Thursday, August 12, 2010
Thursday, August 5, 2010
The Northern Lights Light Up Vancouver
http://www.associatedcontent.com/article/5656058/the_northern_lights_light_up_vancouver.html?cat=8
A solar storm on Aug. 3 and 4 allowed people to see a spectacle that is usually just reserved for those who live in the northernmost regions — the northern lights. Technically referred to as aurora borealis, the
northern lights are a natural phenomenon resulting from the emission of photons and chemicals from the sun's surface that are usually only seen in areas around the north poles, such as in northern Alaska.
A solar storm on Aug. 3 and 4 allowed people to see a spectacle that is usually just reserved for those who live in the northernmost regions — the northern lights. Technically referred to as aurora borealis, the
northern lights are a natural phenomenon resulting from the emission of photons and chemicals from the sun's surface that are usually only seen in areas around the north poles, such as in northern Alaska.
FoldIt
http://arstechnica.com/science/news/2010/08/gamers-beat-algorithms-for-finding-protein-structures.ars
Gamers beat algorithms at finding protein structures
Foldit takes a hybrid approach. The Rosetta algorithm is used to create some potential starting structures, but users are then given a set of controls that let them poke and prod the protein's structure in three dimensions; displays provide live feedback on the energy of a configuration.
Gamers beat algorithms at finding protein structures
Foldit takes a hybrid approach. The Rosetta algorithm is used to create some potential starting structures, but users are then given a set of controls that let them poke and prod the protein's structure in three dimensions; displays provide live feedback on the energy of a configuration.
Wednesday, August 4, 2010
ROC Curve
Receiver operating characteristic (ROC) curve
Exposing the Coadaptive Potential of Protein-protein Interfaces through Computational Sequence Design
Menachem Fromer 1 and Michal Linial 2,*
1School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
2Department of Biological Chemistry, Institute of Life Sciences, Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
*To whom correspondence should be addressed. Michal Linial, E-mail: michall@cc.huji.ac.il
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq412v1?etoc
Sample data
http://mark.goadrich.com/programs/AUC/
Example List file
> AUC
function(ranks, n) {
#ranks : ranks = c( 1,2,3);
#n = 5 ; total number
Npos =length(ranks)
Nneg = n - Npos
AUC = 1 - ( sum(ranks) - Npos*(Npos+1)/2 ) / (Npos * Nneg)
return(AUC)
}
> ROC
function(ranks , n) {
#doesn't work for ties !
TF = rep(0,n)
TF[ranks] = 1;
fp= cumsum(!TF/sum(!TF))
tp=cumsum(TF/sum(TF))
return( list( fp = fp / max(fp), tp = tp))
}
> ROC(x[x$V2==1,'rank'],nrow(x))
$fp
[1] 0.25 0.25 0.50 0.75 0.75 0.75 0.75 1.00 1.00 1.00
$tp
[1] 0.0000000 0.1666667 0.1666667 0.1666667 0.3333333 0.5000000 0.6666667
[8] 0.6666667 0.8333333 1.0000000
> x$rank <- rank(-1*x$V1)
> ROC(x[x$V2==1,'rank'],nrow(x))
$fp
[1] 0.00 0.00 0.25 0.25 0.25 0.25 0.50 0.75 0.75 1.00
$tp
[1] 0.1666667 0.3333333 0.3333333 0.5000000 0.6666667 0.8333333 0.8333333
[8] 0.8333333 1.0000000 1.0000000
> AUC(x[x$V2==1,'rank'],nrow(x))
[1] 0.75
Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction
Richard T. Bradshaw, Bhavesh H. Patel, Edward W. Tate, Robin J. Leatherbarrow and Ian R. Gould1
Department of Chemistry and Chemical Biology Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
1 To whom correspondence should be addressed. E-mail: i.gould@imperial.ac.uk
http://peds.oxfordjournals.org/cgi/content/abstract/gzq047v1?etoc
Comparison study of microarray meta-analysis methods
Anna Campain email and Yee Hwa Yang email
BMC Bioinformatics 2010, 11:408doi:10.1186/1471-2105-11-408
Published: 3 August 2010
http://peds.oxfordjournals.org/cgi/content/abstract/gzq047v1?etoc
Background
Meta-analysis methods exist for combining multiple microarray datasets. However, there are a wide range of issues associated with microarray meta-analysis and a limited ability to compare the performance of different meta-analysis methods.
Results
We compare eight meta-analysis methods, five existing methods, two naive methods and a novel approach (mDEDS). Comparisons are performed using simulated data and two biological case studies with varying degrees of meta-analysis complexity. The performance of meta-analysis methods is assessed via ROC curves and prediction accuracy where applicable.
Conclusions
Existing meta-analysis methods vary in their ability to perform successful meta-analysis. This success is very dependent on the complexity of the data and type of analysis. Our proposed method, mDEDS, performs competitively as a meta-analysis tool even as complexity increases. Because of the varying abilities of compared meta-analysis methods, care should be taken when considering the meta-analysis method used for particular research.
The diagnostic performance of a test, or the accuray of a test to discriminate diseased cases from normal cases is evaluated using Receiver Operating Characteristic (ROC) curve analysis (Metz, 1978; Zweig & Campbell, 1993). ROC curves can also be used to compare the diagnostic performance of two or more laboratory or diagnostic tests (Griner et al., 1981).
http://www.medcalc.be/manual/roc.php
Exposing the Coadaptive Potential of Protein-protein Interfaces through Computational Sequence Design
Menachem Fromer 1 and Michal Linial 2,*
1School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
2Department of Biological Chemistry, Institute of Life Sciences, Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
*To whom correspondence should be addressed. Michal Linial, E-mail: michall@cc.huji.ac.il
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq412v1?etoc
Sample data
http://mark.goadrich.com/programs/AUC/
Example List file
0.9 1 0.8 1 0.7 0 0.6 1 0.55 1 0.54 1 0.53 0 0.52 0 0.51 1 0.505 0Example ROC file for same dataset as above, using 6 pos and 4 neg examples
0 0 0.0 0.16666666666666666 0.0 0.3333333333333333 0.25 0.3333333333333333 0.25 0.5 0.25 0.6666666666666666 0.25 0.8333333333333334 0.5 0.8333333333333334 0.75 0.8333333333333334 0.75 1.0 1.0 1.0
AUC
0.75
> AUC
function(ranks, n) {
#ranks : ranks = c( 1,2,3);
#n = 5 ; total number
Npos =length(ranks)
Nneg = n - Npos
AUC = 1 - ( sum(ranks) - Npos*(Npos+1)/2 ) / (Npos * Nneg)
return(AUC)
}
> ROC
function(ranks , n) {
#doesn't work for ties !
TF = rep(0,n)
TF[ranks] = 1;
fp= cumsum(!TF/sum(!TF))
tp=cumsum(TF/sum(TF))
return( list( fp = fp / max(fp), tp = tp))
}
> ROC(x[x$V2==1,'rank'],nrow(x))
$fp
[1] 0.25 0.25 0.50 0.75 0.75 0.75 0.75 1.00 1.00 1.00
$tp
[1] 0.0000000 0.1666667 0.1666667 0.1666667 0.3333333 0.5000000 0.6666667
[8] 0.6666667 0.8333333 1.0000000
> x$rank <- rank(-1*x$V1)
> ROC(x[x$V2==1,'rank'],nrow(x))
$fp
[1] 0.00 0.00 0.25 0.25 0.25 0.25 0.50 0.75 0.75 1.00
$tp
[1] 0.1666667 0.3333333 0.3333333 0.5000000 0.6666667 0.8333333 0.8333333
[8] 0.8333333 1.0000000 1.0000000
> AUC(x[x$V2==1,'rank'],nrow(x))
[1] 0.75
Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction
Richard T. Bradshaw, Bhavesh H. Patel, Edward W. Tate, Robin J. Leatherbarrow and Ian R. Gould1
Department of Chemistry and Chemical Biology Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
1 To whom correspondence should be addressed. E-mail: i.gould@imperial.ac.uk
http://peds.oxfordjournals.org/cgi/content/abstract/gzq047v1?etoc
Comparison study of microarray meta-analysis methods
Anna Campain email and Yee Hwa Yang email
BMC Bioinformatics 2010, 11:408doi:10.1186/1471-2105-11-408
Published: 3 August 2010
http://peds.oxfordjournals.org/cgi/content/abstract/gzq047v1?etoc
Background
Meta-analysis methods exist for combining multiple microarray datasets. However, there are a wide range of issues associated with microarray meta-analysis and a limited ability to compare the performance of different meta-analysis methods.
Results
We compare eight meta-analysis methods, five existing methods, two naive methods and a novel approach (mDEDS). Comparisons are performed using simulated data and two biological case studies with varying degrees of meta-analysis complexity. The performance of meta-analysis methods is assessed via ROC curves and prediction accuracy where applicable.
Conclusions
Existing meta-analysis methods vary in their ability to perform successful meta-analysis. This success is very dependent on the complexity of the data and type of analysis. Our proposed method, mDEDS, performs competitively as a meta-analysis tool even as complexity increases. Because of the varying abilities of compared meta-analysis methods, care should be taken when considering the meta-analysis method used for particular research.
The diagnostic performance of a test, or the accuray of a test to discriminate diseased cases from normal cases is evaluated using Receiver Operating Characteristic (ROC) curve analysis (Metz, 1978; Zweig & Campbell, 1993). ROC curves can also be used to compare the diagnostic performance of two or more laboratory or diagnostic tests (Griner et al., 1981).
http://www.medcalc.be/manual/roc.php
'Designer Protein' Opens New Door in Cancer Research
http://www.sciencedaily.com/releases/2010/08/100803112813.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29
Recently, the researchers were able to do just that, creating a designer protein that not only targets a specific cell type, but then invades that cell and is drawn directly to a chosen compartment.
Recently, the researchers were able to do just that, creating a designer protein that not only targets a specific cell type, but then invades that cell and is drawn directly to a chosen compartment.
Tuesday, August 3, 2010
New Drug Target for Immune Diseases Discovered
http://www.sciencedaily.com/releases/2010/08/100803132738.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29
Led by Dr. Andrea Cerutti, MD, Professor of Medicine at Mount Sinai School of Medicine, researchers studied human tissue and immune cells from people with mutations of TACI and MyD88, two proteins required to activate the immune system. MyD88 is a signaling protein that alerts the so-called innate immune system -- the immune system encoded at birth that remains unchanged -- to the presence of pathogens. TACI is a receptor protein used to activate immune cells in the so-called adaptive immune system, a more sophisticated immune system than the innate, which is dynamic and combats pathogens.
Led by Dr. Andrea Cerutti, MD, Professor of Medicine at Mount Sinai School of Medicine, researchers studied human tissue and immune cells from people with mutations of TACI and MyD88, two proteins required to activate the immune system. MyD88 is a signaling protein that alerts the so-called innate immune system -- the immune system encoded at birth that remains unchanged -- to the presence of pathogens. TACI is a receptor protein used to activate immune cells in the so-called adaptive immune system, a more sophisticated immune system than the innate, which is dynamic and combats pathogens.
Friday, July 30, 2010
Thursday, July 29, 2010
Tuesday, July 27, 2010
Key Milestone Towards the Development of a New Clinically Useful Antibiotic
http://www.sciencedaily.com/releases/2010/07/100712154426.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29
The producing bacterium, Microbispora corallina, is difficult to work with. It grows very slowly and no tools existed for its genetic manipulation. PhD student Lucy Foulston developed the tools herself. She then took advantage of new developments in genome sequencing to identify and then isolate the M. corallina gene cluster responsible for microbisporicin production.
The producing bacterium, Microbispora corallina, is difficult to work with. It grows very slowly and no tools existed for its genetic manipulation. PhD student Lucy Foulston developed the tools herself. She then took advantage of new developments in genome sequencing to identify and then isolate the M. corallina gene cluster responsible for microbisporicin production.
Tuesday, July 20, 2010
Choosing a Rotation Lab
http://artsci.wustl.edu/~sac/document/ChoosingaRotationLab.htm
http://www.med.upenn.edu/mstp/lab_rotation.shtml
http://thelindberglab.com/papers/rotations.pdf
http://www.med.upenn.edu/mstp/lab_rotation.shtml
http://thelindberglab.com/papers/rotations.pdf
Thursday, July 15, 2010
10 Places to Find Opportunities:
10 Places to Find Opportunities:
1. Job boards & job board aggregators
2. Conferences (Look at vendor lists)
3. Twitter feeds (often people will retweet jobs)
4. Company websites (some companies don’t post their jobs on boards)
5. Linkedin Groups
6. Facebook company pages
7. Business & Investment Blogs
8. Chamber of commerce
9. Local & National newspapers
10. Bumping into opportunity (running into people at coffee shops, sports teams etc)
http://blog.workopolis.com/en/2010/07/ten-places-to-find-career-opportunities.html
1. Job boards & job board aggregators
2. Conferences (Look at vendor lists)
3. Twitter feeds (often people will retweet jobs)
4. Company websites (some companies don’t post their jobs on boards)
5. Linkedin Groups
6. Facebook company pages
7. Business & Investment Blogs
8. Chamber of commerce
9. Local & National newspapers
10. Bumping into opportunity (running into people at coffee shops, sports teams etc)
http://blog.workopolis.com/en/2010/07/ten-places-to-find-career-opportunities.html
Thursday, July 8, 2010
Cholesterol's Other Way out
"In parallel, we believe that the liver also plays a gatekeeper role for nonbiliary fecal sterol loss by repackaging peripheral cholesterol into nascent plasma lipoproteins that are destined for subsequent intestinal delivery."
http://www.sciencedaily.com/releases/2010/07/100707102443.htm
http://www.sciencedaily.com/releases/2010/07/100707102443.htm
Tuesday, July 6, 2010
Avatar / The Last Air Bender
http://www.watchanimeon.com/avatar-the-last-airbender-book-1-chapter-1-2/
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