Thursday, June 30, 2011
Phylop vs Phastcons
PhastCons (region) (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns.
By contrast, phyloP (position) separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).
http://compgen.bscb.cornell.edu/phast/faq.php
http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=200695383&g=cons30way#a_cfg_phastcons
By contrast, phyloP (position) separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).
http://compgen.bscb.cornell.edu/phast/faq.php
http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=200695383&g=cons30way#a_cfg_phastcons
Publishing in the web for free
Google Sites
https://www.google.com/accounts
The key feature of Google Sites is its collaboration abilities
Wordpress
http://wordpress.com/
Powerful design
http://productivewise.com/free-website-building-platforms-compared-wordpress-google-sites/
https://www.google.com/accounts
The key feature of Google Sites is its collaboration abilities
Wordpress
http://wordpress.com/
Powerful design
http://productivewise.com/free-website-building-platforms-compared-wordpress-google-sites/
What Makes You Irresistible to Employers
In a tight market, every job seeker needs to find a way to stand out from the crowd. What separates the "great" from the "good" and makes a particular candidate just too irresistible to pass up?
Oftentimes, it is one of these three things:
- Ability to Prove Worth,
- More than a Simple Knowledge of the Company,
- and Enthusiasm.
http://www.careerbuilder.ca/Article/CB-774-Job-Search-What-makes-you-irresistible-to-employers/?sc_extcmp=cbca_9774&cblang=CAEnglish&SiteId=cbca_9774
Tips for landing higher pay in a new role
Here's how to excel in the art of negotiation:
- Know Your Benchmark
- Set a Minimum Threshold
- Don't Start Too Early
- Demonstrate Your Value
- Be Assertive
BGI to expand into clinical, drug-development services
Earlier this month, Adam Bonislawski at GenomeWeb’s Proteomonitor reported that China-based BGI intends to expand its proteomics offerings and buy 50 new mass spectrometers over the next two years. This diversification into clinical and drug-development services is a forward-thinking move for the genomics/bioinformatics giant and one that should be taken seriously by current proteomics service providers.
http://www.medcitynews.com/2011/06/bgi-to-expand-into-clinical-drug-development-services/
http://www.medcitynews.com/2011/06/bgi-to-expand-into-clinical-drug-development-services/
new generation of ExPASy
SIB Swiss Institute of Bioinformatics just launched the new generation of ExPASy, a web portal which offers a point of entry to more than 120 SIB bioinformatics resources
http://www.expasy.org/
http://www.expasy.org/
Crows learning
Not so bird-brained: Clever crows recognise faces
http://www.google.com/hostednews/afp/article/ALeqM5gDb05xN18drPIMfucOK6FaDQqcog?docId=CNG.b543d6b84be023e079ab0236d9bba908.491
http://www.google.com/hostednews/afp/article/ALeqM5gDb05xN18drPIMfucOK6FaDQqcog?docId=CNG.b543d6b84be023e079ab0236d9bba908.491
Wednesday, June 29, 2011
A New Bioinformatics System Improves Medical Diagnosis
http://www.sciencedaily.com/releases/2011/06/110628094833.htm
The algorithm, called CliDaPa (Clinical Data Partitioning), uses histological and clinical data and pharmacological treatments to partition patients by means of a tree representation for a particular disease (called clinical tree), used to cluster patients according to similar behaviour. It then uses data mining techniques to analyse each patient partition with the associated genetic information.
CliDaPa is a different method of DNA microarray analysis that aims to generate a model representing different patient behaviours (gathered from clinical data). These behaviours will then be examined separately and specifically by means of data mining. New learning methods were also proposed in the course of the research.
The algorithm, called CliDaPa (Clinical Data Partitioning), uses histological and clinical data and pharmacological treatments to partition patients by means of a tree representation for a particular disease (called clinical tree), used to cluster patients according to similar behaviour. It then uses data mining techniques to analyse each patient partition with the associated genetic information.
CliDaPa is a different method of DNA microarray analysis that aims to generate a model representing different patient behaviours (gathered from clinical data). These behaviours will then be examined separately and specifically by means of data mining. New learning methods were also proposed in the course of the research.
Literature mining, ontologies and information visualization for drug repurposing
http://bib.oxfordjournals.org/content/early/2011/06/28/bib.bbr005.abstract?papetoc
Abstract
The immense growth of MEDLINE coupled with the realization that a vast amount of biomedical knowledge is recorded in free-text format, has led to the appearance of a large number of literature mining techniques aiming to extract biomedical terms and their inter-relations from the scientific literature. Ontologies have been extensively utilized in the biomedical domain either as controlled vocabularies or to provide the framework for mapping relations between concepts in biology and medicine. Literature-based approaches and ontologies have been used in the past for the purpose of hypothesis generation in connection with drug discovery. Here, we review the application of literature mining and ontology modeling and traversal to the area of drug repurposing (DR). In recent years, DR has emerged as a noteworthy alternative to the traditional drug development process, in response to the decreased productivity of the biopharmaceutical industry. Thus, systematic approaches to DR have been developed, involving a variety of in silico, genomic and high-throughput screening technologies. Attempts to integrate literature mining with other types of data arising from the use of these technologies as well as visualization tools assisting in the discovery of novel associations between existing drugs and new indications will also be presented.
http://nar.oxfordjournals.org/content/39/suppl_2/W450.abstract?etoc
http://nar.oxfordjournals.org/content/39/suppl_2/W450.abstract?etoc
Prevent ssh connection from disconnecting
$ man ssh_config
$ cat /etc/ssh/ssh_config
...
# ProxyCommand ssh -q -W %h:%p gateway.example.com
SendEnv LANG LC_*
HashKnownHosts yes
# GSSAPIAuthentication yes
# GSSAPIDelegateCredentials no
ServerAliveInterval 30
ServerAliveCountMax 4
$ cat /etc/ssh/ssh_config
...
# ProxyCommand ssh -q -W %h:%p gateway.example.com
SendEnv LANG LC_*
HashKnownHosts yes
# GSSAPIAuthentication yes
# GSSAPIDelegateCredentials no
ServerAliveInterval 30
ServerAliveCountMax 4
Nucleic Acids Research
http://nar.oxfordjournals.org/
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Web Services
http://nar.oxfordjournals.org/
http://nar.oxfordjournals.org/
http://nar.oxfordjournals.org/
Stand Alone Programs
http://nar.oxfordjournals.org/
http://nar.oxfordjournals.org/
http://nar.oxfordjournals.org/
http://nar.oxfordjournals.org/
Monday, June 27, 2011
Sufi Epigram -- lost, left
When the heart grieves over what is has lost, the spirit rejoices over what it has left.
--Sufi Epigram
--Sufi Epigram
Sunday, June 26, 2011
GoVolunteer
SLP Communication Partner
http://govolunteer.ca/cgi/page.cgi?_id=15&posting=23393
Web Designer
Nigel J. Vincent
604 930 4884
nigel@luke15house.com
http://govolunteer.ca/cgi/page.cgi?_id=15&posting=19758
Surrey Art Gallery
http://web.volunteer2.com/public/organization/ListJobs.aspx?OrganizationGUID=ce165d9a-5845-4e0f-bdc0-14d973e4c2f7&VolunteerCenterGUID=&VolunteerCenterReferralTypeID=&AppForm=
http://www.surrey.ca/culture-recreation/1610.aspx
Saturday, June 25, 2011
2011 Steveston Salmon Festival
http://www.richmond.ca/home.htm
Steveston Salmon Festival - 22nd Annual Bullhead DerbyDate:Jun 26, 2011Time:9:00 a.m. Registration 10:00 a.m. to 12:00 p.m. Derby Prizes awarded as soon as results are talliedPlace:Garry Point Park
12011 7th Avenue, Richmond Price:This event is FREE!
Kids ages 12yrs and under and Seniors 65+yrs.
12011 7th Avenue, Richmond Price:This event is FREE!
Kids ages 12yrs and under and Seniors 65+yrs.
2011 Steveston Salmon Festival Schedule of Events.
Main Events (subject to change)
6:30am - 11:30am - Pancake Breakfast
9:30am - Kid's Bicycle Parade
9:55am - Kajaks Salmon Run road race - DETAILS
10:00am - noon - Canada Day Parade
10:00am - 4:00pm - Japanese Cultural Displays
10:00am - 5:00pm - Art Show, Children's Festival, Craft Fair, Trade Show, Community Food Fair, Community Information Tables, Steveston RCMP Child ID Station
11:00am until sold out - Salmon Barbecue
11:00am - 6:00pm - Inflatables and Mini Midway
12:00pm - 5:00pm - Horticulture Show, Youth Rock Fest, Three on Three Hockey
6:30am - 11:30am - Pancake Breakfast
9:30am - Kid's Bicycle Parade
9:55am - Kajaks Salmon Run road race - DETAILS
10:00am - noon - Canada Day Parade
10:00am - 4:00pm - Japanese Cultural Displays
10:00am - 5:00pm - Art Show, Children's Festival, Craft Fair, Trade Show, Community Food Fair, Community Information Tables, Steveston RCMP Child ID Station
11:00am until sold out - Salmon Barbecue
11:00am - 6:00pm - Inflatables and Mini Midway
12:00pm - 5:00pm - Horticulture Show, Youth Rock Fest, Three on Three Hockey
Galaxy tools
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies
https://bitbucket.org/galaxy/galaxy-central/wiki/Home
http://main.g2.bx.psu.edu/
http://screencast.g2.bx.psu.edu/galaxy/flash/Exons_SNP.html
Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 Aug 25;11(8):R86.
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.
https://bitbucket.org/galaxy/galaxy-central/wiki/Home
http://main.g2.bx.psu.edu/
http://screencast.g2.bx.psu.edu/galaxy/flash/Exons_SNP.html
Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 Aug 25;11(8):R86.
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.
FASD - Fetal Alcohol Spectrum Disorder
Fetal alcohol spectrum disorders (FASDs) are a group of conditions that can occur in a person whose mother drank alcohol during pregnancy. These effects can include physical problems and problems with behavior and learning. Often, a person with an FASD has a mix of these problems.
Diagnosing FAS can be hard because there is no medical test, like a blood test, for it.
http://www.cdc.gov/ncbddd/fasd/facts.html
Diagnosing FAS can be hard because there is no medical test, like a blood test, for it.
http://www.cdc.gov/ncbddd/fasd/facts.html
Friday, June 24, 2011
Dolphin-emu
http://code.google.com/p/dolphin-emu/issues/detail?id=2989
, Aug 28, 2010
Compile dolphin: Install this: http://orwell.fiit.stuba.sk/~nou/ati-opencl-dev_2.01.deb http://orwell.fiit.stuba.sk/~nou/ati-opencl-runtime_2.01_amd64.deb Then: sudo apt-get install subversion scons g++ wx2.8-headers libwxbase2.8-0 libwxbase2.8-dbg libwxbase2.8-dev wx2.8-headers libwxgtk2.8-0 libwxgtk2.8-dbg libwxgtk2.8-dev libgtk2.0-dev libsdl1.2-dev g++ wx2.8-headers libwxbase2.8-0 libwxbase2.8-dbg libwxbase2.8-dev libwxgtk2.8-0 libwxgtk2.8-dbg libwxgtk2.8-dev libsdl1.2-dev nvidia-cg-toolkit libxxf86vm1-dbg libxxf86vm-dev libxext6-dbg libxext-dev libglew1.5-dev libcairo2-dbg libcairo2-dev libao2 libao-dev libbluetooth-dev libreadline5-dev nvidia-cg-toolkit libxrandr2-dbg libxrandr-dev libxext6-dbg libxext-dev libglew1.5-dev libcairo2-dbg libcairo2-dev libao2 libao-dev libbluetooth-dev libreadline5-dev libwxbase2.8-0 libwxbase2.8-dbg libwxbase2.8-dev libwxgtk2.8-0 libwxgtk2.8-dbg libwxgtk2.8-dev libgtk2.0-dev libsdl1.2-dev nvidia-cg-toolkit libbluetooth-dev libxrandr2-dbg libxrandr-dev libxext6-dbg libxext-dev libglew1.5-dev libcairo2-dbg libcairo2-dev libao2 libao-dev libreadline-dev sudo svn checkout http://dolphin-emu.googlecode.com/svn/trunk/ dolphin-emu-read-only cd dolphin-emu-read-only sudo scons opencl=true flavor=release sudo chmod -R 777 Binary/Linux-x86_64/
Find libraries in Ubuntu using the 'ldd' command
http://code.google.com/p/google-gadgets-for-linux/issues/detail?id=323
$ldd /usr/bin/ggl-gtk
linux-gate.so.1 => (0xb7f6a000) libgtk-x11-2.0.so.0 => /usr/lib/libgtk-x11-2.0.so.0 (0xb7ba7000) libatk-1.0.so.0 => /usr/lib/libatk-1.0.so.0 (0xb7b8c000) libpangoft2-1.0.so.0 => /usr/lib/libpangoft2-1.0.so.0 (0xb7b62000) libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb7aeb000) libgdk-x11-2.0.so.0 => /usr/lib/libgdk-x11-2.0.so.0 (0xb7a5e000) libgdk_pixbuf-2.0.so.0 => /usr/lib/libgdk_pixbuf-2.0.so.0 (0xb7a44000) libpangocairo-1.0.so.0 => /usr/lib/libpangocairo-1.0.so.0 (0xb7a38000)...
$ldd /usr/lib/google-gadgets/modules/libxml2-xml-parser.so
linux-gate.so.1 => (0xb7f71000) libxml2.so.2 => /usr/lib/libxml2.so.2 (0xb7e19000) libggadget-1.0.so.0 => /usr/local/lib/libggadget-1.0.so.0 (0xb7aa3000)...
Thursday, June 23, 2011
Apple's Steve Wozniak preaches innovation to Concordia grads
“There’s always time for innovation, thinking about how can I do it a little better than I was taught,” Wozniak said. “If you are able to make things simpler, you’ll have done the world a great service.”
Neurodegenerative disease: the value of mouse models
Questions raised about the use of ‘ALS mice’ are prompting a
broad reappraisal of the way that drugs are tested in animal
models of neurodegenerative disease. Jim Schnabel reports.
Scott and his colleagues con-
cluded that the previous positive drug trials in
ALS mice were likely to have been so plagued
by non-drug-related variations in mouse
lifespan that this ‘noise’ was really all they had
measured. In the context of small sample sizes
and a bias against negative results, they noted,
a high degree of noise could easily have led to
the appearance of positive results even when
no drug effect had existed.
mouse was not excluded appropriately from
a study. Such an exclusion should have hap-
pened if, for example, an animal died young of
non-ALS causes — Scott came to believe that
mouse colonies in some academic labs were
“filthy” with infections — or failed to express
enough copies of the mutant SOD1 gene.
“People will do
an experiment once with ten animals and get
a result, and if it’s the right result it gets pub-
lished in a high-profile journal,” says Duff
The wrong model?
http://www.nature.com/nature/journal/v454/n7205/edsumm/e080807-02.html
One of the newly identified genetic variants, SCARB2, is associated with a known Parkinson's disease pathway involving protein degradation.
The other, SREBF1, is not associated with any known Parkinson's pathway.
broad reappraisal of the way that drugs are tested in animal
models of neurodegenerative disease. Jim Schnabel reports.
Scott and his colleagues con-
cluded that the previous positive drug trials in
ALS mice were likely to have been so plagued
by non-drug-related variations in mouse
lifespan that this ‘noise’ was really all they had
measured. In the context of small sample sizes
and a bias against negative results, they noted,
a high degree of noise could easily have led to
the appearance of positive results even when
no drug effect had existed.
mouse was not excluded appropriately from
a study. Such an exclusion should have hap-
pened if, for example, an animal died young of
non-ALS causes — Scott came to believe that
mouse colonies in some academic labs were
“filthy” with infections — or failed to express
enough copies of the mutant SOD1 gene.
“People will do
an experiment once with ten animals and get
a result, and if it’s the right result it gets pub-
lished in a high-profile journal,” says Duff
The wrong model?
Mouse models could therefore end up being
not only more difficult and expensive to use
with acceptable rigour, but at the same time
more narrowly predictive of the human con-
dition.
http://www.nature.com/nature/journal/v454/n7205/edsumm/e080807-02.html
One of the newly identified genetic variants, SCARB2, is associated with a known Parkinson's disease pathway involving protein degradation.
The other, SREBF1, is not associated with any known Parkinson's pathway.
Wednesday, June 22, 2011
We can't change the cards we are dealt with, just how we play our hand. - Randy Pausch, Last Lecture
We can't change the cards we are dealt with, just how we play our hand. - Randy Pausch (Virtual Reality), Last Lecture
fundamentals in football
when you're screwing up and people stop saying anything, then they probably stopped caring
experience is what you get when you didn't get what you wanted
the brick walls are there for a reason: they let us prove how badly we want things,
they're there to stop the 'other' people
Find the best in everybody; wait long enough and people will surprise and impress you
when people are angry at you, you just haven't given them enough time
Disney Imagineering (R & D)
http://corporate.disney.go.com/careers/who_imagineering.html
Found something astounding that your students did? What do you say?
That was amazing but I know you can do better.
respect authority while questioning it
Learning to Program with Alice
http://www.aliceprogramming.net/
Advice for Girls, "Only pay attention to what the guys do, and not what they say."
How to get people to help you. You can't get there alone, and I believe in Karma
Tell the truth
Be earnest
Apologize when you screw up
Focus on others, not yourself
Don't bail; the best gold is at the bottom of barrels of crap
Get a feedback loop and listen to it
Show gratitude
Don't complain; just work harder
Be prepared: "luck" is where preparation meets opportunity
http://www.youtube.com/watch?v=ji5_MqicxSo
fundamentals in football
when you're screwing up and people stop saying anything, then they probably stopped caring
experience is what you get when you didn't get what you wanted
the brick walls are there for a reason: they let us prove how badly we want things,
they're there to stop the 'other' people
Find the best in everybody; wait long enough and people will surprise and impress you
when people are angry at you, you just haven't given them enough time
Disney Imagineering (R & D)
http://corporate.disney.go.com/careers/who_imagineering.html
Found something astounding that your students did? What do you say?
That was amazing but I know you can do better.
respect authority while questioning it
Learning to Program with Alice
http://www.aliceprogramming.net/
Advice for Girls, "Only pay attention to what the guys do, and not what they say."
How to get people to help you. You can't get there alone, and I believe in Karma
Tell the truth
Be earnest
Apologize when you screw up
Focus on others, not yourself
Don't bail; the best gold is at the bottom of barrels of crap
Get a feedback loop and listen to it
Show gratitude
Don't complain; just work harder
Be prepared: "luck" is where preparation meets opportunity
http://www.youtube.com/watch?v=ji5_MqicxSo
Randy Pausch Last Lecture: Achieving Your Childhood Dreams
www.youtube.com/watch?v=ji5_MqicxSo
Carnegie Mellon Professor Randy Pausch (Oct. 23, 1960 - July 25, 2008) gave his last lecture at the university Sept. 18, 2007,
http://www.cs.cmu.edu/~pausch/
-- Randy
Carnegie Mellon Professor Randy Pausch (Oct. 23, 1960 - July 25, 2008) gave his last lecture at the university Sept. 18, 2007,
http://www.cs.cmu.edu/~pausch/
The "Last Lecture"
I am flattered and embarassed by all the recent attention to my "Last Lecture." I am told that, including abridged versions, over six million people have viewed the lecture online. The lecture really was for my kids, but if others are finding value in it, that is wonderful. But rest assured; I'm hardly unique. Send your kids to Carnegie Mellon and the other professors here will teach them valuable life lessons long after I'm gone.-- Randy
Fast interval intersection methodologies
http://biostar.stackexchange.com/questions/99/fast-interval-intersection-methodologies/101#101
Most genomic annotations are specified as intervals along the genome.
http://code.google.com/p/bedtools/#Brief_example
Quinlan, AR and Hall, IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.
Most genomic annotations are specified as intervals along the genome.
- Interval trees have been known to provide an efficient datastructure that allows for very fast overlap querying.
- Nested Containment Lists have been proposed as an even faster alternative
http://code.google.com/p/bedtools/#Brief_example
Quinlan, AR and Hall, IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.
- Intersecting two BED files in search of overlapping features.
- Culling/refining/computing coverage for BAM alignments based on genome features.
- Merging overlapping features.
- Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
- Calculating the depth and breadth of sequence coverage across defined "windows" in a genome.
- Screening for overlaps between "split" alignments and genomic features.
But now you subsequently detect an artifact where false positives are enriched in SNPs having coverage > 100. You refine my original query accordingly.
$ awk '$5 < 100' snps.bed | \ egrep "A/G|C/T" | \ intersectBed -a stdin -b exons.bed | \ intersectBed -v -a stdin -b dbSnp130.bed \ > bonafideNovelSnpsInExons.bed
MOODS: fast search for position weight matrix matches in DNA sequences
http://bioinformatics.oxfordjournals.org/content/25/23/3181.full
http://www.cs.helsinki.fi/group/pssmfind/
http://cs.helsinki.fi/u/prastas/pdf/BIRD-fullC.pdf
J. Korhonen, P. Martinmäki, C. Pizzi, P. Rastas and E. Ukkonen. MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics 25(23), pages 3181-3182. (2009)
http://www.cs.helsinki.fi/group/pssmfind/
http://cs.helsinki.fi/u/prastas/pdf/BIRD-fullC.pdf
J. Korhonen, P. Martinmäki, C. Pizzi, P. Rastas and E. Ukkonen. MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics 25(23), pages 3181-3182. (2009)
Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library.
Availability: The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL).
- based on Pizzi et al. 2007, 2009, standard scoring based on PWM scores (log-odds against background (can be user-defined))
- online algorithm, simple sequential search over target sequence using string matching with lookahead filtration
- "we know without seeing the remaining symbols that the m-segment cannot be a match as the total score will be less than k for any choice of the sequence beyond the location h."
- written in C++, has bindings for BioPerl and BioPython
- return log-odds score or absolute score thresholds
- seems to be good for significant p-values for short-avg-length matrices (4-20 bases), DNA
Comments
- doesn't look like it incorporates any conservation information
- even though it's significantly faster than TFBS and can handle more data, I wonder how similar the results are in terms of predicted positions
TFBS BioPerl extension (Lenhard and Wasserman, 2002) - uses naive algorithm
lookahead scoring search
algorithm of [30] already utilizes the filtering idea.
lookahead scoring search
algorithm of [30] already utilizes the filtering idea.
Bioinformatics workflow tools
Kepler https://kepler-project.org/
- With R functionality
Taverna http://bioinformatics.oxfordjournals.org/content/26/19/2486.full
- With R functionality
Taverna http://bioinformatics.oxfordjournals.org/content/26/19/2486.full
Phenomics, Cognitive ontologies for neuropsychiatric phenomics research.
Several free web applications are available already to support examination and visualisation of cognitive concepts in the literature (PubGraph, PubAtlas, PubBrain) and to aid collaborative development of cognitive ontologies (Phenowiki and the Cognitive Atlas).
http://www.ncbi.nlm.nih.gov/pubmed?term=pubbrain
If the nodes have queries X and Y, the top number is the number of hits for(X AND Y), and the bottom number is the number of hits for (X OR Y). The ratio of these numbers is called theJaccard co-occurrence index; it measures the degree to which the two queries coincide among all publications.
http://www.pubatlas.org/
Consortium for Neuropsychiatric Phenomics
http://phenomics.ucla.edu/projects.asp#wording
http://www.ncbi.nlm.nih.gov/pubmed?term=pubbrain
If the nodes have queries X and Y, the top number is the number of hits for(X AND Y), and the bottom number is the number of hits for (X OR Y). The ratio of these numbers is called theJaccard co-occurrence index; it measures the degree to which the two queries coincide among all publications.
http://www.pubatlas.org/
Consortium for Neuropsychiatric Phenomics
http://phenomics.ucla.edu/projects.asp#wording
Monday, June 20, 2011
APBC2012
APBC2012: The Tenth Asia Pacific Bioinformatics Conference, Melbourne Australia
Deadline Approaching: APBC2012 – The Tenth Asia Pacific Bioinformatics Conference
-------------------------------------------------------------------------------------------------------
The Tenth Asia Pacific Bioinformatics Conference
Melbourne, Australia, 17-19 January 2012
http://homepage.cs.latrobe.edu.au/ypchen/APBC2012/
Important Dates
Paper submission: 20th July 2011 *******
Author Notification: 20th Aug 2011
Final Version due on: 1st Oct 2011
Tutorial submission open: 1st July 2011
Poster submission open: 3rd Oct 2011
Registration open: 22nd Aug 2011
Deadline Approaching: APBC2012 – The Tenth Asia Pacific Bioinformatics Conference
-------------------------------------------------------------------------------------------------------
The Tenth Asia Pacific Bioinformatics Conference
Melbourne, Australia, 17-19 January 2012
http://homepage.cs.latrobe.edu.au/ypchen/APBC2012/
Important Dates
Paper submission: 20th July 2011 *******
Author Notification: 20th Aug 2011
Final Version due on: 1st Oct 2011
Tutorial submission open: 1st July 2011
Poster submission open: 3rd Oct 2011
Registration open: 22nd Aug 2011
Cell graphics images animations
http://cellimagelibrary.org/
http://mgl.scripps.edu/people/goodsell
http://sbarrows.com/Home.html
http://www.xvivo.net/
http://www.invivo.ca/
http://www.hybridmedicalanimation.com/
http://www.hurdstudios.com/
http://multimedia.mcb.harvard.edu/
http://mgl.scripps.edu/people/goodsell
http://sbarrows.com/Home.html
http://www.xvivo.net/
http://www.invivo.ca/
http://www.hybridmedicalanimation.com/
http://www.hurdstudios.com/
http://multimedia.mcb.harvard.edu/
Sunday, June 19, 2011
Betcha by Golly, Wow
"Betcha by Golly, Wow" is a song written by Linda Creed and Thom Bell in 1970, and most notably recorded by the Philadelphia soul group The Stylistics in 1971.
Google Gadgets for Linux
Install Google Gadgets from Ubuntu Software Centre
"Program can't start because it failed to load the following
module(s):
js-script-runtime"
http://code.google.com/p/google-gadgets-for-linux/issues/detail?id=323
, Jul 25, 2009
That's the problem: you have another copy of ggl installed in /usr/local. You need remove all related files in /usr/local: /usr/local/lib/libggadget* /usr/local/lib/google-gadgets /usr/local/bin/ggl* /usr/local/share/google-gadgets
http://code.google.com/p/google-gadgets-for-linux/
http://tombuntu.com/index.php/2008/06/16/install-google-gadgets-for-linux-on-ubuntu/
Google Gadgets for Linux provides a platform for running desktop gadgets under Linux, catering to the unique needs of Linux users. It's compatible with the gadgets written for Google Desktop for Windows as well as the Universal Gadgets on iGoogle. Following Linux norms, this project is open-sourced under the Apache License.
Start Google Gadgets Automatically
To start Google Gadgets when you log in, open System->Preferences->Sessions. Click Add and create a new item for Google Gadgets with the command ggl-gtk.
Leo Buscaglia - Love and differences
"Find the person who will love you because of your differences and not in spite of them and you have found a lover for life."
Saturday, June 18, 2011
Mitochondria - Microsopic Structures Found Inside Cells
http://www.parkinson.bc.ca/Research---Dr-Gordon-Rintoul
Parkinson's disease involves the loss of a select population of brain cells (neurons). My research, funded by Parkinson Society British Columbia, focuses on the involvement of "mitochondria" in this neurodegeneration.
Mitochondria are microscopic structures found within cells. They are often described as the "powerhouses" of cells, as they provide energy for all cellular processes. Recent studies have revealed that mitochondria are very mobile structures within many cells, including neurons. It is thought that the function of this mitochondrial motility is to deliver energy to regions of neurons that require it. In other words, mitochondria act as microscopic "meals on wheels" within neurons. We hypothesize that as neurons age, this energy delivery process is compromised, making neurons in older brains more susceptible to Parkinson's disease.
Our research is directed toward understanding the processes that control mitochondrial motility and determining the contribution of mitochondria to the Parkinson's disease process.
Seqlab
http://sequilab.org/pages/aboutUs.jsf
Sequilab is a leap forward for genetic researchers using online bioinformatics tools. Sequilab is home to a rapidly growing community of researchers working with sequence data, with a wet lab focus, across the breadth of the life sciences field.
The Sequilab research portal presents a simple, seamlessly-integrated interface that combines sequence analysis and manipulation, lab work management (custom notes and projects), and a personal work space with access to social media, personal profiles, community collaboration, as well as information on news, careers, and upcoming conferences. All research on Sequilab can be saved for later use, modified as the research focus changes, printed for sharing with peers, and is accessible via the web from home or on the go. It is also iPhone and Android compatible!
The portal is free and can be accessed at http://www.sequilab.org.
Richard Dawkins - The Selfish Gene
Dawkins came to prominence with his 1976 book The Selfish Gene, which popularised the gene-centered view of evolution and introduced the term meme.
http://en.wikipedia.org/wiki/Richard_Dawkins
A meme (
/ˈmiːm/[1]) is an idea, behavior or style that spreads from person to person within a culture.[2] While genes transmit biological information, memes are said to transmit ideas and belief information.
http://en.wikipedia.org/wiki/Meme
http://en.wikipedia.org/wiki/Richard_Dawkins
A meme (
/ˈmiːm/[1]) is an idea, behavior or style that spreads from person to person within a culture.[2] While genes transmit biological information, memes are said to transmit ideas and belief information.http://en.wikipedia.org/wiki/Meme
Weeds, dandellions
http://www3.botany.ubc.ca/rieseberglab/people/nolan_kane.html
The Asteraceae (Compositae), with nearly 25,000 named species, is the largest plant family, with numerous important crops (sunflower, safflower, lettuce, artichoke, endive, chicory and many more), noxious weeds (e.g. knapweeds, thistles, dandelions) and ecologically important wild species (silverswords, Artemisia, Senecio), yet has no sequenced genome due to the prohibitively large genome sizes of most Asteraceae species. This lack of genomic information has limited our ability to understand the roles of natural selection, artificial selection and gene flow in shaping both wild and domesticated members of the Asteraceae, and to better characterize the enzymes responsible for the diverse secondary metabolites in medicinally important species.
http://www3.botany.ubc.ca/rieseberglab/research.html
Invasive plants represent a major threat to the economy and environment, with annual economic costs to North America of $35-40 billion. In collaboration with laboratories at UBC (S. Otto, J. Whitton, and K. Adams) and Indiana University (Z. Lao, Jim Bever, and K. Clay), we are using common garden experiments, microarray analyses (Genetics 179:1881-1890), and hitchhiking and association mapping with next generation sequence data to identify specific genetic changes associated with invasiveness. By targeting Compositae weeds for this work – diffuse knapweed, starthistle, Canada thistle, ragweed, and common sunflower – we can exploit the genomic tools and resources developed by the Compositae Genome Project (see below).
The Asteraceae (Compositae), with nearly 25,000 named species, is the largest plant family, with numerous important crops (sunflower, safflower, lettuce, artichoke, endive, chicory and many more), noxious weeds (e.g. knapweeds, thistles, dandelions) and ecologically important wild species (silverswords, Artemisia, Senecio), yet has no sequenced genome due to the prohibitively large genome sizes of most Asteraceae species. This lack of genomic information has limited our ability to understand the roles of natural selection, artificial selection and gene flow in shaping both wild and domesticated members of the Asteraceae, and to better characterize the enzymes responsible for the diverse secondary metabolites in medicinally important species.
http://www3.botany.ubc.ca/rieseberglab/research.html
Invasive plants represent a major threat to the economy and environment, with annual economic costs to North America of $35-40 billion. In collaboration with laboratories at UBC (S. Otto, J. Whitton, and K. Adams) and Indiana University (Z. Lao, Jim Bever, and K. Clay), we are using common garden experiments, microarray analyses (Genetics 179:1881-1890), and hitchhiking and association mapping with next generation sequence data to identify specific genetic changes associated with invasiveness. By targeting Compositae weeds for this work – diffuse knapweed, starthistle, Canada thistle, ragweed, and common sunflower – we can exploit the genomic tools and resources developed by the Compositae Genome Project (see below).
Friday, June 17, 2011
Beep code timer
$ alsamixer
enable beep, press m to unmute
$ for v in {1..100} ; do sleep 5; echo $v; beep; done;
enable beep, press m to unmute
$ for v in {1..100} ; do sleep 5; echo $v; beep; done;
500 Days of Summer (2009)
it was that you can't ascribe
great cosmic significance...
to a simple earthly event.
Coincidence. That's all anything ever is.
Nothing more than coincidence.
Tom had finally learned there are no miracles.
There's no such thing as fate.
Nothing is meant to be.
great cosmic significance...
to a simple earthly event.
Coincidence. That's all anything ever is.
Nothing more than coincidence.
Tom had finally learned there are no miracles.
There's no such thing as fate.
Nothing is meant to be.
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
Prateek Kumar, Steven Henikoff, and Pauline C Ng, “Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm,” Nature Protocols 4, no. 7 (2009): 1073-1081.
The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP).
An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5-20 min, depending on the input.
The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP).
An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5-20 min, depending on the input.
8 Ways to negotiate for job perks
8 Ways to negotiate for job perks
http://www.careerbuilder.ca/Article/CB-754-Interviewing-8-Ways-to-negotiate-for-job-perks/?sc_extcmp=cbca_9754&cblang=CAEnglish&SiteId=cbca_9754
Atul Gawande -- "A Townie Speaks"
Excerpts from Atul Gawande -- "A Townie Speaks"
core American idea: Anything is possible in people’s lives. No one should be counted out.
But I think what I really liked was just the idea of being someone important. And you know where that gets you: nowhere.
But over time I learned that there are two very different satisfactions that you can have in your life.
A) One is the satisfaction of becoming skilled at something. It almost doesn’t matter what the terrain is.
Developing a skill is painful, though. It is difficult. And that’s part of the satisfaction. You will only find meaning in what you struggle with.
B) It comes from human connection. It comes from making others happy, understanding them, loving them.
People have layers. You must take the time to find them.
Your strengths as human beings come from both the abilities and the relationships you invest in nurturing. The trick you have had to learn to get through college, that you will have to carry with you for life, is how to turn the distractions away, how to focus at least a little bit every day on stuff that will take awhile.
But somehow they never let themselves be completely defined by the institutions or the way they did things. They were insiders and yet poked at the customs, looking for better ways.
The Checklist Manifesto
well-designed check lists can improve outcomes
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