http://www.sciencedaily.com/releases/2010/08/100818112709.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+(ScienceDaily%3A+Latest+Science+News)
Neuroblastoma, a solid tumour found outside the brain in the nervous system, is the most frequent cause of disease-related death in children.
"We conducted our drug discovery by targeting the cells that we think are responsible for the cancer coming back," says Kaplan, Senior Scientist at SickKids and Professor in the Department of Molecular Genetics at the University of Toronto. "This is a new way of developing drugs for kids, as we are taking the patients' own cancer stem cells and testing them in the lab."
If the clinical trial shows positive results, this could be the beginning of a personalized medicine approach, Kaplan says. "Our dream is that children will come to SickKids, we'll isolate their cancer stem cells, screen them with libraries of drugs and find out whether Patient A will respond to Therapy B.
Kristen M. Smith, Alessandro Datti, Mayumi Fujitani, Natalie Grinshtein, Libo Zhang, Olena Morozova, Kim M. Blakely, Susan A. Rotenberg, Loen M. Hansford, Freda D. Miller, Herman Yeger, Meredith S. Irwin, Jason Moffat, Marco A. Marra, Sylvain Baruchel, Jeffrey L. Wrana, David R. Kaplan. Selective targeting of neuroblastoma tumour-initiating cells by compounds identified in stem cell-based small molecule screens. EMBO Molecular Medicine, 2010; DOI: 10.1002/emmm.201000093
Sunday, August 22, 2010
Thursday, August 19, 2010
Wireless client bridge
http://linksys.custhelp.com/cgi-bin/linksys.cfg/php/enduser/std_adp.php?p_faqid=3733&p_created=1152002311&p_sid=pvAKyxlj&p_accessibility=0&p_redirect=&p_lva=4579&p_sp=cF9zcmNoPTEmcF9zb3J0X2J5PSZwX2dyaWRzb3J0PSZwX3Jvd19jbnQ9MjcsMjcmcF9wcm9kcz0wJnBfY2F0cz0wJnBfcHY9JnBfY3Y9JnBfc2NmXzM9MSZwX3BhZ2U9MSZwX3NlYXJjaF90ZXh0PWNhc2NhZGluZw**&p_li=&p_topview=1
Wireless client bridge
LAN-LAN
1. TEW-432BRP as the main router, 192.168.1.1, DHCP Server enabled
2. Linksys WRT160N as the client router, 192.168.1.2, DHCP Server disabled
Hook up the cable as ethernet port to ethernet port
To get WRT160N to work, I had to enter the correct MAC address from my old router ...
And if you get a blue screen of death in windows while using TEW-424UB, SiS163U WLAN,
802.11 USB Wireless LAN Adapterthe USB key, saying something about sis163u.sys, move this file from c:\windows\system32 over to a c:\temp folder and install
http://www.sis.com/download/agreement.php?url=/download/
Wireless client bridge
LAN-LAN
1. TEW-432BRP as the main router, 192.168.1.1, DHCP Server enabled
2. Linksys WRT160N as the client router, 192.168.1.2, DHCP Server disabled
Hook up the cable as ethernet port to ethernet port
To get WRT160N to work, I had to enter the correct MAC address from my old router ...
And if you get a blue screen of death in windows while using TEW-424UB, SiS163U WLAN,
802.11 USB Wireless LAN Adapterthe USB key, saying something about sis163u.sys, move this file from c:\windows\system32 over to a c:\temp folder and install
http://www.sis.com/download/agreement.php?url=/download/
Monday, August 16, 2010
Saturday, August 14, 2010
Generalized Linear Model
http://www.stat.ubc.ca/~gustaf/stat538.html
Description: Generalized Linear Models (GLMs) extend much of the `niceness' of linear models to situations where the response variable is not continuous. Consequently these models are popular for analysis in the common scenarios of response variables which are binary, categorical, counts, proportions, or directions. GLMs have become a big part of the `statistical toolbox' in most applicaton areas. This course will be a core introduction to GLMs, including a quick review of linear models, the fundamental formulation of GLMs, discussion of link functions, iterative least-squares algorithms, deviance and asymptotic theory, residuals, quasi-likelihood, and quadratic variance functions. A wide range of GLM applications will be discussed.
Description: Generalized Linear Models (GLMs) extend much of the `niceness' of linear models to situations where the response variable is not continuous. Consequently these models are popular for analysis in the common scenarios of response variables which are binary, categorical, counts, proportions, or directions. GLMs have become a big part of the `statistical toolbox' in most applicaton areas. This course will be a core introduction to GLMs, including a quick review of linear models, the fundamental formulation of GLMs, discussion of link functions, iterative least-squares algorithms, deviance and asymptotic theory, residuals, quasi-likelihood, and quadratic variance functions. A wide range of GLM applications will be discussed.
Friday, August 13, 2010
Weaver [Bui, Yu, Thain] a Python workflow app
Weaver [Bui, Yu, Thain] a Python workflow app
* http://bitbucket.org/pbui/weaver/src
* http://cse.nd.edu/~ccl/research/pubs/weaver-clade2010.pdf
* Peter Bui, Li Yu and Douglas Thain. "Weaver: Integrating Distributed Computing Abstractions into Scientific Workflows using Python", CLADE, Chicago Illinois, June 2010.
* http://bitbucket.org/pbui/weaver/src
* http://cse.nd.edu/~ccl/research/pubs/weaver-clade2010.pdf
* Peter Bui, Li Yu and Douglas Thain. "Weaver: Integrating Distributed Computing Abstractions into Scientific Workflows using Python", CLADE, Chicago Illinois, June 2010.
OpenSource project hosting
http://bitbucket.org/ - uses mercurial
http://github.com/ - uses git
http://code.google.com/ - uses svn
http://sourceforge.net/
http://github.com/ - uses git
http://code.google.com/ - uses svn
http://sourceforge.net/
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.
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