BioResource

http://www.stemdb.org/bioresources/index.htm

BioResource Index is an index of commonly used bioinformatics and systems biology databases and software tools. The index covers resources for the analysis of high-throughput genetic, transcriptional, sequence analysis and proteomic profiling. BioResource Index was developed as part of the StemDB database project, funded by the EU FP7 project Eurosystem.

Zeitgeist -- spirit of times

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

Ten Simple Rules for Getting Help from Online Scientific Communities

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

Questioning -- Albert Einstein

“The important thing is not to stop questioning. Curiosity has its own reason for existing”
-Albert Einstein

Live each day as the Last

"Live not one's life as though one had a thousand years, but live each day as the last."

Marcus Aurelius Antoninus

Mouse brain preparation - Mouse Brain Library

Mouse brain preparation - Mouse Brain Library
http://www.mbl.org/tutorials/MBLTrainingManual/index.html

Hit F3 in Ubuntu Nautilus to get a side-by-side file explorer window

Hit F3 in Ubuntu Nautilus to get a side-by-side file explorer window

Writing bad news

http://www.google.com/url?sa=t&source=web&cd=14&ved=0CDEQFjADOAo&url=http%3A%2F%2Femedia.leeward.hawaii.edu%2Fhurley%2Fmodules%2Fmod3%2F3_docs%2Fbadnews.pdf&rct=j&q=telling%20your%20referees%20that%20you%20didn%27t%20get%20the%20scholarship%20or%20the%20job&ei=SlSDTrm1I-nUiAK3ha38DA&usg=AFQjCNHrd3hqDd3uLz7ZHyvtaSqFQ8H4wQ&sig2=3Of3LDwnjmFlQh9skd8H-A&cad=rja

Keep it positive, praise, understanding

Do
Please clarify your request.

Don't
Your request doesn't make any sense.

SADI Semantic Web Services

Semantic Web workshop reading materials
http://sadiframework.org/training/WS2/readingmaterial.html

Dream and Painting

"I dream my painting and then paint my dream."
--

Van Gogh

ImageJ

http://rsbweb.nih.gov/ij/docs/intro.html

Hundreds of plugins, for segmentation, region of interest (ROI) thresholding, cell counting

http://132.187.25.13/home/?category=Download&page=SegmentationEditor

http://rsb.info.nih.gov/ij/plugins/index.html

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

It does geometric transformations such as scaling, rotation and flips. Image can be zoomed up to 32:1 and down to 1:32. All analysis and processing functions are available at any magnification factor. The program supports any number of windows (images) simultaneously, limited only by available memory.

Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.

Intro to neurons

http://www.mind.ilstu.edu/curriculum/neurons_intro/neurons_intro.php

Rose and name

What's in a name? That which we call a rose
By any other name would smell as sweet.
~William Shakespeare, Romeo and Juliet

BCIC New Ventures Competition

http://www.newventuresbc.com/about-nvbc/

The BCIC-New Ventures competition was founded in 2000 under the direction of Wal van Lierop as a means of recognizing and encouraging entrepreneurship in B.C.’s technology sector. The first board included representation from both public and private organizations, and many of the founding organizations and key individuals from the original group have provided continuous support to the competition.

However, it’s not only the winners of the competition who go on to success. Many finalists and round-three competitors use the skills they have learned in the competition to commercialize their business ideas.

Amazon Kindle e-Reader Hacks

http://ireaderreview.com/2008/09/23/top-19-amazon-kindle-tips-do-you-get-the-most-out-of-your-kindle/

Another tip you might want to add is how to access websites that Kindle may not work with nicely (such as a site with lots of frames). A way around this is to go through a mobile proxy site. I use one at http://mowser.com/ and it works well for the Kindle.

- free 3g
- long battery life
- good on the sign
- plays mp3
- light

- but cracks easily
- no color
- can be slow to load
- hard to type

Grand challenges in bioinformatics and computational biology

http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2011.00060/full#B3

profile quantitatively the amounts, activities, spatial locations, and movements of many molecules inside the cells, as well as register multiple parameters describing the whole cells and cell populations

Dating with your brain: Five tips from a neurophysiologist

http://www.sunherald.com/2011/09/22/3452300/dating-with-your-brain-five-tips.html

2. For the guys: Appeal to a woman's brain

"There are key differences in the way sexes choose partners, obviously, and this is because the female and male brains are just wired differently...although this isn't always black and white but rather a continuum. In general men are mostly visual, whereas women are 'cerebral' for a better way of putting it. They require more than just visual stimulation to be attracted to someone."

Funny and smart will get you pretty far with the ladies. It's science!

13 Most Overused Resume Phrases

http://www.careerbuilder.ca/Article/CB-283-Resumes-and-Cover-Letters-13-Most-Overused-R%C3%A9sum%C3%A9-Phrases/?sc_extcmp=cbca_9283&cblang=CAEnglish&SiteId=cbca_9283

Cliché No. 1: "Strong communication, customer service and organizational skills."
Let Sweeney rephrase that: Possess strong communication, customer service and organizational skills, which increased customer satisfaction from 85% to 98% and realized 100% on-time delivery of assigned projects.*

Cliché No. 7: "Team player."
Let Sweeney rephrase that: Possess strong commitment to team environment dynamics with the ability to contribute expertise and follow leadership directives at appropriate times.

hmm ... will these be the next cliche?

Roots and Wings

“Good parents,” Jonas Salk once told me, “give their children roots and wings. Roots to know where home is, wings to fly away and exercise what's been taught them.”

Chicken Soup for the Soul

results in research only begets for more questions

results in research only begets for more questions

Neurological disorder

http://www.ninds.nih.gov/disorders/disorder_index.htm

Translational bioinformatics

2011 AMIA Summit on Translational Bioinformatics

http://jointsummits2011.amia.org/TBI/overview

Exponentially growing biological and bioinformatics data sets present a challenge and an opportunity for researchers to contribute to the understanding of the genetic basis of phenotypes. Due to breakthroughs in microarray technology, it is possible to simultaneously monitor the expressions of thousands of genes, and it is imperative that researchers have access to the clinical data to understand the genetics and proteomics

of the diseased tissue. This technology could be a landmark in personalized medicine, which will provide storage for clinical and genetic data in electronic health records (EHRs). In this paper, we explore the computational and ethical challenges that emanate from the intersection of bioinformatics and healthcare informatics research. We describe the current situation of the EHR and its capabilities to store clinical and genetic data and then discuss the Genetic Information Nondiscrimination Act. Finally, we posit that the synergy obtained from the collaborative efforts between the genomics, clinical, and healthcare disciplines has potential to enhance and promote faster and more advanced breakthroughs in healthcare.

http://perspectives.ahima.org/index.php?option=com_content&view=article&id=166:translational-bioinformatics-and-healthcare-informatics-computational-and-ethical-challenges&catid=42:electronic-records&Itemid=88

MRI Research Demonstrates ALS Attacks Multiple Parts of the Brain

http://www.sciencedaily.com/releases/2011/09/110916131252.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29

Recently published studies by a researcher in the Faculty of Medicine & Dentistry demonstrate that ALS -- known as Lou Gehrig's disease -- damages neurons in parts of the brain responsible for cognition and behaviour.

Kalra uses magnetic resonance imaging (MRI) not to just look at pictures of the brain, but also as a means of measuring the levels of various chemicals in the brain. In his most recently published paper, he looked at two different chemicals called NAA and mIns. NAA is known as a neural marker, which means it is only found in neurons, while levels of mIns increase when there is abnormal scarring in the brain.

His paper published in early 2011 looked at decreasing levels of NAA in the cingulate cortex -- the first time MRI had been used to measure chemicals in this region of the brain in ALS. And his most recently published paper, which came out late this summer, was the first to demonstrate that NAA was decreasing and mIns was increasing in the frontal lobe, even when there weren't signs of cognitive or behavioural issues in patients. The frontal lobe is considered the hub for cognition and behaviour in the brain.

N. Sudharshan, C. Hanstock, B. Hui, T. Pyra, W. Johnston, S. Kalra. Degeneration of the Mid-Cingulate Cortex in Amyotrophic Lateral Sclerosis Detected In Vivo with MR Spectroscopy. American Journal of Neuroradiology, 2010; 32 (2): 403 DOI: 10.3174/ajnr.A2289

Gamers Succeed Where Scientists Fail: Molecular Structure of Retrovirus Enzyme Solved, Doors Open to New AIDS Drug Design

www.sciencedaily.com/releases/2011/09/110918144955.htm

Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. The gamers achieved their discovery by playing Foldit, an online game that allows players to collaborate and compete in predicting the structure of protein molecules.

This class of enzymes, called retroviral proteases, has a critical role in how the AIDS virus matures and proliferates. Intensive research is under way to try to find anti-AIDS drugs that can block these enzymes, but efforts were hampered by not knowing exactly what the retroviral protease molecule looks like.

Firas Khatib, Frank DiMaio, Seth Cooper, Maciej Kazmierczyk, Miroslaw Gilski, Szymon Krzywda, Helena Zabranska, Iva Pichova, James Thompson, Zoran Popović, Mariusz Jaskolski, David Baker. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural & Molecular Biology, 2011; DOI: 10.1038/nsmb.2119

Society for Neuroscience (SFN)

http://www.sfn.org/index.aspx?pagename=brainfacts

Laugh and people

"A laugh is the shortest distance between two people."


-- Victor Borge

Options for collaborating with LaTeX

http://tex.stackexchange.com/questions/4489/what-is-a-good-strategy-for-obtaining-comments-on-a-latex-document-from-non-latex
http://stackoverflow.com/questions/539791/tips-for-collaboratively-editing-a-latex-document
http://luca.cse.ucsc.edu/Style_guidelines_for_student_co-authors

- use latex2rtf to export it to an rtf file which can be opened in word
- export to PDF and have the PDF edited using Acrobat Pro
- add line numbers, manual e-mail of revisions

both will need some manual editing to apply changes back to latex :(

- or do everything in word first, then make the final submission in latex?

latent semantic indexing

latent semantic indexing (lsi) - SVD can be used to cluster documents and carry out information retrieval by using concepts instead of exact word-matching

data encoded in term-frequency matrix (TF)

encode documents to search in a matrix: rows=words, columns=documents, cells=# of words in that document

create a query as a Nx1 vector (N words, mark 1 for matching row index -- word must be in vocabulary), 1 document query

then compare this vector against other documents in the term-frequency matrix to find the document most relevant, use dot product to compare because this avoids the scale problem with finding the euclidean distance

normalization

also, to avoid searching for words that are useless or occur everywhere, eg. "the", use the term frequency:
 total # of times w appears in d / total number of words in d

inverse document frequency:
  idf = log (D / (1+Dw))        D:# of documents in corpus, Dw:# of documents the word appears in

Your Silence Is Hurting Your Company

And here's the cost to our silence — when issues stay unaddressed, stagnant, broken — we all fail. We ship bad products, our brand suffers, and our company performance plummets. In general, things suck. Not just for "them" but for all of "us." The cost of silence is suck-ness.

When we are silent, we are hurting the outcome. You see, minority viewpoints have been proven to aid the quality of decision making in juries, by teams and for the purpose of innovation. Research proves then even when the different points of view are wrong, they cause people to think better, to create more solutions and to improve the creativity of problem solving.

And so here's the opportunity to avoid suck-ness, and the thing I've learned along the way to speak your truth without losing your job. Rather than saying, "This is the problem" which can risk looking the fool and quite possibly pissing someone off, ask this: "Could it be ...that this is the problem?"

"Could it be" is a conversation starter, rather than an assertion. It is the way you put it out there without having to defend it. Could it be allows the issue to be a question for everyone. Could it be allows for a dialogue exchange rather than a yes/no argument.

Could it be....you're ready to speak up?

http://blogs.hbr.org/cs/2011/09/your_silence_is_hurting_your_company.html?utm_source=twitterfeed&utm_medium=twitter

Defend your project / thesis

Need to learn how to defend your project / thesis.

First, if someone hands you a problem, you won't feel that it is yours, you won't have that possessiveness that makes you want to work on it, defend it, fight for it, and make it come out beautifully

Write a Proposal and Get It Criticized.

http://www.yale.edu/eeb/stearns/advice.htm

curiosity vs real investigation

"Physiological experiment on animals is justifiable for real investigation, but not for mere damnable and detestable curiosity."


-- Charles Darwin

The Synaptic Organization of the Brain

The Synaptic Organization of the Brain

Gordon M. Shepherd

details for each brain region, cell populations, cell proportions, brain wiring

Eyes of Love

http://www.chickensoup.com/newsletter.asp?newsid=article-daily-110914&utm_source=CSS_Email&utm_medium=Bulletin&utm_term=20110911&utm_content=1&utm_campaign=daily

Anyone who keeps the ability to see beauty never grows old.
~Franz Kafka

Thesis writing

Style Guides and Computer Tools

http://www.grad.ubc.ca/handbook-graduate-supervision/handbook-graduate-supervision

• Review the literature regularly and keep your literature survey up-to-date
• Maintain exemplary records of your experimental/theoretical work (so that others can replicate
• your results)
• While your supervisor is required to be reasonably available for consultation, it is you responsibility to keep in touch with your supervisor
• Make yourself available to your supervisor for regular meetings at mutually acceptable times
• Follow the university's policy regarding ownership of intellectual property
• "It’s all a matter of perspective. As a student you have little to no control over the administrative part of things, but on the flip side, if you take the time to get to know your administrators, things can be made a lot smoother, especially if someone in the office is willing to sign a form that is late."
• "Ultimately, you are responsible for yourself as a graduate student. It’s time to learn how to self-advocate."
• "Take care of your committee. It sounds corny, but if the student doesn’t care, the committee won’t. For example, set up meetings (time and agenda), give them plenty of information on what you are doing (progress reports), and remind them of past, present, and future important stuff."
• "Don’t expect your committee to care for your emotions. Their role is to put students to the test."
• "Other graduate students are your ticket to a healthy student life. They either have gone through it, are going through it, or will go through it. Sharing feelings and experiences will keep you sane."
• "It’s tough, yet rewarding at the same time, being a graduate student. There are a lot of us at UBC, so competition is high."
• "Be nice to librarians: they are a key resource as your research progresses. You may need their assistance not only during the literature review, but for data analysis, web searches, copyright issues."
• "Use your research to make contacts. Remember, you aren’t just conducting graduate research—you are also entering a field of colleagues."

http://www.grad.ubc.ca/current-students/dissertation-thesis-preparation/style-guides-computer-tools

http://www.grad.ubc.ca/current-students/dissertation-thesis-preparation/thesis-basics

http://www.grad.ubc.ca/current-students/dissertation-thesis-preparation/structure-masters-thesis

Seeing and Giants

If I have seen farther it is by standing on the shoulders of Giants.
— Sir Isaac Newton (1855)

Exome sequencing special issue Genome Biology

• 

  Next-generation human genetics

  Exome and genome sequencing are reshaping the landscape of human genetics; Jay Shendure discusses the lessons learnt and opportunities opened
  

  Genome Biology 2011, 12:408
• 

  Exome issue editorial

  Special Issues Editor, Hannah Stower, introduces Genome Biology's issue on exome sequencing
  

  Genome Biology 2011, 12:407
• 

  Unlocking Mendelian disease using exome sequencing

  In the past 2 years, exome sequencing has provided significant new insights into the causes of both Mendelian and sporadic genetic diseases
  

  Genome Biology 2011, 12:228
• 

  Exome sequencing

  Many computational and statistical methods are now available to narrow down causal variants in exome sequencing data, for both Mendelian and complex diseases
  

  Genome Biology 2011, 12:227
• 

  Exome sequencing: the expert view

  Three leaders in the field of exome sequencing discuss why the approach is so popular and how it is contributing to genomics
  

  Genome Biology 2011, 12:128
• 

  Population exomics and human evolution

  Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality
  

  Genome Biology 2011, 12:127
• 

  Hereditary hearing loss genes

  Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations
  

  Genome Biology 2011, 12:R89
• 

  Wheat exon capture

  Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
  

  Genome Biology 2011, 12:R88
• 

  Mouse exome capture

  In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains
  

  Genome Biology 2011, 12:R86
• 

  Exome linkage analysis

  A method for performing linkage analysis from exome sequencing variant data is presented
  

  Genome Biology 2011, 12:R85
• 

  Rare coding variants

  The 1000 Genomes Project presents exome sequence data for 1000 genes from 700 individuals, better defining low frequency variants
  

  Genome Biology 2011, 12:R84
• 

  The cost of sequencing

  The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
  

  Genome Biology 2011, 12:125

Be yourself -- Oscar Wilde

Be yourself; everyone else is already taken.

-- Oscar Wilde

Math tutorials -- linear algebra

Math tutorials

linear algebra , eigen vectors and eigen values

http://tutorial.math.lamar.edu/sitemap.aspx

SVD in Python

$ sudo apt-get install python-scipy python-matplotlib

from scipy import *
from pylab import *

# load img
img = imread('myimg.png')[:,:,0]
gray()
figure(1)
imshow(img)

# get A = U * S * Vt singular value decomposition
m,n = img.shape
U,S,Vt = svd(img)
S = resize(S,[m,1])*eye(m,n)

# get first 20 eigenvectors
k = 20
figure(2)
imshow(dot(U[:,1:k], dot(S[1:k,1:k], Vt[1:k,:])))
show()

http://www.cs.ubc.ca/~nando/540b-2011/lectures/l2.pdf

Wife -- Thomas Fuller

"Choose a wife by your ear than your eye."
--Thomas Fuller

Love and missing

Love is missing someone whenever you're apart, but somehow feeling warm inside because you're close in heart.
~Kay Knudsen

http://www.chickensoup.com/newsletter.asp?newsid=article-daily-110913&utm_source=CSS_Email&utm_medium=Bulletin&utm_term=20110911&utm_content=1&utm_campaign=daily

Well-known individuals with disabilities inspire readers

http://toolstolife.com/

http://www.delmarvanow.com/article/20110911/NEWS01/109110311/Well-known-individuals-disabilities-inspire-readers

A consistent routine is helpful.

Attitude is everything and I was determined to fight this thing and be optimistic about a cure someday.

Chicken Soup for the Soul

Chicken Soup for the Soul

Brain burdens

Nature 477, 132 (08 September 2011) doi:10.1038/477132a

Published online
07 September 2011

Europe's shocking statistics on neurological and mental disorders demand a shift in priorities.

http://www.nature.com/nature/journal/v477/n7363/full/477132a.html

List of Neuroscience databases

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

Informatics in neuroscience
http://bib.oxfordjournals.org/content/8/6/446.full

http://neuinfo.org/

Why should we hire you

Before answering questions like "Why should we hire you?" and "What accomplishment are you most proud of?" Click Here to prepare for these tough interview questions

Mahatma Gandhi - Mind and freedom

"You can chain me, you can torture me, you can even destroy this body, but you will never imprison my mind."
--Mahatma Gandhi

Newly identified gene mutation linked to Parkinson's

"This discovery provides direct evidence that Parkinson's may result from gene-environmental interactions," Farrer says. "The resulting impairment highlights neuronal recycling systems as a focal point in the effort to develop more effective drugs."

The mutation, EIF4G1, was found in a family from northern France that has a high rate of the disease – more than half of the members of each generation develop it.

http://www.eurekalert.org/pub_releases/2011-09/uobc-nig090711.php 

Cell type-specific gene expression differences in complex tissues

http://en.wikipedia.org/wiki/Deconvolution - recover signal from noise

so in this case, noise is because we mixed all the different cell types together and we can't tell which differential expression is from which cell type

www.nature.com/nmeth/journal/v7/n4/abs/nmeth.1439.html

Shai S Shen-Orr^1,2,10, Robert Tibshirani^3,4,10, Purvesh Khatri¹, Dale L Bodian^5,9, Frank Staedtler⁶, Nicholas M Perry⁷, Trevor Hastie^3,4, Minnie M Sarwal^1,2, Mark M Davis^2,8,10 & Atul J Butte^1,10

---

Abstract

We describe cell type–specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.

Nature Methods 7, 287 - 289 (2010)
Published online: 7 March 2010 | doi:10.1038/nmeth.1439


whole-blood cell types: lymphocytes, monocytes, neutrophils, eosinophils and basophils
two groups: 15 acute rejection of kidney, 9 stable after kidney transplant
cell type frequencies: from Coulter counter measurements used for complete blood counts

Probabilistic retrieval and visualization of biologically relevant microarray experiments

http://bioinformatics.oxfordjournals.org/content/25/12/i145.full

content based search instead of searching through annotations


so give gene expression data set instead of just typing words

Motivation: As ArrayExpress and other repositories of genome-wide experiments are reaching a mature size, it is becoming more meaningful to search for related experiments, given a particular study. We introduce methods that allow for the search to be based upon measurement data, instead of the more customary annotation data. The goal is to retrieve experiments in which the same biological processes are activated. This can be due either to experiments targeting the same biological question, or to as yet unknown relationships.

Results: We use a combination of existing and new probabilistic machine learning techniques to extract information about the biological processes differentially activated in each experiment, to retrieve earlier experiments where the same processes are activated and to visualize and interpret the retrieval results. Case studies on a subset of ArrayExpress show that, with a sufficient amount of data, our method indeed finds experiments relevant to particular biological questions. Results can be interpreted in terms of biological processes using the visualization techniques.

Availability: The code is available from http://www.cis.hut.fi/projects/mi/software/ismb09.

Contact: jose.caldas@tkk.fi


----------------------
http://www.biomedcentral.com/1471-2164/10/411

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

Conclusion

GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at http://cgs.pharm.kyoto-u.ac.jp/services/network webcite.

------------------------------

CellMontage: similar expression profile search server

Summary: The establishment and rapid expansion of microarray databases has created a need for new search tools. Here we present CellMontage, the first server for expression profile similarity search over a large database—69 000 microarray experiments derived from NCBI's; GEO site. CellMontage provides a novel, content-based search engine for accessing gene expression data. Microarray experiments with similar overall expression to a user-provided expression profile (e.g. microarray experiment) are computed and displayed—usually within 20 s. The core search engine software is downloadable from the site.

http://cellmontage.cbrc.jp


http://bioinformatics.oxfordjournals.org/content/23/22/3103.abstract

Job search no no's Job search no no’s: A check-list of the things candidates shouldn't be doing

http://www.workopolis.com/advice/article/854-job-search-no-no-s-a-check-list-of-the-things-candidates-shouldn-t-be-doing

Neurotransmitters

- excitatory - glutamate
- inhibitory - GABA (GABAergic)
- modulatory - dopamine (dopaminergic), acetylcholine (cholinergic)

Basal Ganglia

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

The main components of the basal ganglia are the striatum (also called neostriatum) composed of caudate and putamen, globus pallidus or pallidum composed of globus pallidus externa (GPe) and globus pallidus interna (GPi), substantia nigra composed of both substantia nigra pars compacta (SNc) and substantia nigra pars reticulata (SNr), and the subthalamic nucleus (STN).^[5]

caudate nucleus, putamen, and nucleus accumbens are very similar in their internal structure and are often referred together as the neostriatum and take up the most volume of the basal ganglia

The basal ganglia play a central role in a number of neurological conditions, including several movement disorders. The most notable are Parkinson's disease, which involves degeneration of the melanin-pigmented dopamine-producing cells in the substantia nigra pars compacta (SNc), and Huntington's disease, which primarily involves damage to the striatum.^[1][5]

The basal ganglia have a limbic sector whose components are assigned distinct names: the nucleus accumbens (NA), ventral pallidum, and ventral tegmental area (VTA). VTA efferents provide dopamine to the nucleus accumbens (ventral striatum) in the same way that the substantia nigra provides dopamine to the dorsal striatum. Because there is much evidence that it plays a central role in reward learning, the VTA→NA dopaminergic projection has attracted a great deal of attention. For example, a number of highly addictive drugs, including cocaine, amphetamines, and nicotine, are thought to work by increasing the efficacy of the VTA→NA dopamine signal. There is also evidence implicating overactivity of the VTA dopaminergic projection in schizophrenia.^[6]

Nervous system review

http://www.dmacc.edu/instructors/rbwollaston/Chapter_8_Nervous_System.htm

Discovery suggests way to block fetal brain damage produced by oxygen deprivation

Examining brain damage that occurs when fetuses in the womb are deprived of oxygen, researchers at The Scripps Research Institute have discovered that damage does not occur randomly but is linked to the specific action of a naturally occurring fatty molecule called LPA, acting through a receptor that transfers information into young brain cells.


—specifically, the receptor for the phospholipid molecule lysophosphatidic acid (LPA) 


What Chun and his colleagues found, however, is that hypoxia causes the neurons to become overstimulated, mimicking effects produced by excessive LPA exposure. Genetically removing the receptors for LPA or blocking them through drugs stopped these effects.


http://medicalxpress.com/news/2011-09-discovery-block-fetal-brain-oxygen.html

NeuronRegistry

http://pons.neurocommons.org/page/Working_Pages#Neuron_Registry_TF

This group is responsible for working with the Representation and deployment TF to put structure into place for a knowledge base of neuronal cell types, providing a formal means for describing and quantifying existing cell types from their properties, e.g., a cell registry, and populating it with information from the literature. This knowledge base will serve as a resource for comparing potentially new neuronal types with known types and for constructing statistical representations of neuronal cell types based on known instances. We will create conventions and specify tools to aid in naming new cell types based on defining characteristics. This group will examine and flesh out requirements and review what has already been done in related areas and based on this, determine what might be reused and identify what needs to be built in order to create this structure.

Neuron Registry TF
* Toward an Ontology for Neurons
* Neuron Registry Operating Principles
* Naming Convention
* Definitions
* Definition of Cell Type
* Neuron Registry Specifications
* Neuron Registry Template
* Neuron Registry Interface

Seattle shuttle bus

http://www.quickcoach.com/fares.htm

Work ethic: The 24/7 lab

Working weekends. Leaving at midnight. Friday evening meetings. Does science come out the winner?
Heidi Ledford

http://www.nature.com/news/2011/110831/full/477020a.html

Quiñones-Hinojosa — had no such qualms. His work ethic is no secret: a 2007 essay in the New England Journal of Medicine1 and several television and newspaper reports have traced his path from 19-year-old illegal immigrant from Mexico, labouring in the fields of California, to neurosurgeon at one of the United States' leading research hospitals. He did not get there by working 9 to 5.

Every so often, he asks a cancer patient or his or her family to join the lab meeting. It is a chance for the patients to learn about the research being done with their tumours. And for the lab, it is a reminder of the urgency of their work.

"When someone says 'I'm going to die in six months', it really hits them."

Quiñones-Hinojosa, though, says that he has nothing against holidays. "Vacations are great," he says. "Take a weekend off."

Human Subjects Training (PHRP course)

Protecting Human Research Participants (PHRP)

NIH's online version of human subjects training (PHRP Course). It can take as little as an hour to complete the training. It’s free & available online here:

http://phrp.nihtraining.com/users/login.php

GENSAT - Gene Expression Nervous System ATlas, Sense Lab

http://www.ncbi.nlm.nih.gov/gensat

GENSAT stands for Gene Expression Nervous System ATlas. The GENSAT project aims to map the expression of all genes expressed in the mouse brain at various stages of development. The project focuses on two techniques
Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in-situ hybridization.
Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene

The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques.

http://neuronbank.org
The NeuronBank Wiki is place for Neuroscientists to describe neurons and neural circuitry. It works like Wikipedia, in that all pages are available to be edited by registered users of NeuronBank. The ultimate goal is advance the field of Neuromics by creating an encyclopedia of neurons and neural circuitry.

http://senselab.med.yale.edu/NeuronDB/ndbCanExpl.aspx
Canonical neurons and their parts
The abbreviations for the canonical parts of a neuron are: D, dendrite; S, soma (cell body); AH, axon hillock-initial segment of the axon; A, axon; T, axon terminal.
The simplest case is a single dendrite, represented as an equivalent cylinder (e) consisting of a chain of three compartments, designated as (p) proximal, (m) middle, and (d) distal with respect to the cell body

Cells have various forms. eg. Nigral dopaminergic cell has Canonical form 3

ModelDB, models of a particular neuron, citations, etc.
http://senselab.med.yale.edu/ModelDB/FindByRegionList.asp

borad cell types: Neuron, glia, muscle, gland

Hotwire - Cheap discount travels, deals, hotels, car rentals, etc

Can't know exactly the details of the hotel before purchasing, but cheap, site looks credible enough

http://www.hotwire.com/deals/index.jsp

Courting connections

http://www.nature.com.proxy.lib.sfu.ca/naturejobs/2011/110825/full/nj7361-479a.html?WT.ec_id=NATUREjobs-20110901

The theme connecting these ideas is that the way to gain recognition as a scientist is to act like one. Although being in the lab or at your computer is necessary for your research project, budgeting time week-to-week to engage with the scientific community at home and on the outside is not a diversion but an essential activity, part of the life of every working scientist. It is also how you establish your own old boy network.

It is better to court invitations to apply for the research job you would like — and a successful courtship is not an overnight project.

The 6 Most Frequently Quoted Brain Facts (That Are Total BS) Read more: The 6 Most Frequently Quoted Brain Facts (That Are Total BS) | Cracked.com http://www.cracked.com/article_19370_the-6-most-frequently-quoted-brain-facts-that-are-total-bs_p2.html#ixzz1Wj9vJqvW

http://www.cracked.com/article_19370_the-6-most-frequently-quoted-brain-facts-that-are-total-bs_p2.html