n0b3l1a

Metagenomics - a guide from sampling to data analysis

2012-02-14T09:52:00.001-08:00

http://www.microbialinformaticsj.com/content/2/1/3/abstract

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.

Nervous tissue

2012-02-13T16:58:00.001-08:00

http://faculty.rmc.edu/aconway/public_html/BIOL%20432%20HO%20Nervous%20Tissue.pdf

supporting cells (glia) are small relative to neurons

Doctor's practice

2012-02-13T09:46:00.001-08:00

"Isn't it a bit unnerving that doctors call what they do "practice"?"
--George Carlin

2010 Large-scale Applied Research Project Competition

2012-02-10T14:42:00.000-08:00

www.genomebc.ca/index.php/download_file/view/607/909

BrainStars

2012-02-07T11:25:00.000-08:00

http://brainstars.org/supplement/

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions.

For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2).

These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database.

Takeya Kasukawa*, Koh-hei Masumoto*, Itoshi Nikaido*, Mamoru Nagano, Kenichiro D. Uno, Kaori Tsujino, Carina Hanashima, Yasufumi Shigeyoshi, and Hiroki R. Ueda: Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain, PLoS ONE 6(8), e23228, 2011. (Journal page) ( doi:10.1371/journal.pone.0023228) *equally contributed

Understanding the Human Brain

2012-02-07T10:45:00.000-08:00

http://www.sciencemag.org/content/334/6056/567.full

The human brain contains an estimated 86 billion neurons and an equal number of glial cells. The complete structure of the enormously simpler 302-neuron network of the nematode worm Caenorhabditis elegans was published in 1986.

Although expensive bets are being placed on explaining the diversity of human behavior and mental disorders with genetic polymorphisms, gene mutations, and chromosomal rearrangements, the results so far have been modest

The Society for Neuroscience, which convenes its annual meeting next week, will soon launch BrainFacts.org, a reliable source of information about the brain. In-depth interviews with neuroscientists can be found online at thesciencenetwork.org.

ssh / sftp rsa public key

2012-02-07T10:00:00.000-08:00

~/.ssh/config

Host hostworld
Port 22
User username
HostName hostname.world.ca

$ ssh hostworld

$ ssh-keygen
# just hit enter on passphrase

$ scp .ssh/id_rsa.pub hostworld:~

$ ssh hostworld

$ cat id_rsa.pub >> .ssh/authorized_keys

sftp://hostworld/home/username

sftp://username@hostname.world.ca:22/home/username

Diseases caused by mutations that causes repeat expansion in non-coding regions

2012-02-06T09:51:00.000-08:00

Mutations that causes repeat expansion in non-coding regions contribute to neurogenerative diseases such as fragile X syndrome (OMIM #300624) and myotonic dystrophy (OMIM #160900).

.0004 FRAGILE X MENTAL RETARDATION SYNDROME
FRAGILE X TREMOR/ATAXIA SYNDROME, INCLUDED
PREMATURE OVARIAN FAILURE 1, INCLUDED

FMR1, (CGG)n EXPANSION

Kremer et al. (1991) demonstrated that the presence of an unstable expanded trinucleotide repeat sequence, designated p(CCG)n, in the 5-prime untranslated region of the FMR1 gene is the basis of fragile X syndrome (300624). The authors showed that normal X chromosomes have about 40 +/- 25 copies of p(CCG)n and that within these limits the sequence is a stable DNA polymorphism. The fragile X genotype was characterized by an increased amount of unstable DNA that maps to the repeat. The mutation causing fragile X syndrome contains over 200 CCG repeats (Devys et al., 1992).

myotonic dystrophy (OMIM #160900)

A number sign (#) is used with this entry because myotonic dystrophy-1 (DM1) is caused by a heterozygous trinucleotide repeat expansion (CTG)n in the 3-prime untranslated region of the dystrophia myotonica protein kinase gene (DMPK; 605377) on chromosome 19q13.

A repeat length exceeding 50 CTG repeats is pathogenic (Musova et al., 2009).

http://www.junkdna.com/junkdna_diseases.html

Statistical Approaches to RNA Secondary Structure Prediction and Applications

2012-02-06T08:49:00.000-08:00

Title: Statistical Approaches to RNA Secondary Structure Prediction and Applications
Speaker: Ye Ding
Wadsworth Center, New York State Department of Health

Abstract

Abstract: RNAs are versatile regulators of gene expression. RNA secondary structures are known to be important for regulatory functions by various types of RNAs. An RNA molecule, particularly a long-chain mRNA, may have a population of structures in the cell. Furthermore, multiple structures have been demonstrated to play important functional roles. Thus a representation of the ensemble of probable structures is of interest. We developed a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures, and introduced the notion of centroid structures as a new class of structure predictors. These approaches can overcome inherent limitations in conventional algorithms and are the bases for our Sfold RNA folding program (http://sfold.wadsworth.org).

MicroRNAs are small non-coding RNAs that repress protein synthesis by binding to target mRNAs in multicellular eukaryotes. Target identification of microRNA targets is essential to fully understand this new dimension of the complex gene regulatory networks. By employing a two-step model for modeling microRNA:target hybridization, we found that target secondary structure has a major impact on target recognition by microRNAs. Based on analyses of large microRNA targeting data using the model parameters and other sequence and conservation features, we have recently developed a novel computational framework that offers major improvement over established algorithms for prediction of microRNA targets. Computational tools are available through Sfold web server.

http://www.cs.ubc.ca/labs/beta/Courses/BioinfoReadingGroup/winter2011/07Feb2012.html

not really protein structure but mRNA structure ...

Far away friend

2012-02-06T08:45:00.001-08:00

"A friend who is far away is sometimes much nearer than one who is at hand. Is not the mountain far more awe-inspiring and more clearly visible to one passing through the valley than to those who inhabit the mountain?"
--Khalil Gibran

Remote control (slide changer) for Powerpoint or for OpenOffice

2012-02-05T19:20:00.002-08:00

PowerPoint OpenOffice Remote

http://www.vrallev.net/do/apps/android/pptodp_remote/instruction

http://www.vrallev.net/do/download?path=dropbox__ppt_odp_remote&file=PowerPointOpenOfficeRemote_PC_v3.0.0.jar (14 MB)

basically,
1. Download the PC and Android App
2. Run PC App with jar -jar PowerPointOpenOfficeRemote_PC_v3.0.0.jar
3. Run the Android App and read the IP address
4. Enter the IP address in the PC app
5. Open your PowerPoint presentation in full screen, already presenting, don't close, switch back to the PC app
6. Enter the number of slides
7. Connect
8. 'Start Presentation' on your phone

You can toggle buttons in the phone to see back/forward buttons, or just tap on your phone to advance, swipe left to right to go back

dislikes
- large jar file, needs java
- play on watching videos?
- mess up with animations
- setup can be tricky
- the screenshots on the phone doesn't look right, they just look like the desktop for all of them but not important (on linux, openoffice)

Other remote PC apps
http://slodive.com/freebies/android-remote-desktop-apps/ android-vnc-viewer
https://help.ubuntu.com/community/VNC/Servers go to System > Preferences > Remote Desktop

possible issues with these:
- time-outs / disconnects
- hard issue a left arrow key command without a trackball on your phone --> You can actually use the volume button on your phone for this!

Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life

2012-02-05T17:36:00.001-08:00

http://bib.oxfordjournals.org.proxy.lib.sfu.ca/content/early/2012/02/03/bib.bbr080.abstract

This article reviews recent advances in ‘microbiome studies’: molecular, statistical and graphical techniques to explore and quantify how microbial organisms affect our environments and ourselves given recent increases in sequencing technology. Microbiome studies are moving beyond mere inventories of specific ecosystems to quantifications of community diversity and descriptions of their ecological function. We review the last 24 months of progress in this sort of research, and anticipate where the next 2 years will take us. We hope that bioinformaticians will find this a helpful springboard for new collaborations with microbiologists.

Conditional Random Fields applied to protein fold recognition

2012-02-04T08:27:00.000-08:00

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.394

CRFs are “undirected” graphical models (also known as random fields, as opposed to directed graphical models such as HMMs) to compute the conditional likelihood P (y|x) directly.

Protein folds are frequent arrangement pattern of several secondary structure elements: some elements
are quite conserved in sequences or prefer a specific length, while others might form hydrogen bonds with
each other, such as two β-strands in a parallel β-sheet. To model the protein fold better, it would be natural
to think of each secondary structure element as one observation, corresponding to one node in the graph,
and the edges between elements as indicating their interactions in 3-D. Then, given a protein sequence,
we can search for the best segmentation defined by the graph and determine whether the protein adopts
the fold or not.

Mouse atlas

2012-02-03T21:44:00.001-08:00

http://mouse.brain-map.org/iav/atlas#plate=100960301&atlas=1&structure=961

Synapses, Receptor Cells, and Brain

2012-02-03T14:59:00.001-08:00

http://www.bem.fi/book/05/05.htm

Immunology

2012-02-03T14:39:00.000-08:00

http://www.microbiology.ubc.ca/system/files/MICB%20302%20-%20Immunology.pdf

Learning objectives: By the end of the course, you should be able to:
1. Identify the major mechanisms (inflammatory responses, cytotoxic T cells, antibodies) by which
immune cells protect us from different types of pathogens (viruses, extracellular bacteria,
intravesicular bacteria, parasites) or from cancer cells.
2. Understand how immune cells detect the presence of pathogens and cancer cells (pattern
recognition receptors, antigen receptors, antigen presentation pathways, NK cell receptors).
3. Describe processes that lead to the elimination of pathogens (e.g. opsonization, phagocytosis,
neutralization, complement activation, cell-mediated cytotoxicity).
4. Describe the structure and function of key molecules that mediate immune responses including
antibodies, antigen receptors, Toll-like receptors, MHC proteins, cytokines, chemokines.
5. Describe the main cell types of the immune system including their development, function, and for lymphocytes, how they generate antigen receptors.
6. Describe how defects in immune cell regulation can lead to immunodeficiency diseases or
autoimmune diseases.
7. Describe the topics of current immunological interest including vaccines, immune tolerance,
allergies, and transplantation.
8. Describe the basis for and application of current experimental approaches in immunology
including flow cytometry, monoclonal antibodies, immunofluorescence, knockout and transgenic
mice, adoptive transfer of immune cells, and gene expression profiling.
9. Relate processes that occur in immune cells to similar processes that occur in all cell types and which have been described in previous cell biology courses (e.g. mRNA splicing, protein
secretion, receptor signaling).

http://www.microbiology.ubc.ca/Murphy

Gastrointestinal flora and gastrointestinal status in children with autism -- comparisons to typical children and correlation with autism severity

2012-02-03T14:08:00.000-08:00

http://www.biomedcentral.com/1471-230X/11/22

Abstract

Background

Children with autism have often been reported to have gastrointestinal problems that are more frequent and more severe than in children from the general population.

Methods

Gastrointestinal flora and gastrointestinal status were assessed from stool samples of 58 children with Autism Spectrum Disorders (ASD) and 39 healthy typical children of similar ages. Stool testing included bacterial and yeast culture tests, lysozyme, lactoferrin, secretory IgA, elastase, digestion markers, short chain fatty acids (SCFA's), pH, and blood presence. Gastrointestinal symptoms were assessed with a modified six-item GI Severity Index (6-GSI) questionnaire, and autistic symptoms were assessed with the Autism Treatment Evaluation Checklist (ATEC).

Results

Gastrointestinal symptoms (assessed by the 6-GSI) were strongly correlated with the severity of autism (assessed by the ATEC), (r = 0.59, p < 0.001). Children with 6-GSI scores above 3 had much higher ATEC Total scores than those with 6-GSI-scores of 3 or lower (81.5 +/- 28 vs. 49.0 +/- 21, p = 0.00002).

Children with autism had much lower levels of total short chain fatty acids (-27%, p = 0.00002), including lower levels of acetate, proprionate, and valerate; this difference was greater in the children with autism taking probiotics, but also significant in those not taking probiotics. Children with autism had lower levels of species of Bifidobacter (-43%, p = 0.002) and higher levels of species of Lactobacillus (+100%, p = 0.00002), but similar levels of other bacteria and yeast using standard culture growth-based techniques. Lysozyme was somewhat lower in children with autism (-27%, p = 0.04), possibly associated with probiotic usage. Other markers of digestive function were similar in both groups.

Conclusions

The strong correlation of gastrointestinal symptoms with autism severity indicates that children with more severe autism are likely to have more severe gastrointestinal symptoms and vice versa. It is possible that autism symptoms are exacerbated or even partially due to the underlying gastrointestinal problems. The low level of SCFA's was partly associated with increased probiotic use, and probably partly due to either lower production (less sacchrolytic fermentation by beneficial bacteria and/or lower intake of soluble fiber) and/or greater absorption into the body (due to longer transit time and/or increased gut permeability).

Due to antibiotics used to treat ASD?
Oral antibiotics were primarily used for treating otitis media (ear infections), which may suggest an impaired immune system. Commonly used oral antibiotics eliminate almost all of the normal gut microbiota, which play an important role in the breakdown of plant polysaccharides, promoting gastrointestinal motility, maintaining water balance, producing some vitamins, and competing against pathogenic bacteria. Loss of normal gut flora can result in the overgrowth of pathogenic flora, which can in turn cause constipation and other problems.

Science is refinement thinking

2012-02-02T10:18:00.001-08:00

"The whole of science is nothing more than a refinement of everyday thinking."
--Albert Einstein

Roche takeover bid poses challenge to Illumina

2012-02-02T10:07:00.001-08:00

http://www.nature.com/news/roche-takeover-bid-poses-challenge-to-illumina-1.9928?WT.ec_id=NATUREjobs-20111219

A merger could stifle innovation, say observers.

for US$5.7 billion

Covariance vs Correlation

2012-02-01T10:33:00.000-08:00

http://www.riskglossary.com/link/correlation.htm

The covariance is defined by the expectation

where and are the means of and .

The correlation is defined as

where and are the standard deviations of and .

The Cell Biology of Synaptic Plasticity

2012-02-01T09:53:00.000-08:00

http://www.sciencemag.org/content/334/6056/623.full

Synaptic plasticity is the experience-dependent change in connectivity between neurons that is believed to underlie learning and memory. Here, we discuss the cellular and molecular processes that are altered when a neuron responds to external stimuli, and how these alterations lead to an increase or decrease in synaptic connectivity. Modification of synaptic components and changes in gene expression are necessary for many forms of plasticity. We focus on excitatory neurons in the mammalian hippocampus, one of the best-studied model systems of learning-related plasticity.

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

2012-01-31T10:54:00.000-08:00

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

2012-01-31T10:15:00.001-08:00

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

2012-01-30T08:42:00.000-08:00

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

2012-01-27T13:50:00.001-08:00

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

2012-01-27T11:04:00.001-08:00

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)inputvenn(input)

Become wealthy

2012-01-27T10:49:00.000-08:00

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

Enterpreneurship

2012-01-26T21:01:00.000-08:00

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/

2012-01-24T10:17:00.000-08:00

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

2012-01-23T11:26:00.001-08:00

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

Peace

2012-01-23T11:02:00.000-08:00

"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

2012-01-20T14:36:00.000-08:00

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

2012-01-20T13:39:00.001-08:00

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

2012-01-20T13:13:00.001-08:00

Full name
Linda Lanyon
Affiliation
INCF Secretariat

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

age of conquerors tips and hotkeys

2012-01-20T11:46:00.000-08:00

* 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

Praise the bridge

2012-01-20T10:48:00.001-08:00

"Praise the bridge that carried you over."

Brain viewers

2012-01-19T16:50:00.000-08:00

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/

encephalization

2012-01-19T16:15:00.001-08:00

"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

2012-01-17T10:13:00.000-08:00

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

2012-01-17T10:07:00.001-08:00

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

2012-01-17T10:03:00.001-08:00

"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

2012-01-16T20:39:00.001-08:00

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

2012-01-16T18:31:00.000-08:00

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

2012-01-16T10:59:00.001-08:00

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

2012-01-16T10:21:00.001-08:00

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

2012-01-16T08:42:00.001-08:00

"In ourselves are triumph and defeat."

You can -- Henry Ford

2012-01-16T08:38:00.001-08:00

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

Viral miRNA

2012-01-16T08:34:00.001-08:00

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

2012-01-14T12:13:00.001-08:00

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

2012-01-11T11:51:00.000-08:00

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

2012-01-11T10:11:00.000-08:00

* 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

2012-01-11T09:56:00.000-08:00

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

branched DNA and Affymetrix QuantiGene

2012-01-10T13:48:00.000-08:00

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

2012-01-10T11:43:00.000-08:00

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

2012-01-10T11:15:00.000-08:00

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

2012-01-10T10:58:00.000-08:00

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

2012-01-09T15:32:00.000-08:00

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

2012-01-09T11:00:00.000-08:00

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

Stars and feet

2012-01-06T09:13:00.001-08:00

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

Convert gene IDs between different species

2012-01-05T13:59:00.000-08:00

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)

2012-01-05T10:54:00.001-08:00

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

2012-01-05T10:41:00.000-08:00

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

2012-01-05T10:32:00.000-08:00

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

2012-01-05T10:13:00.001-08:00

"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

2012-01-05T10:04:00.000-08:00

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

2012-01-05T10:00:00.000-08:00

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

2012-01-04T10:30:00.000-08:00

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

2012-01-03T16:14:00.001-08:00

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

2012-01-03T15:57:00.000-08:00

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

2012-01-03T15:47:00.001-08:00

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.

2012-01-03T15:28:00.001-08:00

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

2012-01-03T15:25:00.000-08:00

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

2012-01-03T15:00:00.000-08:00

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.

2012-01-03T14:56:00.001-08:00

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

2012-01-03T14:35:00.000-08:00

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

2012-01-03T14:18:00.001-08:00

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

2012-01-03T13:43:00.001-08:00

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

Cell signalling caught in the act

2012-01-03T13:22:00.000-08:00

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

2012-01-03T12:57:00.000-08:00

"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

2012-01-03T12:52:00.001-08:00

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

2012-01-03T11:46:00.000-08:00

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.

2012-01-03T11:27:00.000-08:00

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

2012-01-03T10:52:00.001-08:00

"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

2012-01-03T10:41:00.000-08:00

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

2012-01-03T10:33:00.001-08:00

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

Disconnect

2011-12-31T18:22:00.001-08:00

https://addons.mozilla.org/en-US/firefox/addon/disconnect/

Google Disconnect

Facebook Disconnect

Stop major third parties from tracking the webpages you go to (built with WebMynd).

Viber

2011-12-31T18:12:00.001-08:00

http://www.viber.com/

http://lifehacker.com/5706423/viber-makes-free-iphone-calls-over-3g-and-wi+fi

https://addons.mozilla.org/en-US/firefox/addon/disconnect/

When you use Viber, your phone calls and text messages to any other Viber users are free! The sound quality is also much better than a regular call.

50 Things Women Wish Men Knew

2011-12-30T14:15:00.001-08:00

50 Things Women Wish Men Knew
By: Lisa Jones

http://www.menshealth.com/mhlists/what_women_want_from_men/What_She_Wishes_You_Knew_50.php?page=5

Words with a Q not followed by a U

2011-12-29T17:56:00.000-08:00

qaid
quintar
quindar
qoph
qiviut

http://www.scrabble.org.au/words/ulessq.htm

Words with a Q not followed by a U

2-letter Words
QI

3-letter Words
QAT QIS SUQ

4-letter Words
QADI QAID QATS QOPH SUQS WAQF

5-letter Words
BURQA FAQIR NIQAB QADIS QAIDS QIBLA QOPHS QORMA TALAQ TRANQ UMIAQ WAQFS

6-letter Words
BURQAS BUQSHA FAQIRS NIQABS QABALA QANATS QASIDA QAWWAL QIBLAS QIGONG
QINDAR QINTAR QIVIUT QORMAS QWERTY SHEQEL TALAQS TRANQS UMIAQS YAQONA

7-letter Words
BUQSHAS INQILAB QABALAH QABALAS QASIDAS QAWWALI QAWWALS QIGONGS
QINDARS QINTARS QIVIUTS QWERTYS SHEQELS TSADDIQ TZADDIQ YAQONAS

8-Letter Words
INQILABS MBAQANGA MUQADDAM QABALAHS QAIMAQAM QALAMDAN
QAWWALIS QINDARKA QWERTIES SHEQALIM TSADDIQS TZADDIQS

9-letter Words
MBAQANGAS MUQADDAMS QABALISM QABALIST QAIMAQAMS QALAMDANS QINGHAOSU
TSADDIQIM TZADDIQIM

Statistical analysis of co-expression properties of sets of genes in the mouse brain

2011-12-29T16:37:00.001-08:00

Statistical analysis of co-expression properties of sets of genes in
the mouse brain

http://arxiv.org/abs/1111.6200

A cell-type based model explaining co-expression patterns of genes in the brain
Pascal Grange, Jason Bohland, Hemant Bokil, Sacha Nelson, Benjamin Okaty, Ken Sugino, Lydia Ng, Michael Hawrylycz, Partha P. Mitra

http://arxiv.org/abs/1111.6217

Virtual Windows system + ITunes.

2011-12-29T08:29:00.001-08:00

Virtual Windows system + ITunes.

I installed virtualbox 4 and set up a Windows XP. To use the USB drivers I installed the Oracle Expansion Pack. The Licence changes from OSE (Open Source Edition) to PUEL (Personal Use and Evaluation License).

Plugin the Ipod to your Ubuntu System. Start the VM with Windows and Itunes. Under "Devices" in the Virtual Box select your ipod nano. Windows and Itunes will find it.

I also shared my music-library with a virtualbox shared folder and mountet it under windows.

This works for me but I am unhappy with the situation too.

http://askubuntu.com/questions/26353/how-can-i-sync-with-an-ipod-nano-6g

Spotify
http://www.engadget.com/2011/05/04/spotify-launches-download-service-with-ipod-sync-puts-itunes-on/

PlayOnLinux (Wine frontend) > Multimedia > Spotify
http://www.makeuseof.com/tag/spotifys-free-version-working-linux/

VirtualBox windows on Ubuntu
http://www.blog.arun-prabha.com/2007/05/07/installing-virtualbox-and-windows-using-virtualbox-in-ubuntu/

A handle on neurodegenerative disease complexity

2011-12-28T10:01:00.000-08:00

http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1847.html?WT.ec_id=NMETH-201201

Erika Pastrana

Nature Methods
doi:10.1038/nmeth.1847

Published online
28 December 2011

Combining experiments and calculations makes it possible to measure the prognostic value of toxic protein species in the cell.

It is still not clear though, whether these aggregates are toxic to the cell or whether they represent a way for the cell to cope with the misfolded mutant proteins. Mutant Htt proteins are continuously shifting from one conformation to another, and it is unclear which of the conformational states (or protein species) exist at a given time in the cell and to what extent each of them contributes to the cell's degeneration.

These are not easy questions to address, and as Steven Finkbeiner and his team at the University of California, San Francisco, noted, methods for such investigations have been lacking. To date, a lot of work has focused on looking at aggregation of purified proteins in a test tube. However, “the environment in which proteins fold and misfold inside cells is very different from the one in vitro,” says Finkbeiner. The group set out to develop new tools and methods that would enable labeling the different protein species of Htt that exist in situ and estimating the pathogenic contribution of each of them.

Brain scarring may help explain obesity battle, study finds

2011-12-28T09:10:00.001-08:00

http://www.montrealgazette.com/health/Brain+scarring+help+explain+obesity+battle+study+finds/5916860/story.html

Scientists are linking obesity with inflammation and scarring in the key brain area that controls weight, which could explain why it's so hard to lose weight and keep it off.

When researchers switched mice and rats genetically bred to become obese from low-fat chow to high-fat and highly palatable chow, they began showing signs of inflammation in the hypothalamus within 24 hours.

The hypothalamus takes signals from body fat and other tissues that tell the brain we need food or we've had enough. It also regulates how much fat we burn.

"We saw direct evidence of neuron injury and, ultimately, after months on the diet, a loss of neurons in this hypothalamic area that's vital for body weight control," said lead researcher Dr. Michael Schwartz, professor of medicine and director of the Diabetes and Obesity Center of Excellence at the University of Washington, Seattle.

talkatone

2011-12-23T09:14:00.001-08:00

http://www.talkatone.com/faq.html

Free voice and text using Wifi or 3G

Power of Love

2011-12-22T09:04:00.001-08:00

"Whenever you are confronted with an opponent, conquer him with love."

ANOVA

2011-12-21T08:47:00.001-08:00

http://www.gardenersown.co.uk/Education/Lectures/R/anova.htm#anova

http://www.personality-project.org/r/r.anova.html

A special case of the linear model is the situation where the predictor variables are categorical. In psychological research this usually reflects experimental design where the independent variables are multiple levels of some experimental manipulation (e.g., drug administration, recall instructions, etc.)

The first 5 examples are adapted from the guide to S+ developed by TAs for Roger Ratcliff. For more detail on data entry consult that guide. The last three examples discuss how to reorganize the data from a standard data frame into one appropriate for within subject analyses. For this discussion, I assume that appropriate data files have been created in a text editor and saved in a subjects x variables table.

Microarray data analysis

2011-12-20T23:31:00.000-08:00

http://discover.nci.nih.gov/microarrayAnalysis/Exploratory.Analysis.jsp

Exploratory Analysis
Pattern-Finding
Exploratory analysis aims to find patterns in the data that aren’t predicted by the experimenter’s current knowledge or pre-conceptions. Some typical goals are to identify groups of genes expression patterns across samples are closely related; or to find unknown subgroups among samples. A useful first step in all analyses is to identify outliers among samples – those that appear suspiciously far from others in their group. To address these questions, researchers have turned to methods such as cluster analysis, and principal components analysis, although these have often been used inappropriately.
The first widely publicized microarray studies aimed to find uncharacterised genes, which act at specific points during the cell cycle. Clustering is the natural first step in doing this. Unfortunately many people got the impression that clustering is the 'right' thing to do with microarray data; the confusion has been perpetuated, since many software packages have catered to this impression. The proper way to analyze data is the way that addresses the goal at which the study was aimed. Clustering is a useful exploratory technique for suggesting resemblances among groups of genes, but it’s not a way of identifying the differentially regulated genes in an experimental study.

The Virtual Fly Brain Browser and Query Interface.

2011-12-20T11:02:00.001-08:00

www.virtualflybrain.org

Bioinformatics. 2011 Dec 16. [Epub ahead of print]
The Virtual Fly Brain Browser and Query Interface.
Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD.
Source

School of Informatics, University of Edinburgh, UK.
Abstract
MOTIVATION:

Sources of neuroscience data in Drosophila are diverse and disparate making integrated search and retrieval difficult. A major obstacle to this is the lack of a comprehensive and logically structured anatomical framework and an intuitive interface.
RESULTS:

We present an online resource that provides a convenient way to study and query fly brain anatomy, expression and genetic data. We extended the newly developed BrainName nomenclature for the adult fly brain into a logically structured ontology that relates a comprehensive set of published neuron classes to the brain regions they innervate. The Virtual Fly Brain interface allows users to explore the structure of the Drosophila brain by browsing 3D images of a brain with sub-regions displayed as coloured overlays. An integrated query mechanism allows complex searches of underlying anatomy, cells, expression and other data from community databases.
AVAILABILITY:

Virtual Fly Brain is freely available on-line at www.virtualflybrain.org.

Extraordinary

2011-12-20T07:56:00.001-08:00

"I can't believe that God put us on this earth to be ordinary." -- Lou Holtz

polypyrimidine tract

2011-12-19T20:59:00.000-08:00

The polypyrimidine tract is a region of messenger RNA (mRNA) that promotes the assembly of the spliceosome, the protein complex specialized for carrying out RNA splicing during the process of post-transcriptional modification. The region is rich with pyrimidine nucleotides, especially uracil, and is usually 15-20 base pairs long, located about 5-40 base pairs before the 3' end of the intron to be spliced.[1]

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