Eric Lander - founding director of the Broad Institute of Harvard and M.I.T.

Power in Numbers

Dr. Lander’s story can be told as a linear narrative of lucky breaks and perfect opportunities. But he doesn’t subscribe to that sort of magical thinking. To him, biography is something of a confection: “You live your life prospectively and tell your story retrospectively, so it looks like everything is converging.”

“It is very easy to be an expert in a new field where there are no experts,” Dr. Lander said. “All you have to do is raise your hand.”

Even before the Human Genome Project ended, Dr. Lander was thinking of how to keep what he saw as a wonderful collaboration among scientists going. There were, by his count, about 65 collaborations among young scientists in Cambridge and Boston, all outside the usual channels.

http://www.nytimes.com/2012/01/03/science/broad-institute-director-finds-power-in-numbers.html?_r=1

Genome Biology - Genomics in 2011: challenges and opportunities

http://genomebiology.com/2011/12/12/137

Abstract

As we come to the end of 2011, Genome Biology has asked some members of our Editorial Board for their views on the state of play in genomics. What was their favorite paper of 2011? What are the challenges in their particular research area? Who has had the biggest influence on their careers? What advice would they give to young researchers embarking on a career in research?

Business cards

http://psd.tutsplus.com/tutorials/designing-tutorials/making-a-print-ready-business-card-using-only-photoshop/

http://www.snap2objects.com/2009/01/20/business-cards-101-everything-you-need-to-know-about-it/

http://www.jukeboxprint.com/shipping_rates.php

http://www.vistaprint.ca

http://www.businessknowhow.com/marketing/business-card.htm
Simple is best. Sort out the information and keep only what's totally necessary for someone to know your name, your company, what you do, and why they should use you -- but don't skimp on your contact information; you want to be easy to reach.

http://www.canville.net/article.html?article=business-card-advice
Include your title

http://www.jobdig.com/articles/791/Enhance_Your_Job_Search_with_Business_Cards.html
answer the question, "Why should I be interested in contacting you?"

http://content.photojojo.com/tips/12-awesome-photography-business-card-ideas/

Prey - anti-theft

http://preyproject.com/

Silent but deadly

Basically you install a tiny agent in your PC or phone, which silently waits for a remote signal to wake up and work its magic.

This signal is sent either from the Internet or through an SMS message, and allows you to gather information regarding the device's location, hardware and network status, and optionally trigger specific actions on it. Next

Venn diagrams in R - gplots.venn

http://www.oga-lab.net/RGM2/func.php?rd_id=gplots:venn


##
## Example using a list of item names belonging to the
## specified group.
##

## construct some fake gene names..
oneName <- function() paste(sample(LETTERS,5,replace=TRUE),collapse="") geneNames <- replicate(1000, oneName()) ## GroupA <- sample(geneNames, 400, replace=FALSE) GroupB <- sample(geneNames, 750, replace=FALSE) GroupC <- sample(geneNames, 250, replace=FALSE) GroupD <- sample(geneNames, 300, replace=FALSE) input <-list(GroupA,GroupB,GroupC,GroupD) input venn(input)

Become wealthy

http://www.claytoncramer.com/rich/BecomeWealthy.html

Enterpreneurship

Meetup - Startup Drinks
http://www.meetup.com/Vancouver-Tech-Co-Founders/

http://www.nrc-cnrc.gc.ca/eng/ibp/irap/about/advisors.html

UpStart Labs: a place for Start Ups to foment
UpStart Labs brings together entrepreneurs with a post-graduate educational background. The perfect place to grow your network, share ideas, and build relationships with others who share your entrepreneurial spark - and who just may have that idea or piece of knowledge that complements your own!

http://upstartlabs.ca

Roger Patterson

Scientific Research and Experimental Development — Tax Incentive Program (SR&ED)
http://www.canadabusiness.ca/eng/summary/1226/

Industrial Research Assistance Program (IRAP)
http://www.canadabusiness.ca/eng/summary/6440/

Free voting system - simplyvoting.com/

simplyvoting.com/

Simply Voting is a web-based online voting system that will help you manage your elections easily and securely. Try casting a ballot in our demo or sign up to run a free test vote. Got a question? Our Rapid Support team is standing by!

Business and Art

"To open a shop is easy, to keep it open is an art."
--Chinese Proverb

Peace

"Peace is not unity in similarity but unity in diversity, in the comparison and conciliation of differences."
--Mikhail Gorbachev

Gene clustering using Latent Semantic Indexing of MEDLINE abstracts

http://memphis.edu/binf/RaminWebpage.htm

Gene clustering using Latent Semantic Indexing of MEDLINE abstracts

Recent advances in genomics and DNA microarray technology enable investigators to simultaneously analyze the expression of thousands of genes under different experimental conditions. However understanding the functional relationships between co-regulated genes presents a formidable task to investigators, requiring first hand knowledge of the biological characteristics of ea`ch gene. There are a variety of public electronic resources from which investigators may assemble gene information. For instance, there are over 10,000 annotated human genes in LocusLink and nearly 13 million citations archived in MEDLINE. However, better automated tools are needed to aid in extraction and utilization of gene information from these databases. My lab has been collaborating with Dr. Michael Berry (Professor of Computer Science at The University of Tennessee, Knoxville; http://www.cs.utk.edu/~berry/) to develop a new software environment called Semantic Gene Organizer?(SGO) ( http://shad.cs.utk.edu/sgo/sgo.html ) to automatically extract gene relationships from titles and abstracts in MEDLINE citations. SGO utilizes a variant of the vector-space model of information retrieval called Latent Semantic Indexing (LSI). LSI implements a classical factorization method from linear algebra (singular value decomposition) to identify conceptual relationships between documents. Our studies have provided proof-of-principle that LSI is a robust automated method for identification of gene-to-keyword and gene-to-gene relationships from the biological literature. Future aims of this project include: 1) expansion of the gene-document collection to include all genes in the LocusLink database; 2) Utilize SGO to expand gene ontology terms and functional gene annotation.

Duplication hotspots - genomic hotspots

The human genome is enriched in interspersed segmental duplications that sensitize approximately 10% of our genome to recurrent microdeletions and microduplications as a result of unequal crossing over. We review the recent discovery of recurrent rearrangements within these genomic hotspots and their association with both syndromic and non-syndromic diseases. Studies of common complex genetic disease show that a subset of these recurrent events plays an important role in autism, schizophrenia and epilepsy. The genomic hotspot model may provide a powerful approach for understanding the role of rare variants in common disease.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746670/?tool=pubmed

microdeletions, segmental duplication, array CGH

Linda Lanyon - INCF

Full name
Linda Lanyon
Affiliation
INCF Secretariat

http://www.incf.org/community/people/lindal/person_view

age of conquerors (age of empires 2) tips and hotkeys

Fix screen resolution
http://www.sevenforums.com/gaming/191362-age-empires-ii-conquerors-high-resolution-music-fix-win7-64-a.html
http://www.gamespot.com/age-of-empires-ii-the-conquerors-expansion/answers/how-to-fix-the-resolution-18760/
http://www.wsgf.org/forum/5528/age-empires-2-conquerors-aoe2-widescreen-fix?page=1

no-cd works on multiplayer only

http://www.allgame.com/game.php?id=25838&tab=controls

* attack by patroling or hitting z - by either clicking the patrol button itself, or hitting z (standard hotkey for patrol). Patrolling in units is the most popular way to attack because all the units in the same group will target and attack the closest enemy unit to that group together, making it a smart way to attack, without requiring too much micromanagement.
* press H+Shift+C while the game is still loading
* when attacked, amass army away from the action, update rally points
* don't be afraid to runaway from loosing battles, wait for more units before attacking again
* build house on where the villager is standing
* set rally points of TCs on buildings that needs to be built
* setup building rally points of military buildings in front of TCs even before the bulding is completely built
* number them by pressing Ctrl+Number even before the bulding is completely built
* house bug - click a house and try building it on the enemy, it will turn red if there's already a building
* build buildings side by side to protect the other sides and easy management
* build markets early if black forest or michi, sell things cheap in early stages of the game
* map control
* best way to kill villies is with scouts
* two builders don't build twice as fast
* triangle-walling half-built walls to protect villagers while building castles

http://aok.heavengames.com/university/strategy/deathmatch/dm-game-overview/

Backspace Key return to the last 10 map locations
Ctrl + 1-9 Keys assign group number to units
1-9 Key select group assigned to this number
Shift + 1-9 Keys select this group in addition to currently selected units
F11 Key display game time
F2 Key display online tech tree
F4 Key display score

Home Key or Middle Mouse Button cycle through last five sound events
. Key cycle through idle villagers
, Key cycle through idle military units
Ctrl + B Keys cycle through barracks
Ctrl + M Keys cycle through markets
Ctrl + A Keys cycle through archery ranges
Spacebar center view on selected unit
Left Mouse Button (twice) select all units of one type
Alt Key + Right Mouse Button (on building) garrison selected units
Delete Key delete selected unit or building
Pause Key pause
Enter Key display chat interface
H Key select town center
F9 Key insert chapters in a recorded game
Print Scrn Key capture screenshot
Ctrl + F12 Keys capture screenshot of entire game map
B then E Key build house
B then F Key build farm
B then T Key build tower
B then Building Hotkey build building
B then Military Building Hotkey build military building
Right Mouse Button rebuild farm

http://www.allgame.com/game.php?id=19528&tab=controls



http://www.youtube.com/watch?v=5IT2Qpu1BJ8&feature=related

hotkeys
http://webcache.googleusercontent.com/search?q=cache:RhROxflDFr0J:forums.ageofempiresonline.com/forums/ThreadNavigation.aspx%3FPostID%3D199495%26NavType%3DPrevious+&cd=2&hl=en&ct=clnk
put all military buildings in 1 group and use tab to switch between them nub. ???? doesn't seem to work on 1.0c .... Probably from AOE1 only http://aoe.heavengames.com/academy/hotkeysandcommands/shortcuts.shtml

i leave them. but u want to use the ones on the left side of ur keyboard (so there close to ur other hotkeys) so once u get to like 6 u should stop using them.
my control groups:
1 scout
2 military buildings
3 dock
4 ranged units
5 inf units
6 cav
7 sometimes (2nd cav gorup for raiding)

http://www.lclan.com/forums/archive/index.php/t-18460.html

Praise the bridge

"Praise the bridge that carried you over."

Brain viewers

Harvard FreeSurfer
http://surfer.nmr.mgh.harvard.edu/

Allen BrainExplorer
http://mouse.brain-map.org/static/brainexplorer

Bede
http://www.neuinfo.org/tutorials/brede/brede_tutorial.shtm
http://neuro.imm.dtu.dk/services/jerne/brede/

http://www.mccauslandcenter.sc.edu/mricro/mricro/linux.html#native
http://neuroimage.usc.edu/neuro/BrainSuite
http://neuromorphometrics.org:8080/nvm/
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewInterface

encephalization

"The increase of brain size relative to body size—encephalization—is intimately linked with human evolution. However, two genetically different evolutionary lineages, Neanderthals and modern humans, have produced similarly large-brained human species.

http://en.wikipedia.org/wiki/Olfactory_bulb

Discovering transcription factor regulatory targets using gene expression and binding data

http://bioinformatics.oxfordjournals.org/content/28/2/206.abstract?etoc


Abstract

Motivation: Identifying the target genes regulated by transcription factors (TFs) is the most basic step in understanding gene regulation. Recent advances in high-throughput sequencing technology, together with chromatin immunoprecipitation (ChIP), enable mapping TF binding sites genome wide, but it is not possible to infer function from binding alone. This is especially true in mammalian systems, where regulation often occurs through long-range enhancers in gene-rich neighborhoods, rather than proximal promoters, preventing straightforward assignment of a binding site to a target gene.

Results: We present EMBER (Expectation Maximization of Binding and Expression pRofiles), a method that integrates high-throughput binding data (e.g. ChIP-chip or ChIP-seq) with gene expression data (e.g. DNA microarray) via an unsupervised machine learning algorithm for inferring the gene targets of sets of TF binding sites. Genes selected are those that match overrepresented expression patterns, which can be used to provide information about multiple TF regulatory modes. We apply the method to genome-wide human breast cancer data and demonstrate that EMBER confirms a role for the TFs estrogen receptor alpha, retinoic acid receptors alpha and gamma in breast cancer development, whereas the conventional approach of assigning regulatory targets based on proximity does not. Additionally, we compare several predicted target genes from EMBER to interactions inferred previously, examine combinatorial effects of TFs on gene regulation and illustrate the ability of EMBER to discover multiple modes of regulation.

Availability: All code used for this work is available at http://dinner-group.uchicago.edu/downloads.html

Contact: dinner@uchicago.edu

Supplementary Information: Supplementary data are available at Bioinformatics online.

Zipcar - car rentals

www.zipcar.com/
Welcome to Zipcar. Zipcar is the world's largest car sharing and car club service. It is an alternative to traditional car rental and car ownership.

Doors

"In the universe, there are things that are known, and things that are unknown, and in between, there are doors."

William Blake

Karaoke with scoring system online

http://www.karaokeparty.com/en/songs

Karaoke - Online and Free
Sing karaoke online and get a score based on your performance. Practice your singing and increase your score. Challenge your friends in becoming the next karaoke champion. All you need is a microphone, built in or connected to your computer.

Age of Empires 2: Battle Tips and Tactics

http://www.youtube.com/watch?v=CoHlZAbCc8c
http://www.youtube.com/watch?v=i8dXGH0PRw4
http://www.youtube.com/watch?v=ep68deMwNVI&feature=mfu_in_order&list=UL
http://www.youtube.com/watch?v=FSTJZxrhAgI&feature=mfu_in_order&list=UL
http://www.voobly.com
http://www.gameranger.com/about/

http://www.youtube.com/watch?feature=endscreen&NR=1&v=I0t0t4t9G6g

Jia You 加油

en.wikipedia.org/wiki/Jiayou


Jiayou (Chinese: 加油; pinyin: jiāyóu) is a Chinese figure of speech or idiom, meaning "be stronger!"

jiā means "to add", and yóu means oil or fuel. Therefore jiayou literally means "add oil" or "add fuel", as in refuelling a motor vehicle; by anology jiayou is used to encourage someone to put more effort into a certain task.

BrainInfo

http://braininfo.rprc.washington.edu/Default.aspx

BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it.

Henry Wadsworth -- Triumph

"In ourselves are triumph and defeat."

You can -- Henry Ford

"Whether you think you can or think you can't, you're right."

Viral miRNA

http://homepage.usask.ca/~vim458/advirol/SPCV/miRNA/miRNA.html#References

Abstract

RNA interference (RNAi) is a natural response to the presence of double stranded RNA (dsRNA) which results in the sequence-specific silencing of gene expression. RNAi is a nucleic-acid based immune defense against viruses, transgenes and transposons. In eukaryotic cells, RNAi is triggered either by short interfering RNAs (siRNA) or by micro RNAs (miRNA) molecules. Recent findings reveal that certain viruses encode their own miRNAs that are processed by cellular RNAi machinery. However, it was unclear what the roles of these virus-encoded miRNAs play and whether some cellular miRNAs play a role in viral replication and phatogenicity. Here I have reviewed the current findings on virus-encoded miRNAs, and their roles in viral replication. I have also examined the role of cellular miRNA in the virus replicative cycle, mechanisms of virus countradefense as well as roles of viral miRNAs in cancer development and latest achievements in antiviral therapy using miRNA analogs.


Since miRNAs have been discovered and their role in gene regulation established, it has been theorized that viruses could generate miRNAs as well and that these viral encoded miRNAs could regulate cellular mechanisms and viral replication. There are several lines of evidence to support this theory:

Kang Eun-Kyung - Korean Drama Writer

http://asianmediawiki.com/Kang_Eun-Kyung

Glory Jane | Yeongkwangui Jaein (KBS2 / 2011)
Bread, Love and Dreams | Jeppangwang Kim Tak Goo (KBS2 / 2010)
Formidable Rivals | Kangcheok deul (KBS2 / 2008)
Dalja's Spring | Daljaui Bom (KBS2 / 2007)
Hello God | Annyeonghaseyo Haneunim (KBS2 / 2006)
Oh! Phil Seung Bong Soon Young | O! Pilseung Bongsoon Young (KBS2 / 2004)
Glass Slippers | Yuri Goodu (SBS / 2002)
Hotelier | Hotelrieo (MBC / 2001)
Ghost | Goseuteu (SBS / 1999)
White Nights 3.98 | Baek Ya 3.98 (SBS / 1998)

RNA spike-in

Known amounts of RNA spike-ins are mixed with the experiment sample during preparation. Subsequently the measured degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA.

http://en.wikipedia.org/wiki/RNA_spike-in

Arts and Science

* SpongeLab Interactive Games and Videos http://www.spongelab.com/browse/
* Development of the Brain Comic http://scienceblogs.com/neurophilosophy/brain%20development%20infographic2.jpg
* mort.art.meseum medicine and art
* NIA Alzheirmer’s CGI Animation (Jannis Productions) http://www.youtube.com/watch?v=LQNCzSuRPZQ
* Science Magazine Feb 2010 http://www.sciencemag.org/content/vol327/issue5968/index.dtl
* Artsy Science www.curiocity.ca/

Brain Development by Dwayne Godwin and Jorge Cham

http://scienceblogs.com/neurophilosophy/brain%20development%20infographic2.jpg

branched DNA and Affymetrix QuantiGene

http://en.wikipedia.org/wiki/Branched_DNA_assay


In biology, a branched DNA assay is a signal amplification assay (as opposed to a target amplification assay) that is used to detect nucleic acid molecules.


Diagrammatically, we have Base -> Capture Probe -> Extender -> Target -> label extender -> pre-amplifier -> amplifier

Affymetrix QuantiGene - DNA Copy Number

Dopaminergic neurons for Parkinson's therapy

http://www.nature.com/nbt/journal/v30/n1/full/nbt.2077.html?WT.ec_id=NBT-201201


* Olle Lindvall1

DOI:
doi:10.1038/nbt.2077


A differentiation protocol guided by developmental principles produces more-authentic dopaminergic neurons for transplantation in patients.

A recent report in Nature by Studer and colleagues2 describes the conversion of human embryonic stem cells (hESCs) into substantia nigra dopaminergic neurons that ameliorate Parkinson's disease symptoms in animal models without forming tumors. From the clinical perspective, this new differentiation protocol, which generates large numbers of transplantable dopaminergic neurons of the correct phenotype, represents a major advance toward the first application of hESC-derived dopaminergic neurons for grafting in patients.

A critical issue for clinical translation is safety. The protocol for generating dopaminergic neurons should be fully chemically defined, and the components of animal origin eliminated. The potential for graft-induced dyskinesias after transplantation should be assessed in appropriate animal models.

Big data in small places

http://www.nature.com/nbt/journal/v30/n1/full/nbt.2079.html?WT.ec_id=NBT-201201

* Daniel MacLean1
* & Sophien Kamoun1

DOI:
doi:10.1038/nbt.2079

Published online
09 January 2012

Dealing with big data sets can be abstracted into three main tasks: we must be able to manage, understand and analyze. 'Managing' is to carry out the computer science–based transfer and storage of data. 'Understanding' implies a clear knowledge of the biological context and caveats of the data as well as the functioning and limitations of the methods. And 'analyzing' refers to the application of the various bioinformatics methods to specific biological questions and data. Our support model distributes labor between bioinformaticians and bench scientists to optimize the delivery of these three tasks.

NCBI GEO2R

NCBI generated annotation is available for many records. These annotations are derived by extracting stable sequence identification information from the Platform and periodically querying against the Entrez Gene and UniGene databases to generate consistent and up-to-date annotation. Gene symbol and Gene title annotations are selected by default. Other categories of NCBI generated annotation include GO terms and chromosomal location information.

Submitter supplied annotation is available for all records. These represent the original Platform annotations provided by the submitter. Note that there is a lot of diversity in the style and content of submitter supplied annotations and they may not have been updated since the time of submission.

http://www.ncbi.nlm.nih.gov/geo/info/geo2r.html

GEO2R is an interactive web tool that allows users to compare two or more groups of Samples in a GEO Series in order to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.

HCI - Human Computer Interaction

http://www.cs.ubc.ca/~cs444/schedule.html

Android tutorial
http://www.cs.ubc.ca/~cs444/tutorials/cs444_lab_Android_StudentSchedule.pdf
http://developer.android.com/resources/tutorials/hello-world.html

Chi-square test

http://www.itl.nist.gov/div898/handbook/eda/section3/eda358.htm

Engineering statistics Handbook

A chi-square test ( Snedecor and Cochran, 1983) can be used to test if the standard deviation of a population is equal to a specified value.

The chi-square distribution results when nu independent variables with standard normal distributions are squared and summed.

When items are classified according to two or more criteria, it is often of interest to decide whether these criteria act independently of one another.

Statistic
X1 = sigma (Oi-Ei)^2/Ei

Oi are the observed values and Ei are the expected values according to some hypothesis, then X1 ~ chi-square. The statistic X1 is known as a goodness of fit statistic, and has n-1 degrees of freedom (df) if no parameters are estimated from the observed data.

http://67.159.209.94/Courses/Genetics_and_statistics.doc
http://67.159.209.94/Courses/Statistics_and_math_notation.doc

Pearson's chi-squared is used to assess two types of comparison: tests of goodness of fit and tests of independence.

• A test of goodness of fit establishes whether or not an observed frequency distribution differs from a theoretical distribution.
• A test of independence assesses whether paired observations on two variables, expressed in a contingency table, are independent of each other—for example, whether people from different regions differ in the frequency with which they report that they support a political candidate.

http://en.wikipedia.org/wiki/Pearson%27s_chi-squared_test

Use Fisher's exact test for smaller contingency tables
http://en.wikipedia.org/wiki/Fisher%27s_exact_test

So in Fisher's original example, one criterion of classification could be whether milk or tea was put in the cup first; the other could be whether Dr Bristol thinks that the milk or tea was put in first. We want to know whether these two classifications are associated – that is, whether Dr Bristol really can tell whether milk or tea was poured in first.
To determine if the distribution of differentially expressed genes across the functional groups within each taxonomy differs significantly from the distribution of detected genes, the sum of the χ² distances between the two distributions was calculated and compared with the sums calculated for 10,000 sets of genes randomly selected from all genes with detectable expression. According to this criterion, all three taxonomies were significantly changed (p < 0.0001).

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509255/?tool=pubmed


Applied Statistics for Bioinformatics using R
Wim P. Krijnen
November 10, 2009

Example 2. In the year 1866 Mendel observed in large number of exper-
iments frequencies of characteristics of different kinds of seed and their off-
spring. In particular, this yielded the frequencies 5474, 1850 the seed shape



of ornamental sweet peas. A crossing of B and b yields off spring BB, Bb and
bb with probability 0.25, 0.50, 0.25. Since Mendel could not distinguish Bb
from BB, his observations theoretically occur with probability 0.75 (BB and
Bb) and 0.25 (bb). To test the null hypothesis H0 : (π1 , π2 ) = (0.75, 0.25)
against H1 : (π1 , π2 ) = (0.75, 0.25), we use the chi-squared test6 , as follows.
> pi <- c(0.75,0.25)
> x <-c(5474, 1850)
> chisq.test(x, p=pi)

Chi-squared test for given probabilities

data: x

X-squared = 0.2629, df = 1, p-value = 0.6081

From the p-value 0.6081, we do not reject the null hypothesis.

Stars and feet

"Keep your eyes on the stars and your feet on the ground."

Convert gene IDs between different species

http://bogdan.org.ua/2010/10/27/batch-retrieve-entrezgene-homologs-using-ncbi-homologene-and-r.html

1. Install the annotationTools R package:
source(“http://bioconductor.org/biocLite.R”)
biocLite(“annotationTools”)
2. Download full HomoloGene data file from ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current
3. library(annotationTools)
4. homologene = read.delim(“homologene.data”, header=FALSE)
5. mygenes = read.table(“file with one entrez ID of the source organism per line.txt”)
6. getHOMOLOG(unlist(mygenes), taxonomy_ID_of_target_organism, homologene) [alternatively, wrap the call to getHOMOLOG into unlist to get a vector]


##get mouse (species ID 10090) orthologs of several human (species ID 9606)

Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)

http://bib.oxfordjournals.org/content/13/1/83.full

Abstract

The receiver operating characteristic (ROC) has emerged as the gold standard for assessing and comparing the performance of classifiers in a wide range of disciplines including the life sciences. ROC curves are frequently summarized in a single scalar, the area under the curve (AUC). This article discusses the caveats and pitfalls of ROC analysis in clinical microarray research, particularly in relation to (i) the interpretation of AUC (especially a value close to 0.5); (ii) model comparisons based on AUC; (iii) the differences between ranking and classification; (iv) effects due to multiple hypotheses testing; (v) the importance of confidence intervals for AUC; and (vi) the choice of the appropriate performance metric. With a discussion of illustrative examples and concrete real-world studies, this article highlights critical misconceptions that can profoundly impact the conclusions about the observed performance.

ROC analysis measures a model's ability to rank positive and negative cases relative to each other.


http://rss.acs.unt.edu/Rdoc/library/verification/html/roc.plot.html

a<- c(0,0,0,1,1,1,0,1,1,0,0,0,0,1,1) b<- c(.8, .8, 0, 1,1,.6, .4, .8, 0, 0, .2, 0, 0, 1,1) c<- c(.928,.576, .008, .944, .832, .816, .136, .584, .032, .016, .28, .024, 0, .984, .952) A<- data.frame(a,b,c) names(A)<- c("event", "p1", "p2") http://www.inmet.gov.br/documentos/cursoI_INMET_IRI/Climate_Information_Course/References/Mason%2BGraham_2002.pdf

Tools for managing and analyzing microarray data

http://bib.oxfordjournals.org/content/13/1/46.abstract?etoc

Tools for managing and analyzing microarray data

Abstract

The microarray-based analysis of gene expression has become a workhorse for biomedical research. Managing the amount and diversity of data that such experiments produce is a task that must be supported by appropriate software tools, which led to the creation of literally hundreds of systems. In consequence, choosing the right tool for a given project is difficult even for the expert. We report on the results of a survey encompassing 78 of such tools, of which 22 were inspected in detail and seven were tested hands-on. We report on our experiences with a focus on completeness of functionality, ease-of-use, and necessary effort for installation and maintenance. Thereby, our survey provides a valuable guideline for any project considering the use of a microarray data management system. It reveals which tasks are covered by mature tools and also shows that important requirements, especially in the area of integrated analysis of different experimental data, are not yet met satisfyingly by existing systems.

Challenges in translational research

http://www.nature.com/news/last-minute-wins-for-us-science-1.9696?WT.ec_id=NATUREjobs-20120105


Bill tops up health, energy and translational-science spending.

http://en.wikipedia.org/wiki/Translational_research

Challenges in translational research

To flourish translational research requires a knowledge-driven ecosystem, in which constituents generate, contribute, manage and analyze data available from all parts of the landscape. The goal is a continuous feedback loop to accelerate the translation of data into knowledge. Collaboration, data sharing, data integration and standards are integral. Only by seamlessly structuring and integrating these data types will the complex and underlying causes and outcomes of illness be revealed, and effective prevention, early detection and personalized treatments be realized.

Translational research requires that information and data flow from hospitals, clinics and participants of studies in an organized and structured format to repositories and research-based facilities and laboratories. Furthermore, the scale, scope and multi-disciplinary approach that translational research requires means a new level of operations management capabilities within and across studies, repositories and laboratories. Meeting the increased operational requirements of larger studies, with ever increasing specimen counts, larger and more complex systems biology data sets, and government regulations, precipitates an informatics approach that enables the integration of both operational capabilities and clinical and basic data. Most informatics systems in use today are inadequate in terms of handling the tasks of complicated operations and contextually in data management and analysis.

Finding what you need

"A man travels the world over in search of what he needs, and returns home to find it."

--George Moore

Is it old age or Alzheimer’s? Study alarms health-care experts

http://www.thestar.com/article/1110158--is-it-old-age-or-alzheimer-s-study-alarms-health-care-experts

According to Alzheimer Society statistics, the economic costs of dementia in Canada will increase tenfold by 2038, from the current $15 billion to $153 billion a year.

“Early diagnosis also enables us to monitor changes in the patient so that medication, if appropriate, can be started earlier instead of later,” Lemire adds. “It is possible to live with this disease and have a reasonable quality of life, if detected in the early stages.”

Video captures a fish mimicking a mimic octopus that mimics fish

http://www.csmonitor.com/Science/2012/0105/Video-captures-a-fish-mimicking-a-mimic-octopus-that-mimics-fish

mimic octopus (Thaumoctopus mimicus)- impersonate toxic lionfish, flatfish
jawfish (Stalix histrio) - fish mimicking

Avoiding kids' "self-entitlement" mentality

http://www.news1130.com/news/national/article/316078--avoiding-kids-self-entitlement-mentality#Comments

--parenting expert Christie Barnes

"It ends up in college, with college graduates refusing to take an entry-level job because of these false rewards given to them all along the way," she adds.

Her 12 New Year's resolutions for kids (she suggests choosing one each month):

1) Helping around the house is a normal necessity (like eating and sleeping). I just have to do it because it needs to be done without a reward. College kids complain when their clothes don’t automatically pick themselves up. No one will be there to give them a cookie for cleaning when they grow up. Some kids have never spent a night away from home until college because of worried, doting parents.

2) I will not force my parents to bribe me to do things I know I should do. Ask them to help make the list with you and get the items so they are involved and not just passive, bored observers.

3) If I do something good, I should have a reward but not money or extravagant presents. If your child does help, get good grades (or at least works hard) allow them some free time or some special time with you. You could even break your one-hour of TV or computer time on a school night as long as they are on track. Just don’t offer money and things.

4) I do not deserve to cut the line at the front when I am late because I am wonderful, my parents tell me that. Yes, your child is wonderful but you need to teach your child to respect others. Some parents encourage grab-all-you-can-get and encourage anything from cutting in line to cheating to get ahead. One mom had so little respect for others that she demanded that her teen daughter cut the 12-person long Starbucks line because “she is so beautiful and she is late for school.” Then don’t get Starbucks…

5) I won’t be the best at everything. I will be good at some things and not others and I will recognize that. Parents, please instill realistic self-esteem. Some things will be harder for your children than others. A stocky kid may be great at wrestling or football but not basketball. We are all born with different strengths that we can play to.

6) I won’t quit something I like doing because I am not the best. (For example, girls who don’t win the top awards are prone to give up hobbies they like, like painting, swimming, gymnastics, music because they feel they failed if they weren’t first.)

7) I do not need a reward for a grocery store trip. Parents, don’t give in.

8) I do not need something from the gift shop for every trip to the zoo or theme park. It can be as hard for a parent as a kid to pass up that huge-eyed stuffed baby tiger from the zoo gift shop

9) I do not need to be praised every time I do something good. I know it myself when I am happy and it makes me happy. As an adult, we are not praised for everything we do right on the job. Young adults often have a hard time with this. Some think of quitting a job because they aren’t praised and cannot tell from within themselves that they are doing well by accomplishing tasks.

10) Sometimes a science expert is needed, sometimes a math one, or a cook, or an artist. I will be the best I can be at my specialty and I won’t beat myself up that I can’t succeed at everything. Parents tell their kids they can do or be anything. Kids have many options but they really can’t be and do everything.

11) If I work as hard as I can, I still probably won’t be the best in the world. That sounds cruel but only one person can be the best quarterback in the world, or the best lawyer, or the best top model. Or just a few will achieve the heights of fame and wealth. Don’t shatter dreams by creating false ones. Focus on the process, the journey and not a destination that is probably unrealistic. If your child does become a Hollywood superstar, that is the icing on the cake; he or she needs to just enjoy the acting work along the way.

12) I will take an entry level job at no pay. Graduates today have lost the concept of starting at the bottom and working their way up.

365 days: Images of the year

http://www.nature.com/news/365-days-images-of-the-year-1.9620?WT.ec_id=NEWS-20120103

CELLULAR CHRISTMAS
Donna Stolz created a festive wreath by assembling images of mammalian cells from more than 25 experiments. The picture adorned her Christmas card last year and won recognition for the University of Pittsburgh biologist in the 2011 Nikon Small World photography contest.

D. STOLZ/Univ. Pittsburgh/Nikon Small World

BeadArray Expression Analysis Using Bioconductor

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002276

Abstract Top

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered.

A Tale of Two Stories: Astrocyte Regulation of Synaptic Depression and Facilitation

Synaptic plasticity is the capacity of a preexisting connection between two neurons to change in strength as a function of neuronal activity. Because it admittedly underlies learning and memory, the elucidation of its constituting mechanisms is of crucial importance in many aspects of normal and pathological brain function. Short-term presynaptic plasticity refers to changes occurring over short time scales (milliseconds to seconds) that are mediated by frequency-dependent modifications of the amount of neurotransmitter released by presynaptic stimulation. Recent experiments have reported that glial cells, especially hippocampal astrocytes, can modulate short-term plasticity, but the mechanism of such modulation is poorly understood. Here, we explore a plausible form of modulation of short-term plasticity by astrocytes using a biophysically realistic computational model. Our analysis indicates that astrocytes could simultaneously affect synaptic release in two ways. First, they either decrease or increase the overall synaptic release of neurotransmitter. Second, for stimuli that are delivered as pairs within short intervals, they systematically increase or decrease the synaptic response to the second one. Hence, our model suggests that astrocytes could transiently trigger switches between paired-pulse depression and facilitation. This property explains several challenging experimental observations and has a deep impact on our understanding of synaptic information transfer.

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002293

BioGPS: A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.

http://biogps.org/#goto=welcome

BioGPS: A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.

Su Lab

http://sulab.org/research/

Our lab’s activities can be broadly separated into two categories: creating tools to accelerate biomedical research, and direct engagement in biomedical discovery.

Tools. Figuring out how to harness the collective efforts of the biology community is the primary emphasis of the biomedical tools that we build. These “community intelligence” initiatives have the potential to scale with the explosive growth of data generation in sciencie. For more details, read about the Gene Wiki and BioGPS.

Biomedical discovery. Our group embraces the data mining challenges that have resulted from high-throughput biology. We have many past and ongoing research projects that span multiple disease areas, from immunology to metabolism to neurobiology. These projects are based on high-throughput transcriptomics, sequencing, genotyping, and phenotyping.

Flash cards and learning www.funnelbrain.com

www.funnelbrain.com

FunnelBrain gives you and your friends a new way to learn. You can form study teams, play games, take quizzes, and show off your intellectual prowess. It's fun, it's free and you'll do better in class. Check it out...

The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Search&doptcmdl=Citation&defaultField=Title%20Word&term=Shannon[author]%20AND%20The%20Gaggle%3A%20an%20open-source%20software%20system%20for%20integrating%20bioinformatics%20software%20and%20data%20sources.

Abstract
BACKGROUND:

Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing.
RESULTS:

In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools.
CONCLUSION:

We have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found at http://gaggle.systemsbiology.net.

Rare diseases

http://www.socialstyrelsen.se/rarediseases

In the database for rare diseases of the Swedish National Board of Health and Welfare you can find information about diseases or disorders which affect fewer than 100 people per million, and which lead to a marked degree of disability.

Human genetics: Genomes on prescription

http://www.nature.com/news/2011/111005/full/478022a.html

As prices fall further, some say that prescribing a genome sequence or analysis will become akin to requesting a magnetic resonance imaging (MRI) scan. "It's just like any other test in medicine. There's nothing remotely special about it," says David Bick, a clinical geneticist at the Medical College of Wisconsin in Milwaukee. But, he adds, "people will cry and scream and yell about that statement". That's true: unlike the results of most medical tests, a genome sequence provides a vast amount of difficult-to-interpret data, not all of which will be necessary for diagnosing or treating the patient's condition and which could provide unwanted clues to future health risks.

they identified a mutation on the X chromosome in a gene called X-linked inhibitor of Apoptosis, or XIAP (ref. 3). A deficiency of the protein encoded by this gene is known to put patients at high risk for a deadly immune-cell disorder,
http://www.nature.com/news/2011/111005/full/478022a.html#B3

Nature 365 days: 2011 in review

http://www.nature.com/news/365-days-2011-in-review-1.9684?WT.ec_id=NEWS-20120103

Cell signalling caught in the act

http://www.nature.com/news/2011/110719/full/475273a.html

The structure of this complex could finally reveal how one of biology's most important signalling mechanisms, G-protein-coupled receptors (GPCRs), do their job. This structure, published online in Nature1 by a team led by Kobilka at Stanford University in California and Roger Sunahara at the University of Michigan in Ann Arbor, now reveals the complete three-dimensional atomic structure of an activated GPCR — the β2 adrenergic receptor (β2AR) — in a complex with its G protein.

GPCRs sit in the membranes of cells throughout the body, where they detect signals from the outside world — such as light, odours and flavours — and signals from within the body, such as hormones and neurotransmitters. These signals are transmitted to the inside of the cell where they activate intracellular G proteins, which then trigger a variety of biochemical pathways.

The β2AR is activated by the hormones adrenaline and noradrenaline, and kicks off the body's fight-or-flight response by speeding up the heart and opening airways. It is a key target for anti-asthma drugs. Kobilka's X-ray crystallographic snapshot of β2AR associated with its G protein reveals some surprises, and could help in the design of more effective medicines — GPCRs are targeted by between one-third and one-half of all drugs on the market, including most of the best-sellers.

communicating your work is essential

"However, the best advice I can
probably give you is that if you feel the reviewers didn't understand your
work, it is most likely because you didn't explain it as well as you
should. If you feel the reviewers did not understand the significance or
coolness of your work, it is most likely because you failed to communicate
it. The one big lesson I hope you get from this is that communicating your
work is essential. People with good communication skills have a far higher
chance of succeeding in industry, business and/or academia. " --
Nando, cpsc540

Flexible, foldable, actively multiplexed, high-density electrode array for mapping brain activity in vivo

http://www.nature.com/neuro/journal/v14/n12/full/nn.2973.html

Arrays of electrodes for recording and stimulating the brain are used throughout clinical medicine and basic neuroscience research, yet are unable to sample large areas of the brain while maintaining high spatial resolution because of the need to individually wire each passive sensor at the electrode-tissue interface. To overcome this constraint, we developed new devices that integrate ultrathin and flexible silicon nanomembrane transistors into the electrode array, enabling new dense arrays of thousands of amplified and multiplexed sensors that are connected using fewer wires. We used this system to record spatial properties of cat brain activity in vivo, including sleep spindles, single-trial visual evoked responses and electrographic seizures. We found that seizures may manifest as recurrent spiral waves that propagate in the neocortex. The developments reported here herald a new generation of diagnostic and therapeutic brain-machine interface devices.

Democrat vs Republican

http://www.diffen.com/difference/Democrat_vs_Republican

Obama is a democrat (social)
Bush is a republican (individual, corporate)

Differences in Philosophy

While there may be several differences in opinion between individual Democrats and Republicans on certain issues, what follows is a generalization of their stand on several of these issues. A Democrat is typically known as a supporter of a broader range of social services in America than those advocated by Republicans. Republican philosophy is based on a limited influence of government and a dominant foreign policy.

Republicans are considered on the "right" end of the political spectrum while Democrats are on the "left." The far right generally is pro-religion, anti-bureaucracy, pro-military, pro-business and pro-personal responsibility.

Republicans, are usually considered conservative (fiscally as well as socially), maybe a little pious, pro-business and against the bureaucracy often associated with big government. They see big governments as wasteful and an obstacle to getting things done. Their approach is Darwinian in that the strong shall survive, cream rises to the top, etc.

To the far left of the spectrum are the extreme liberal, or the most extreme democrats. Democrats are considered more liberal. Democrats tend to favor an active role for government in society and believe that such involvement – be it environmental regulations against polluting or anti-discrimination laws – can improve the quality of people’s lives and help achieve the larger goals of opportunity and equality. On the other hand, Republicans tend to favor a limited role for government in society and believe that such reliance on the private sector (businesses and individuals) – be it avoiding unnecessary environmental regulations or heavy-handed anti-discrimination laws – can improve economic productivity and help achieve the larger goals of freedom and self-reliance

365 days: Nature's 10 - Ten people who mattered this year.

http://www.nature.com/news/365-days-nature-s-10-1.9678

Dario Autiero: Relativity challenger
Sara Seager: Planet seeker
Lisa Jackson: Pollution cop
Essam Sharaf: Science revolutionary
Diederik Stapel: Fallen star (fraudulent research, a psychologist from Tilburg University in the Netherlands) (as well as Marc Hauser, Harvard, evolutionary psychologist)
Rosie Redfield: Critical enquirer (Canadian microbiologist) "a propensity to say what was on her mind"
Danica May Comacho: Child of the times (7-billionth baby) in the Philippines
Mike Lamont: The Higgs mechanic
Tatsuhiko Kodama: Fukushima's gadfly (gadfly: a fly that annoys horses and other livestock)
John Rogers: Tech exec

perseverance

"You've got to say, I think that if I keep working at this and want it badly enough I can have it. It's called perseverance."

Functional Genomics Laboratory: Gingeras Group

http://gingeraslab.cshl.edu/

Expression and Proliferation Program. We are located in the Genome Center on the Woodbury campus. Our laboratory employs empirical and computational approaches to study the organization of information found within genomes and the roles non-protein coding RNAs assume both as part of the informational content and regulation of the protein coding content. Central to these studies is the analysis of the transcriptional content expressed by cells (transcriptomes) and the epigenetic marks found on both genomes and chromatin that influence the expression levels and timing of transcriptomes. These studies require whole genome analyses using high density microarray and deep nucleotide sequencing. The generation of such very large sets has prompted us to develop and to utilize novel computational tools: to store, to analyze, to curate, to graphically display and to make these data sets available for the scientific community.

Electrical 'deep brain' depression treatment safe, effective: Research

An experimental treatment first performed in Canada that uses electrical currents to reset the brain can ease the torment of treatment-resistant depression for at least two years, new research suggests.

http://www.vancouversun.com/health/Electrical+deep+brain+depression+treatment+safe+effective+Research/5936610/story.html