http://bluebrain.epfl.ch/page-56882-en.html
Blue Brain is a resounding success. In five years of work, Henry
Markram’s team has perfected a facility that can create realistic models
of one of the brain’s essential building blocks. This process is
entirely data driven and essentially automatically executed on the
supercomputer. Meanwhile the generated models show a behavior already
observed in years of neuroscientific experiments. These models will be
basic building blocks for larger scale models leading towards a complete virtual brain.
www.ncbi.nlm.nih.gov/pubmed/15192011
Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex.
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034786#pone.0034786-ToledoRodriguez1
Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons
Friday, April 13, 2012
Why you should consider being a jerk What you can learn from the jerks at work
Having an opinion and taking credit for your own (not other people's) ideas can make you stand out at work. Being assertive and speaking out when you have something to say can make you look like a leader.
Just remember there is a fine line between being assertive and being pushy, and the aggressive loudmouth on the team who nobody likes generally doesn't last too long. So learn from the jerks, but don't become one.
http://www.workopolis.com/content/advice/article/2178-what-you-can-learn-from-the-jerks-at-work?CID=721:19L:14946
Microbial Genomics, Pangenomics, and Metagenomics in Disease and in Health
http://www.vanbug.org/2012/william-hsiao/
Abstract:
As DNA sequencing technologies continue to improve, sequencing of microbial genomes can now be done routinely. We have gone from a group of researchers spending years to generated and study one bacterial genome to an individual researcher comparing tens or hundreds of similar genomes at a time with the help of bioinformatic applications. Pangenomic analysis allows us to decipher how a bacterium evolves and how certain small mutations could have a large impact on disease outcome. In recent years, we have also started to sequence the genetic material directly isolated from a microbial community (microbiota) in order to bypass culturing. The International Human Microbiome Consortium and associated efforts are trying to decipher the interactions between our bodies and our microbiotas. The metagenomics approach allows researchers to study an entire microbial community in relation to health and diseases but new challenges arise on how to assign taxonomic and functional information to incomplete and sometimes novel sequences. With the increased scale of sequencing, new bioinformatics and statistical tools are needed to facilitate data process and interpretation. In this talk, I’ll discuss the progress and challenges of microbial genomic analysis with examples drawn from my own research and from literature. Through this talk, I wish to demonstrate that microbial genomics has benefit greatly from the technological improvements over the years and there is a bright future in applying microbial genomics to improve human health.
Abstract:
As DNA sequencing technologies continue to improve, sequencing of microbial genomes can now be done routinely. We have gone from a group of researchers spending years to generated and study one bacterial genome to an individual researcher comparing tens or hundreds of similar genomes at a time with the help of bioinformatic applications. Pangenomic analysis allows us to decipher how a bacterium evolves and how certain small mutations could have a large impact on disease outcome. In recent years, we have also started to sequence the genetic material directly isolated from a microbial community (microbiota) in order to bypass culturing. The International Human Microbiome Consortium and associated efforts are trying to decipher the interactions between our bodies and our microbiotas. The metagenomics approach allows researchers to study an entire microbial community in relation to health and diseases but new challenges arise on how to assign taxonomic and functional information to incomplete and sometimes novel sequences. With the increased scale of sequencing, new bioinformatics and statistical tools are needed to facilitate data process and interpretation. In this talk, I’ll discuss the progress and challenges of microbial genomic analysis with examples drawn from my own research and from literature. Through this talk, I wish to demonstrate that microbial genomics has benefit greatly from the technological improvements over the years and there is a bright future in applying microbial genomics to improve human health.
Wednesday, April 11, 2012
Jaccard index
The Jaccard index, also known as the Jaccard similarity coefficient (originally coined coefficient de communauté by Paul Jaccard), is a statistic used for comparing the similarity and diversity of sample sets.
http://en.wikipedia.org/wiki/Jaccard_index
The Jaccard coefficient measures similarity between sample sets, and is defined as the size of the intersection divided by the size of the union of the sample sets:
http://en.wikipedia.org/wiki/Jaccard_index
The Jaccard coefficient measures similarity between sample sets, and is defined as the size of the intersection divided by the size of the union of the sample sets:
Brain Talks
http://braintalks.wordpress.com/talks/
Talks take place monthly at Vancouver General Hospital. Wine and cheese are complimentary in a casual setting starting at 530 pm, and the speakers begin at 6 pm. Please RSVP to be updated on the location.
Talks take place monthly at Vancouver General Hospital. Wine and cheese are complimentary in a casual setting starting at 530 pm, and the speakers begin at 6 pm. Please RSVP to be updated on the location.
Thursday, April 5, 2012
How job hopping can be good for your career (and for your employers)
http://www.workopolis.com/content/advice/article/2124-how-job-hopping-can-be-good-for-your-career-and-for-your-employers?CID=721:19L:14946
But that's not all. I actually think even intentional job hoppers can make better employees.
But that's not all. I actually think even intentional job hoppers can make better employees.
Tuesday, April 3, 2012
Blue sky science
Blue skies research (also called blue sky science) is scientific research in domains where "real-world" applications are not immediately apparent. It has been defined as "research without a clear goal"[1] and "curiosity-driven science." It is sometimes used interchangeably with the term "basic research."[2]
http://en.wikipedia.org/wiki/Blue_skies_research
http://en.wikipedia.org/wiki/Blue_skies_research
Phil Bourne - Professor, Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego
*Featured speaker*: Philip Bourne, Professor, Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego
Associate Director, RCSB Protein Data Bank and Adjunct Professor, Burnham Institute
Title: What Really Happens When We Take a Drug?
This is a question which, after generic clinical trials, is still very much answered by observing patient outcomes. Methods from bioinformatics and systems biology are making some inroads into answering this question more systematically through integration of a variety of data sources and important algorithmic developments. I will dig in to some of our work in this area, but if you cant wait refer to Xie et al. (2012) Annual Review of Pharmacology and Toxicology 52: 361-379. I’ll also describe the importance of open science to this collective effort.
http://www.vanbug.org/talk_ppts/2011-12/201204_PhilBourne.pdf
http://www.vanbug.org/talk_ppts/2011-12/201204_PhilBourne/201204_PhilBourne.html
http://www.sdsc.edu/~bourne/
Associate Director, RCSB Protein Data Bank and Adjunct Professor, Burnham Institute
Title: What Really Happens When We Take a Drug?
This is a question which, after generic clinical trials, is still very much answered by observing patient outcomes. Methods from bioinformatics and systems biology are making some inroads into answering this question more systematically through integration of a variety of data sources and important algorithmic developments. I will dig in to some of our work in this area, but if you cant wait refer to Xie et al. (2012) Annual Review of Pharmacology and Toxicology 52: 361-379. I’ll also describe the importance of open science to this collective effort.
http://www.vanbug.org/talk_ppts/2011-12/201204_PhilBourne.pdf
http://www.vanbug.org/talk_ppts/2011-12/201204_PhilBourne/201204_PhilBourne.html
http://www.sdsc.edu/~bourne/
Monday, April 2, 2012
doMC: Foreach parallel adaptor for the multicore package
doMC: Foreach parallel adaptor for the multicore package
The doMC package is a “parallel backend” for the foreach package. It provides a mechanism needed
to execute foreach loops in parallel. The foreach package must be used in conjunction with a
package such as doMC in order to execute code in parallel. The user must register a parallel backend
to use, otherwise foreach will execute tasks sequentially, even when the %dopar% operator is used.1
Sunday, April 1, 2012
Helping hand
"Remember, if you ever need a helping hand, it's at the end of your arm, as you get older, remember you have another hand: The first is to help yourself, the second is to help others."
--Audrey Hepburn
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