (Source: The Biotech Weblog)
Source: The Biotech Weblog - December 2, 2009 Category: Medical Scientists Tags: Genomics, Proteomics and Bioinformatics Source Type: blogs
Next Generation DNA Sequencing Made Me Do It or How I learned to Stop Worrying and Love MicroarraysEmail this article to a colleague.
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For many years, I've been perfectly content to work with small numbers of things. Working with one gene or one protein is great. Even small groups of genes are okay. I'm fine with alternatively spliced genes with multiple transcripts, or multiple polymorphisms, or genes in multi-gene families, or groups of genes in operons.
But I never trusted microarrays. 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 - December 2, 2009 Category: Medical Scientists Tags: Bioinformatics Source Type: blogs
Has our quest for completeness made things too complicated?Email this article to a colleague.
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In my opinion, yes. Let me elaborate.
My current job is very much focused on “data integration”. What this means is that we have a large amount of diverse data from different “-omics” experiments: microarrays, protein mass spectrometry, DNA sequencing – really, whatever you like, but it’s all aimed at answering the same question. Namely: which of these biological entities (transcripts, proteins, metabolites) are markers for various human disease states?
Somehow, we have to pull all of these data into a common framework so that it can be analysed using statistics. The problem: whilst a l...
Source: What You're Doing Is Rather Desperate - December 2, 2009 Category: Bioinformaticians Authors: nsaunders Tags: bioinformatics research diary data integration databases Source Type: blogs
DIALIGN-TX has all the problems with scientific softwareEmail this article to a colleague.
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Image via Wikipedia
Yes, DIALIGN-TX has all the problems with scientific software. All of them in 1.8 Mb of data, and I’m being kind. Let me explain that. I have this small project, and DIALIGN-TX is one of the programs I want to check. I compiled fine, or so I think: it runs ok on the Mac, shows me the parameters to run it, in a large list of options. Most of these options have a “DEFAULT” value, which means they are not needed to run the program. And there’s an usage example
Usage: dialign-t [OPTIONS] []
(notice the error on the usage, I just copied and pasted)
I tried every possible combinati...
Source: Blind.Scientist - November 26, 2009 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion alignment problems Science Source Type: blogs
Merck Seeks Medical Informatics Flunkie On The Cheap @ $30/hrEmail this article to a colleague.
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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 Dud On The Cheap @ $30/hrEmail this article to a colleague.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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(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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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“… 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.
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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
