Wednesday, February 29, 2012

Mining and integration of pathway diagrams from imaging data

http://bioinformatics.oxfordjournals.org/content/28/5/739.full

Abstract

Motivation: Pathway diagrams from PubMed and World Wide Web (WWW) contain valuable highly curated information difficult to reach without tools specifically designed and customized for the biological semantics and high-content density of the images. There is currently no search engine or tool that can analyze pathway images, extract their pathway components (molecules, genes, proteins, organelles, cells, organs, etc.) and indicate their relationships.
Results: Here, we describe a resource of pathway diagrams retrieved from article and web-page images through optical character recognition, in conjunction with data mining and data integration methods. The recognized pathways are integrated into the BiologicalNetworks research environment linking them to a wealth of data available in the BiologicalNetworks' knowledgebase, which integrates data from >100 public data sources and the biomedical literature. Multiple search and analytical tools are available that allow the recognized cellular pathways, molecular networks and cell/tissue/organ diagrams to be studied in the context of integrated knowledge, experimental data and the literature.
Availability: BiologicalNetworks software and the pathway repository are freely available at www.biologicalnetworks.org.
Supplementary information: Supplementary data are available at Bioinformatics online.
                   

The process of image recognition, data extraction and integration consists of several steps (Supplementary Fig. S1). First, objects and relations are extracted from the image, together with their coordinates. This is done using mathematical morphology and binary analysis routines of ImageJ (http://rsbweb.nih.gov/ij/). The image is transferred to binary gray-scale 32-bit RGB mode by applying a threshold adjustment with a Huang Filter. Special mathematical morphology ‘Opening’ after ‘Closing’ operations are applied to reduce the number of domains for recognition by removing areas that are too small. Finally, an ‘analyze particles’ procedure applied to the last image retrieves all possible candidates for nodes as objects represented by points of an enclosing polygon.
                    
Text recognition is done separately with preliminary image processing (Kou et al., 2007; Li et al., 2008). Cleaning non-textual elements using properties that characterize horizontal text objects, such as alignment, height–width ratio, character separation and connectedness, is performed. ‘Cognitive OpenOCR (Cuneiform)’ (http://en.openocr.org) software is used for batch image text recognition and ‘AutoIt v3’ (http://www.autoitscript.com) for automated batch operations. The scanning procedure is executed both horizontally and vertically to extract horizontal and vertical text.                    


The next step involves the extracted text, objects and relations being sent to the IntegromeDB (Baitaluk et al., 2010) (back-end database) data integration pipeline to check the consistency of the data (Supplementary Fig. S2 and Table S1). We check that all recognized objects are genes/proteins, processes, cell types, diseases or any other object type constituting BioNets ontology (Baitaluk et al., 2010; Kozhenkov et al., 2011) in our database. Recognized relations are compared with the existing (literature or pubic databases) interactions, reactions and relations integrated in the IntegromeDB from >100 of public databases. Only those recognized relations that are supported by at least one type of evidence from our integrated database are included in the final pathway.

We scanned a collection of >150 journals, 50 000 articles and ~25 000 figures available in PubMed Central and WWW through the Google Image service API by querying terms from Pathway Ontology (e.g. ‘Nicotine pathway’), Gene Ontology Biological Process (e.g. ‘molecular synthesis’), ‘$GeneName pathway’ (e.g. ‘NF-B pathway’), etc. After filtering out images not containing objects/relations, top 1012 pathway/network diagrams (richest in number of literature-supported relations) are stored on a remote server and the Lucene open-source search engine (http://lucene.apache.org) is used to index, retrieve and rank the image text descriptions (using the default statistical ranking). In case of publication, the image description is the image legend, whereas in the case of a web page, the specifically designed algorithm retrieves the most appropriate description from the web page text surrounding the image. Image publication date and source journal are stored as separate fields that can also be used to sort the results.                      

Google history

http://www.thestar.com/business/article/1138594--google-youtube-let-s-forgive-and-forget-how-to-purge-your-history-before-the-new-privacy-policy

https://www.google.com/history


 Go to https://www.youtube.com
  Login to your Google account
  Click your icon (in the upper right corner where your user name is)
  Click “Video Manager”
  Click “History” from the menu on the left
  Click “Clear all viewing history”
  Click “Pause all viewing history”
  Click “Search history” from the menu on the left
  Click “Clear all search history”
  Click “Pause all search history”

Alacrity Foundation

The Alacrity Foundation is devoted to advance the education of Entrepreneurship, Business and Management studies and practices. It provides an intensive training environment with mentors and industry partners to prepare graduates for entrepreneurship in the technology sector. The Alacrity Foundation model in Canada operates as a non-profit organization out of British Columbia.



Bioinformatics Graduate Diploma Program

http://students.sfu.ca/calendar/molecular-biology-and-biochemistry/bioinformatics-grad-dipl.html


Department of Molecular Biology and Biochemistry | Faculty of Science
Simon Fraser University Calendar 2012 Summer

The Department of Molecular Biology and Biochemistry and the School of Computing Science co-operate to offer this program which provides advanced education in bioinformatics for students with a bachelor’s degree in molecular biology, cell biology, biochemistry, computer science, mathematics, or related disciplines. Admission is highly competitive.
This program supports students sponsored by the Canadian Institutes of Health Research (CIHR) Bioinformatics in Health Science Training Grant in which Simon Fraser University is a full partner with the University of BC and the BC Genome Sciences Centre. Students who are not part of the program are strongly encouraged to choose their courses from those offered at Simon Fraser University.

Stones and mountains

"The man who removes a mountain begins by carrying away small stones."
--William Faulkner

Monday, February 27, 2012

Testing the ortholog conjecture with comparative functional genomic data from mammals.

http://www.ncbi.nlm.nih.gov/pubmed/21695233

A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the "ortholog conjecture"). Many methods used to computationally predict protein function are based on this assumption, even though it is largely untested. Here we present the first large-scale test of the ortholog conjecture using comparative functional genomic data from human and mouse. We use the experimentally derived functions of more than 8,900 genes, as well as an independent microarray dataset, to directly assess our ability to predict function using both orthologs and paralogs. Both datasets show that paralogs are often a much better predictor of function than are orthologs, even at lower sequence identities. Among paralogs, those found within the same species are consistently more functionally similar than those found in a different species. We also find that paralogous pairs residing on the same chromosome are more functionally similar than those on different chromosomes, perhaps due to higher levels of interlocus gene conversion between these pairs. In addition to offering implications for the computational prediction of protein function, our results shed light on the relationship between sequence divergence and functional divergence. We conclude that the most important factor in the evolution of function is not amino acid sequence, but rather the cellular context in which proteins act.

Feb. 29 - Rare disease day

http://www.novartis.com/

Thousands of disorders fit the definition of “orphan diseases” established by health authorities around the world. Each orphan condition is rare, affecting hundreds or thousands of people – a far cry from the millions of patients with hypertension or type 2 diabetes. The collective impact on public health is immense, however, and the vast majority of rare diseases still lack effective treatment options.

orphan drugs <- personalized medicine?


BPN 2012 - BioPartnering North America 2012

The following companies are registered to attend BPN 2012:

Company Name

Industry

Country

20/20: NSERC Ophthalmic Mat. Net.
3P Biopharmaceuticals, S.L.
A. Menarini I.F.R. Srl
AAIPharma Services
Abbott Biotech Ventures, Inc.
Abbott Laboratories
Accelerator Corporation
Accelerator Corporation
Actelion Pharmaceuticals Ltd.
Actelion Pharmaceuticals Ltd.
Actelion Pharmaceuticals Ltd.
Actlabs
Adimab, Inc.
Advanced Biopharma Consulting
Advenchen Laboratories, LLC
Affilogic
Akron Biotechnology, LLC
Alberta Innovates - Tech. Futures
Alberta Innovates - Tech. Futures
Alder BioPharmaceuticals, Inc.
Allergan, Inc.
Allphase Clinical Research Inc.
Alpha Cancer Technologies (ACT)
Alphora Research Inc.
Alsace BioValley
Alsace BioValley
Amicrobe
Amorfix Life Sciences Ltd.
AMRI
Amunix, Inc.
AnaptysBio, Inc.
Angelini
Apex Healthcare Consulting
Apoplogic Pharmaceuticals, LLC
Apotex Fermentation Inc.
Aptalis Pharmaceutical Technologies
Aquinox Pharmaceuticals Inc.
ARC Medical Devices
Areta International srl
Arete Strategies
Ariana Pharmaceuticals
Artenga Inc.
ASEBIO, Spanish Bioindustry Assn.
Aslan Pharmaceuticals
AstraZeneca
AstraZeneca
AstraZeneca
aTyr Pharma Inc.
Australian Research Network
Bayer HealthCare
Bayer HealthCare
BC Cancer Agency
BELTAS Clinical Research
Berkley Canada Inc.
BGL Group Inc./VeriScience
Bio Business Magazine
BioAlberta
BIOALTERNATIVES
BioCentury Publications, Inc.
Biocepta Corp.
BioEnsemble
Biominas Brasil
BioNova
BioPartner.co.uk
BioPharm Insight
Bio-Sino Biotech. & Science Inc.
Bio-Synectics Inc.
BioTalent Canada
BIOTECanada
Biotechnology Focus
Biothera
Boehringer Ingelheim
Bristol-Myers Squibb Co.
British Columbia Int'l Trade & Inv.
Business Devel. Bank of Canada
Business Wire
Cambridge Healthtech Institute
Campbell Alliance
Canadian Consulate General
Canadian Embassy
Canadian Embassy
Canadian Embassy
Canadian Embassy
Canadian Institutes of Health Res.
Caprion Proteomics, Inc.
Cardiome Pharma Corp.
Catalent Pharma Solutions, Inc.
Catalonia Competitiveness Agency
Ceapro Inc.
Celgene Corporation
Centre for Drug Research & Devel.
Charles River
Chelsea Therapeutics Inc.
ChemRoutes Corporation
China Nat'l Vaccine & Serum Inst.
Chiome Bioscience Inc.
Cipher Pharmaceuticals Limited
CiToxLAB North America
Clera Inc.
Clinical Network Services (CNS)
Cohiro
Contact Canada
Cooley LLP
Cornerstone Therapeutics Inc
Creative Antibiotics AB
Critical Outcome Technologies Inc.
CrystalGenomics, Inc.
CTI Life Sciences Fund
Current Partnering
Cyterion, Inc.
Cytochroma Inc.
Daebong LS, Ltd.
Dalton Pharma Services, Inc.
Del Mar Pharmaceuticals
Deloitte & Touche LLP
Deloitte Recap LLC
DepoMed, Inc.
DiaMedica Inc.
DLA Piper LLP
DLVR Therapeutics Inc.
Dr. Reddy's Laboratories Ltd
EastHORN Clinical Services in CEE
EastHORN Clinical Services in CEE
Echogen, Inc.
EMBLEM Tech Transfer
Emerald Biostructures
Emory University
enGene, Inc.
Enterprise Saskatchewan
Enzon Pharmaceuticals
ERA Consulting (UK) Ltd
Essa Pharma
EUCODIS Bioscience GmbH
EUCODIS Bioscience GmbH
Eurasante
EvaluatePharma
EVER Neuro Pharma
Everett Laboratories, Inc.
Ezose Sciences Inc.
Farris, Vaughan, Wills & Murphy
Ferrer Internacional SA
Fish & Richardson P.C.
Flamel Technologies S.A.
Foreign Affairs & Int'l Trade Canada
Forest Laboratories, Inc.
FreeMind Group
French Consulate
Fresenius Kabi Deutschl & GmbH
Galderma Laboratories, L.P.
Gebro Pharma
Genentech, Inc.
Genome BC
Genome Canada
Germany Trade & Invest
GlaxoSmithKline plc
Globe Laboratories Inc
Government of British Columbia
GP20
Groove BioPharma
GrĂ¼nenthal Central Europe GmbH
GVK Biosciences Private Limited
GVK Biosciences Private Limited
Han Wha Pharma Co., Ltd.
HanAll Biopharma Co., Ltd.
Horizon Discovery Ltd
Horizon Discovery Ltd
HungaroTrial CRO
Hutchison MediPharma Limited
iBio, Inc.
IE Singapore
Ie Sung International
Ikaria, Inc.
Indel Therapeutics Inc.
Industry Canada
Informa plc
Innovaro Pharmalicensing Ltd.
Insymbiosis
Intelligent Pharma
Intercell AG
Intercell AG
International Trade & Inv. Attraction
Intrexon Corporation
Invest in Western France
Isotechnika Inc.
Jamesway Incubator Co.
Japan Technology Group, Inc.
Japan Tobacco, Inc.
Jubilant Biosys
Kalexsyn, Inc.
KalGene Pharma Inc.
KaloBios, Inc.
Kane Biotech Inc.
KBI Biopharma, Inc.
KMT Hepatech Inc.
Korea B.C. Trade & Inv. Repr. Off.
Korea Prime Pharm Co., Ltd.
Kowa Research Institute, Inc.
Kyorin Pharmaceutical Co. Ltd
La Jolla Inst. for Allergy & Immun.
Laboratorios Bioprofarma
Landsteiner Scientific
Lanzhou Institute of Bio. Products
Lesley Phillips Services
Life Science Association of Manitoba
Life Sciences Ontario
LifeSciences British Columbia
Lilly Ventures
Linear Clinical Research Ltd
LMBRI, LLC
LPC Consulting International
Lumira Capital
Luye Pharma Group
MaRS Discovery District
Maxia Strategies, LLC
McGill University
MedGenesis Therapeutix Inc.
MedImmune, Inc
MEDUNIK
Medytox
Menarini Biotech Srl
MenoGeniX, Inc.
Merck
Merck
Meridian Life Science, Inc.
Merrill DataSite
Metabolys
Microbion Corporation
Micromyx, LLC
Min. of Econ. Dev. & Inno. - Ontario
Min. of Econ. Dev. & Trade - Ontario
Mirna Therapeutics Inc.
MPI Research
MRM Proteomics
MSI Methylation Sciences Inc.
Naegis Pharmaceuticals Inc.
National Cheng Kung University
National Research Council Canada
National University of Singapore
Natrix Separations
Navigen Pharmaceuticals
NDA Group
Nektar Therapeutics
Neurodyn Inc.
NeuroSearch A/S
NKT Therapeutics
North Carolina Canadian Office
Northern Lipids Inc.
NovAliX
Novartis International AG
Novartis International AG
Novo A/S
Novo Nordisk A/S
Novozymes Biopharma
NS Pharma, Inc.
Nucro-Technics Incorporated
Nycomed; a Takeda Company
OMT
Oncolytics Biotech Inc.
Oncomed Pharmaceuticals Inc
OncoSec Medical Incorporated
Ono Pharmaceutical Co. Ltd.
ORA, Inc.
Oragenics Inc
Organovo Inc.
Osteometabolix Pharmaceuticals Inc.
Owl Genomics
Oxford Expression Technologies Ltd
Oxford Pharmascience Group Plc
Paladin Labs Inc.
Pan-Provincial Vaccine Enterprise
Pendopharm, a div of Pharmascience
PeptiVir, Inc.
Pfenex Inc
Pfizer Inc
Pfizer Inc
PharmaEssentia Corp.
Pharmatek Laboratories, Inc.
PharmaVoice
PharmaWave Ltd
PhysioStim
Plant Advanced Technologies
PlantForm Corporation
PolyMedix Inc.
Polypeptide Group
PolyTherics Ltd
Presage Biosciences
Prestwick Chemical, Inc.
Priaxon AG
PricewaterhouseCoopers LLP
Prime Pharm Korea, Hanyang Univ.
Prince Edward Isl & BioAlliance
ProBioGen AG
ProImmune Ltd.
PROOF Centre of Excellence
Protagonist Therapeutics
Purdue Pharma
PX'Therapeutics
QLT Inc.
Qu Biologics
Rentschler Biotechnologie GmbH
RepliCel Life Sciences
Resolve Therapeutics
Resverlogix Corp.
Ribomed Biotechnologies, Inc.
Rick Hansen Institute
Ritter Pharmaceuticals Inc.
Rna Diagnostics Inc.
Roowin SA
S&oz GmbH
SAFC
Salient Pharmaceuticals Inc
Samedan Limited
Sanofi
Sanofi
Saskatchewan Research Council
Sernova Corp
SGS Life Science Services
Shanghai GuoChuang Pharmaceutical
Shire Pharmaceuticals Group Ltd.
Siegfried AG
Siena Biotech S.p.A.
Sigma-Aldrich Pty Ltd
SignalChem Lifesciences Corporation
Sihuan Pharma. Holdings Group
Sinoveda Canada Inc.
Sirona Biochem (TFChem)
SiteOne Therapeutics
Sprint Bioscience
StemCell Technologies
sterna biologicals
Stiris Research, Inc.
SuppreMol GmbH
Swedish Orphan Biovitrum AB
Synergy Pharmaceuticals, Inc.
Takeda Pharmaceutical Company
Takeda Ventures, Inc.
TapImmune Inc
Targacept, Inc.
TC Scientific Inc.
TDO, Provincial Health Serv. Auth.
TEC Edmonton
TetraQ
The Hos. for Sick Children Res. Inst.
The Jackson Laboratory
The Student Biotech. Network (SBN)
Theraclone Sciences
Therapure Biopharma Inc.
Thomson Reuters
TransTech Pharma, Inc.
Tzamal Bio Pharma Ltd
Tzamal Bio Pharma Ltd
Ubifrance /French Trade Commission
Unigene Laboratories Inc.
Union Korea Pharma
University of Alberta
University of British Columbia
University of Calgary
University of Manitoba
University of Saskatchewan
University of Waterloo
UVic Industry Partnerships
Ventria Bioscience
Ventures West Capital Ltd.
Verona Pharma plc
Vical Incorporated
Vifor Pharma Ltd
Viracor-IBT Laboratories
Vivalis
WBBA
Wiley-Blackwell
WRF Capital
Wuhan Institute of Bio. Products
WuXi AppTec Co., Ltd
Xediton Pharmaceuticals Inc
Xenon Pharmaceuticals Inc.
XenoPort, Inc.
Your Bio Team
Zalicus, Inc.
Zymeworks Inc.
Zyngenia, Inc.
ZZ Alztech
Academic
Contract Org.
Pharmaceutical
Contract Org.
Venture Capital
Pharmaceutical
Venture Capital
Biotechnology
Pharmaceutical
Pharmaceutical
Pharmaceutical
Service
Biotechnology
Service
Biotechnology
Biotechnology
Biotechnology
Contract Org.
Contract Org.
Biotechnology
Pharmaceutical
Contract Org.
Biotechnology
Contract Org.
Reg. Econ. Devel.
Reg. Econ. Devel.
Biotechnology
Biotechnology
Contract Org.
Biotechnology
Biotechnology
Biotechnology
Consultancy
Biotechnology
Contract Org.
Pharmaceutical
Biotechnology
Biotechnology
Biotechnology
Consultancy
Pharmaceutical
Biomed Device
Trade Assoc.
Biotechnology
Pharmaceutical
Pharmaceutical
Pharmaceutical
Biotechnology
Consultancy
Pharmaceutical
Pharmaceutical
Academic
Contract Org.
Service
Service
Media
Trade Assoc.
Contract Org.
Media
Biotechnology
Consultancy
Reg. Econ. Devel.
Trade Assoc.
Trade Assoc.
Media
BioSupply
Biotechnology
Trade Assoc.
Trade Assoc.
Media
Biotechnology
Pharmaceutical
Pharmaceutical
Government
Inv. Bank
Media
Media
Consultancy
Government
Government
Government
Government
Government
Government
Biotechnology
Pharmaceutical
Contract Org.
Government
Biotechnology
Pharmaceutical
Academic
Contract Org.
Biotechnology
Biotechnology
Biotechnology
Biotechnology
Biotechnology
Contract Org.
Biotechnology
Contract Org.
Biotechnology
Media
Legal
Biotechnology
Biotechnology
Biotechnology
Pharmaceutical
Venture Capital
Service
Biotechnology
Biotechnology
Pharmaceutical
Contract Org.
Biotechnology
Service
Consultancy
Biotechnology
Biotechnology
Legal
Biotechnology
Pharmaceutical
Contract Org.
Contract Org.
Biotechnology
Tech Transfer
Contract Org.
Academic
Biotechnology
Government
Biotechnology
Consultancy
Pharmaceutical
Contract Org.
Contract Org.
Reg. Econ. Devel.
Service
Pharmaceutical
Pharmaceutical
Biotechnology
Legal
Pharmaceutical
Legal
Biotechnology
Government
Pharmaceutical
Consultancy
Government
Pharmaceutical
Pharmaceutical
Pharmaceutical
Pharmaceutical
Academic
Non-Profit Org.
Government
Pharmaceutical
Contract Org.
Government
Consultancy
Biotechnology
Pharmaceutical
Contract Org.
Contract Org.
Pharmaceutical
Pharmaceutical
Biotechnology
Biotechnology
Contract Org.
Biotechnology
Biotechnology
Government
Consultancy
Biotechnology
Biotechnology
Government
Media
Consultancy
Contract Org.
Contract Org.
Pharmaceutical
Pharmaceutical
Government
Biotechnology
Biotechnology
Biotechnology
Service
Tech Transfer
Pharmaceutical
Pharmaceutical
Contract Org.
Biotechnology
Biotechnology
Biotechnology
Contract Org.
Contract Org.
Government
Pharmaceutical
Contract Org.
Pharmaceutical
Academic
Biotechnology
Pharmaceutical
Pharmaceutical
Consultancy
Trade Assoc.
Trade Assoc.
Trade Assoc.
Venture Capital
Non-Profit Org.
Consultancy
Consultancy
Venture Capital
Pharmaceutical
Non-Profit Org.
Consultancy
Academic
Biotechnology
Pharmaceutical
Pharmaceutical
Pharmaceutical
Pharmaceutical
Biotechnology
Pharmaceutical
Pharmaceutical
BioSupply
Service
Service
Biotechnology
Contract Org.
Government
Government
Biotechnology
Contract Org.
Contract Org.
Biotechnology
Biotechnology
Academic
Government
Academic
Biotechnology
Biotechnology
Consultancy
Biotechnology
Biotechnology
Biotechnology
Biotechnology
Reg. Econ. Devel.
Contract Org.
Biotechnology
Pharmaceutical
Pharmaceutical
Venture Capital
Pharmaceutical
Biotechnology
Pharmaceutical
Contract Org.
Pharmaceutical
Biotechnology
Biotechnology
Biotechnology
Biotechnology
Pharmaceutical
Contract Org.
Biotechnology
Biotechnology
Drug Delivery
Biotechnology
Biotechnology
Drug Delivery
Pharmaceutical
Non-Profit Org.
Pharmaceutical
Biotechnology
Biotechnology
Pharmaceutical
Pharmaceutical
Biotechnology
Contract Org.
Media
Consultancy
Contract Org.
Biotechnology
Biotechnology
Biotechnology
Contract Org.
Biotechnology
Biotechnology
Contract Org.
Contract Org.
Accounting
Biotechnology
Bus. Incubator
Contract Org.
Biotechnology
Non-Profit Org.
Biotechnology
Pharmaceutical
Contract Org.
Pharmaceutical
Biotechnology
Contract Org.
Biotechnology
Biotechnology
Biotechnology
Biotechnology
Non-Profit Org.
Biotechnology
Biotechnology
Contract Org.
Pharmaceutical
Contract Org.
Biotechnology
Media
Pharmaceutical
Pharmaceutical
Government
Biotechnology
Contract Org.
Pharmaceutical
Pharmaceutical
Contract Org.
Biotechnology
BioSupply
Biotechnology
Pharmaceutical
Pharmaceutical
Biotechnology
Biotechnology
Biotechnology
Biotechnology
Biotechnology
Service
Biotechnology
Pharmaceutical
Biotechnology
Pharmaceutical
Venture Capital
Biotechnology
Biotechnology
Contract Org.
Academic
Tech Transfer
Contract Org.
Academic
Biotechnology
Academic
Biotechnology
Contract Org.
Media
Biotechnology
Pharmaceutical
Pharmaceutical
Reg. Econ. Devel.
Biotechnology
Pharmaceutical
Academic
Academic
Academic
Academic
Academic
Academic
Tech Transfer
Biotechnology
Venture Capital
Biotechnology
Biotechnology
Pharmaceutical
Service
Biotechnology
Trade Assoc.
Media
Venture Capital
Biotechnology
Contract Org.
Pharmaceutical
Biotechnology
Biotechnology
Consultancy
Biotechnology
Biotechnology
Biotechnology
Pharmaceutical
Canada
Spain
Italy
USA
USA
USA
USA
USA
Brazil
Canada
Switzerl&
Canada
USA
USA
USA
France
USA
Canada
Canada
USA
USA
Canada
Canada
Canada
France
USA
USA
Canada
USA
USA
USA
Italy
UK
USA
Canada
USA
Canada
Canada
Italy
USA
France
Canada
Spain
Singapore
Canada
Sweden
USA
USA
Australia
Germany
USA
Canada
New Zeal&
Canada
Canada
Canada
Canada
France
USA
Canada
USA
Brazil
Canada
UK
USA
China
Rep. of Korea
Canada
Canada
Canada
USA
USA
USA
China
Canada
Canada
USA
USA
USA
China
Germany
Italy
Japan
Canada
Canada
Canada
USA
Canada
Canada
Canada
Canada
USA
USA
Canada
China
Japan
Canada
Canada
Canada
Australia
France
Canada
USA
USA
Sweden
Canada
Rep. of Korea
Canada
UK
USA
Canada
Rep. of Korea
Canada
Canada
Canada
USA
USA
Canada
USA
Canada
USA
Cyprus
Czech Rep.
USA
Germany
USA
USA
Canada
Canada
USA
UK
Canada
Austria
USA
France
USA
Austria
USA
USA
Canada
Spain
USA
USA
Canada
USA
USA
Canada
Germany
USA
Spain
USA
Canada
Canada
USA
Canada
Canada
Canada
USA
USA
Austria
India
USA
Rep. of Korea
Rep. of Korea
UK
USA
Hungary
Hong Kong
USA
USA
Rep. of Korea
USA
Canada
Canada
UK
UK
Canada
Spain
Austria
USA
Canada
USA
France
Canada
Canada
Japan
USA
India
USA
Canada
USA
Canada
USA
Canada
Rep. of Korea
Rep. of Korea
USA
USA
USA
Argentina
Mexico
China
Canada
Canada
Canada
Canada
USA
Australia
USA
Canada
Canada
China
Canada
Switzerl&
Canada
Canada
USA
Canada
Rep. of Korea
Italy
USA
Canada
USA
USA
USA
France
USA
USA
Canada
Canada
USA
USA
Canada
Canada
Canada
Taiwan
Canada
Singapore
Canada
USA
UK
USA
Canada
Denmark
USA
Canada
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France
Switzerl&
USA
USA
USA
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Canada
Canada
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USA
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Spain
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UK
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USA
Taiwan
USA
USA
UK
France
France
Canada
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USA
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USA
France
Germany
Canada
Rep. of Korea
Canada
Germany
USA
Canada
USA
Canada
France
Canada
Canada
Germany
Canada
USA
Canada
USA
Canada
USA
Canada
France
Austria
USA
USA
UK
Brazil
USA
Canada
Canada
Canada
China
USA
USA
Italy
Canada
Canada
China
Canada
Canada
USA
Sweden
Canada
Germany
Canada
Germany
Sweden
USA
Japan
USA
USA
USA
Canada
Canada
Canada
Australia
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USA
Canada
USA
Canada
UK
USA
Israel
USA
Canada
USA
Rep. of Korea
Canada
Canada
Canada
Canada
Canada
Canada
Canada
USA
Canada
UK
USA
Canada
USA
France
USA
UK
USA
China
China
Canada
Canada
USA
USA
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Canada
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USA

Applied Biological Materials

BC Bioenergy Network

Bioinformatics Training Program, Genome Sciences Centre, BCCA

Cardiome Pharma Corp.

iData Research

KPMG MSLP

NSERC-CRSNG

Response Biomedical

SFU Beedie School of Business

SFU Innovation Office

STEMCELL Technologies, Inc.

TAITLABS

UBC Master of Management – Early Career Masters

Brain Dictionary - Rodent Brain Protein Atlas

http://rodent.proteinatlas.org/dictionary.php

The rodent brain atlas shows expression and localization of proteins in a large variety of normal and colchicine treated rodent brain tissues with the aid of immunohistochemistry (IHC) images.  

impossible to upgrade from 386system to a Pentium

"Last time you said love is a game. Teach me the rules," she said.
"I can't do that," he said.
"You can't?"
"That's rite, I said I can't,"
"Why can't u? What's the reason?"
"The reason? It's because it's impossible to upgrade from 386system to a Pentium. Your brain might stop functioning, from a fatal error,"
"Are you telling me that my brain is a 386?"

http://www.fanfiction.net/s/4915026/1/Seducing_Mr_Perfect

Wrinkles from laughter

"With mirth and laughter let old wrinkles come."
--William Shakespeare

Saturday, February 25, 2012

Friends too late

"I hate it in friends when they come too late to help." --Euripides

Friday, February 24, 2012

Foosball - How to stop a ball

Recommended Practice: Start slow at first. Lift up all of the guys in between your 2-man defense bar and your 3-man offensive bar. Practice hitting the ball all the way from the back to the front and stop the ball with your 3-bar. You can use a slight forward wrist-flick motion to cushion the ball as it approaches its target. This motion needs to be quicker as you increase the speed that the ball is traveling. Increase the speed of your hit until you can hit it at near full speed and can stop the ball dead at your 3-bar.
Learn to Cut Off as Much of the Goal as You Can From Your Opponent: The old defensive adage holds true in foosball: "Stay between the ball and the goal." Notice I did not say, "Stay between your man and the goal." Follow the ball and stagger your defender and goalie to block as much area of the goal as you can. This can require different degrees of stagger and swapping

http://www.helium.com/items/487779-how-to-beat-your-friends-at-foosball?page=2


Catching Lane passes


http://www.youtube.com/watch?v=NH0aui39bxc&feature=results_video&playnext=1&list=PL5907AACCAD1FFB95

http://www.youtube.com/watch?v=jA5oWri-RZk

http://www.youtube.com/watch?v=pkVH6sJkNec&feature=related

http://www.youtube.com/watch?v=aGiTpAgTqYk

Deadball shot
http://www.youtube.com/watch?v=6sDsyBPboWc

Chip passing
http://www.youtube.com/watch?v=QOGz6IBTxDg

Aptamers - strong binding of single-stranded oligos

Latin ‘aptus’ meaning “to fit” and is based on the strong binding of single stranded oligos to specific targets based on structural conformation.

http://www.genelink.com/newsite/products/aptamers.asp

Do not track in browsers

http://support.mozilla.org/en-US/kb/how-do-i-turn-do-not-track-feature

Thursday, February 23, 2012

GEO Annotation URL

ftp://ftp.ncbi.nih.gov/pub/geo/DATA/annotation/platforms/GPL570.annot.gz

GMiner - biomedical ontology, search GEO

http://gminer.mcw.edu

GEO samples

http://geossdev.med.virginia.edu/research/teaching/2011/R/source-R-tutorial-Day2-bioconductor.R
http://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE10784
http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/

# Version info: R 2.12.1, Biobase 2.12.1, GEOquery 2.18.0, limma 3.8.1
# R scripts generated Thu Feb 23 16:57:44 EST 2012

# Unable to generate script analyzing differential expression.
# Invalid input: at least two groups of samples should be selected.

################################################################
# Boxplot for selected GEO samples
library(Biobase)
library(GEOquery)

# load series and platform data from GEO
gset <- getGEO("GSE10784", GSEMatrix =TRUE)

if (length(gset) > 1) idx <- grep("GPL1261", attr(gset, "names")) else idx <- 1 gset <- gset[[idx]]

 #Download GPL file, put it in the current directory, and load it:
gpl1261 <- getGEO('GPL1261', destdir=".") 

#show probe_id and corresponding gene symbol
Table(gpl1261)[1:10,c("ID",'Gene.Symbol')]
# ID Gene.Symbol
#1 1415670_at Copg
#2 1415671_at Atp6v0d1

 # set parameters and draw the plot
dev.new(width=4+dim(gset)[[2]]/5, height=6) par(mar=c(2+round(max(nchar(sampleNames(gset)))/2),4,2,1))
title <- paste ("GSE10784", '/', annotation(gset), " selected samples", sep ='')
boxplot(exprs(gset), boxwex=0.7, notch=T, main=title, outline=FALSE, las=2)
legend("topleft", labels, fill=palette(), bty="n")
featureNames(gset)[1:10]

 # Get sample names
sampleNames(gset)

 # Get phenotype data of samples
pData(gset)

 # read CEL files
gsm272325 <- ReadAffy('GSM272325.CEL')  # downloaded from GEO, untar and unzipped, one sample

 # http://www.biostat.iupui.edu/~XiaochunLi/Portugal/Biocon_lab1/Biocon_lab1.pdf
#Next we use rma to background correct, normalize, and summarize the probe level data
#into an expression measure for each probe set (gene) on each of the six arrays. The
#expression values are in log base 2 scale.
eset <- rma(gsm272325)
e <- exprs(eset)
dim(e)

Free webiste mockup tools

http://speckyboy.com/2010/01/11/10-completely-free-wireframe-and-mockup-applications/

Pencil Project
Web Site Wireframe Tool

Get up, stand up

"Get up, stand up, Stand up for your rights. Get up, stand up, Don't give up the fight."
--Bob Marley

Tuesday, February 21, 2012

History of Biology

June 08, 2011
The New Spongelab platform is now in open Public Beta (www.spongelab.com). Users of the new platform will be able to access the 'History of Biology' game but will not be able to access their saved game data. It will function like you are starting from the beginning. Current users should continue to access the History of Biology game through this site. Having said that - we'd love you feedback on the new site so please register and send us you comments! We're looking to users as well as contributors - points and credits are awarded - and yet again, the game is afoot! www.spongelab.com

ClearSea Free Video Conferencing

http://www.clearsea.com/

On any device. On any network. Connect to H.323 and SIP devices. Today!

A personal video conferencing solution on any network and any device.

Here at Mirial we always had a clear vision about video conferencing being a personal tool. We feel that each individual should be able to connect in video from any network and any device, and that is fundamental to be able to reach the hundreds of thousands H.323-based room systems to provide a real value to the enterprise market.

The ClearSea in the Cloud service removes all the complexities thanks to the SaaS (Software as a Service) approach.



ClearSea is also available as on-premises solution for all the companies willing to manage autonomously all aspects of their video conferencing infrastructure. Learn more.

Nanopore genome sequencer makes its debut

http://www.nature.com/news/nanopore-genome-sequencer-makes-its-debut-1.10051?WT.ec_id=NEWS-20120221

Technology that its parent company says will sequence a human genome in just 15 minutes opened its first data run to scrutiny today.

Oxford Nanopore Technologies, based in Oxford, UK, revealed the initial results from its GridION system at the Advances in Genome Biology and Technology meeting in Marco Island, Florida. The firm expects to start selling its new machine in the second half of this year and also plans to launch the world’s first miniaturized, disposable sequencer — the MinION — which will retail for less than US$900.

The potential advantages of the nanopore system are that it could deliver real-time seqeuncing of single molecules at low cost, and should not damage the DNA, so in theory the same molecule can be reanalysed, said Brown.

The technology has a 4% error rate, meaning that 4% of the bases are read incorrectly, but Brown says that the company is working to cut this down to 0.1– 1% by the time the system launches, which would make it more competitive with current systems.

Cancer-causing mutations yield their secrets

http://www.nature.com/news/cancer-causing-mutations-yield-their-secrets-1.10029?WT.ec_id=NEWS-20120221

The mystery of how mutations in a gene called isocitrate dehydrogenase 1 (IDH1) cause brain cancer and leukaemia is beginning to be unravelled. Researchers have discovered that the mutations cause the production of an enzyme that can reconfigure on–off switches across the genome and stop cells from differentiating.

Monday, February 20, 2012

Hans Rosling

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

Rosling co-founded the Gapminder Foundation together with his son Ola Rosling and daughter-in-law Anna Rosling Rönnlund. Gapminder developed the Trendalyzer software that converts international statistics into moving, interactive graphics. His lectures using Gapminder graphics to visualise world development have won awards.

Hans Rosling's new insights on poverty
http://www.ted.com/talks/hans_rosling_reveals_new_insights_on_poverty.html

RIKEN / Fantom3 Transcription Start Sites CAGE Analysis Viewer

http://gerg02.gsc.riken.jp/gev-promoter/gbrowse/hg17/

http://gerg01.gsc.riken.jp/cage_analysis/hg17prmtr/TESummary.php?te_id=15897

Cap-Analysis Gene Expression (CAGE)

New chemical reagent turns mouse brain transparent

http://www.riken.jp/engn/r-world/info/release/press/2011/110830_3/index.html

Combined with fluorescence labeling, new approach produces 3D images at unprecedented depth and levels of spatial detail

Never regret

"Never regret. If it's good, it's wonderful. If it's bad, it's experience."
--Victoria Holt

Saturday, February 18, 2012

BC Clinical Genomics Conference

http://bccgn.ca/news-events/Conference.htm

BCCGN holds a conference every spring to facilitate education and research in the area of clinical genomics

BCCGN’s third annual conference, GENOMICS IN MEDICINE 2015 was held on Wednesday April 27th, 2011 at the Vancouver Convention Center. Attending physicians recieved 6 CME credits. It attracted 210 delegates including family physicians and specialists (23%), many of whom (18%) travelled from outside the lower mainland. Also attending were health professionals, researchers and students. Feedback from delegates was very positive for the overall conference program.

Here's some quotes from physicians who attended:-

“I am better prepared for discussion with patients about what genomics can and cannot do for them right now.”

“I learned about the “Fast pace of genomic technology and our lack of preparedness to deal with it.”

Love that never ceases

"The steadfast love of the Lord never ceases, his mercies never come to an end; they are new every morning."
--Lamentations

Friday, February 17, 2012

2011 Alzheimer’s disease facts and figures

http://www.sciencedirect.com/science/article/pii/S1552526011000367

Alzheimer's Association, Thies W, Bleiler L.
Source

william.thies@alz.org

Abstract

Alzheimer’s disease (AD) is the sixth leading cause of all deaths in the United States and is the fifth leading cause of death in Americans aged ≥65 years. Although other major causes of death have been on the decrease, deaths because of AD have been rising dramatically. Between 2000 and 2008 (preliminary data), heart disease deaths decreased by 13%, stroke deaths by 20%, and prostate cancer-related deaths by 8%, whereas deaths because of AD increased by 66%.

An estimated 5.4 million Americans have AD; approximately 200,000 people aged <65 years with AD comprise the younger-onset AD population. Every 69 seconds, someone in America develops AD; by 2050, the time is expected to accelerate to every 33 seconds. Over the coming decades, the baby boom population is projected to add 10 million people to these numbers. In 2050, the incidence of AD is expected to approach nearly a million people per year, with a total estimated prevalence of 11 to 16 million people. Dramatic increases in the numbers of “oldest-old” (those aged ≥85 years) across all racial and ethnic groups will also significantly affect the numbers of people living with AD.

In 2010, nearly 15 million family and other unpaid caregivers provided an estimated 17 billion hours of care to people with AD and other dementias, a contribution valued at more than $202 billion. Medicare payments for services to beneficiaries aged ≥65 years with AD and other dementias are almost 3 times higher than for beneficiaries without these conditions. Total payments in 2011 for health care, long-term care, and hospice services for people aged ≥65years with AD and other dementias are expected to be $183 billion (not including the contributions of unpaid caregivers).

This report provides information to increase understanding of the public health effect of AD, including incidence and prevalence, mortality, health expenditures and costs of care, and effect on caregivers and society in general. The report also examines the current state of AD detection and diagnosis, focusing on the benefits of early detection and the factors that present challenges to accurate diagnosis.

Allan Jones: A map of the brain

http://www.ted.com/talks/allan_jones_a_map_of_the_brain.html

Ed Boyden: A light switch for neurons
http://www.ted.com/talks/ed_boyden.html

ResearchGate - Facebook for research

http://www.researchgate.net

Thursday, February 16, 2012

Google refine

Google Refine is a power tool for working with messy data, cleaning it up, transforming it from one format into another, extending it with web services, and linking it to databases like Freebase.

http://code.google.com/p/google-refine/

has clustering, groupings, merging, undos, expressions on numeric facet

refine messy data

desktop application even though using a browser

microRNA: The microcosmos of cancer

http://www.nature.com/nature/journal/v482/n7385/full/nature10888.html?WT.ec_id=NATURE-20120216

The discovery of microRNAs (miRNAs) almost two decades ago established a new paradigm of gene regulation. During the past ten years these tiny non-coding RNAs have been linked to virtually all known physiological and pathological processes, including cancer. In the same way as certain key protein-coding genes, miRNAs can be deregulated in cancer, in which they can function as a group to mark differentiation states or individually as bona fide oncogenes or tumour suppressors. Importantly, miRNA biology can be harnessed experimentally to investigate cancer phenotypes or used therapeutically as a target for drugs or as the drug itself.

Personalized medicine: Bring clinical standards to human-genetics research

http://www.nature.com/nature/journal/v482/n7385/full/482300a.html?WT.ec_id=NATURE-20120216

Study protocols need to be rigorous, because more than science is at stake. Sometimes participants' lives depend on the results, writes Gholson J. Lyon.

I was not her physician; I was a researcher, and I had done this work on a research basis, not following the specific protocol required for performing validated clinical or diagnostic tests. I couldn't be totally sure that her individual results were accurate. Should I share them with her anyway, knowing the devastation they could cause? What if I was wrong, and she terminated the pregnancy?

There are increasingly limited resources for biomedical research, and it can take 20 years or more to translate genetic discoveries into new drugs or other treatments. So why not help the families and research participants now, by deriving the highest possible value from every DNA sample we sequence?

We cannot forget the wise words of the late geneticist Charles Epstein, from his 2001 William Allan award lecture: “the operative word in 'human genetics' is 'human.' Human genetics is about human beings — about humanity and humaneness.”3

Allen school expanding

http://www.nature.com/naturejobs/science/articles/10.1038%2Fnj7385-431c?WT.ec_id=NATUREjobs-20120216

hire 13 researchers to detect emerging cross-species diseases, develop vaccines and work on transmission control, says director Guy Palmer.

http://globalhealth.wsu.edu/

Biostatistics: Revealing analysis

http://www.nature.com/naturejobs/science/articles/10.1038%2Fnj7384-263a?WT.ec_id=NATUREjobs-20120216

As the challenges of analysing genomic data evolve, statistical expertise has become more valuable than ever.

As a result, statistical geneticists are now mining sequence data for directly causative mutations, rather than for SNPs. And geneticists are starting to combine data from different types of studies, using a method called integrative genomics — for instance, studying combinations of SNPs, the protein-coding genes surveyed in exome studies, epigenetic factors (heritable information not found in the DNA sequence), gene-expression factors and environmental interactions. “This field has ballooned and changed to a ridiculous degree in the past ten years, because there have been multiple waves of technological revolution,” says Gilean McVean, a statistical geneticist at the University of Oxford, UK. “As genomics becomes a much more integrated part of health care, things are going to change again and new opportunities will open up, so it's a good time to be a statistical geneticist.”

The challenge is to find true associations within the huge volumes of data without getting duped by the errors that tend to affect data sets of this magnitude, says Lucia Hindorff, an epidemiologist at the US National Human Genome Research Institute (NHGRI) in Bethesda, Maryland.

Companies such as Pacific Biosciences, Illumina in San Diego, California, and Life Technologies in Carlsbad, California, are developing new methods for sequencing and need people who can come up with ways to analyse the new forms of data that will be produced.

“There's a massive amount of data being generated, particularly by next-generation sequencing platforms, and the cost of the analysis is now greater than the cost of the data generation,” she says. “Finding the right people to analyse those data is a challenge.”

“The more you understand software and computer science, the better off you are; writing software is 90% of what we're doing,” says Alexander.

No excuse for failure

"We have forty million reasons for failure, but not a single excuse."
--Rudyard Kipling

Wednesday, February 15, 2012

The ups and downs of alpha-synuclein mRNA expression.

Neystat et al. 1999 iPD: 9/con.: 8 Substantia nigra/frontal cortex RPA VMAT2 Diminished α-synuclein mRNA levels in the substantia nigra of PD cases, no changes in the cortex

Dachsel et al. 2006 iPD: 9/ con.: 5 Amygdala/occipital lobe/striatum/ RT-PCR Synaptop./YWHAZ/HPRT/GAPDH Strongly reduced α-synuclein mRNA levels in PD substantia nigra, moderate but significant decrease in PD putamen and occipital lobe, no change in amygdala

Kingsbury et al. 2004 Cortex: iPD: 8/ con.: 4 midbrain: iPD: 7/ con.: 4 Cortex/midbrain Semiquant. in situ hybridization α-synuclein mRNA expression significantly reduced in melanized neurons in substantia nigra and frontal cortex in PD

Brodmann’s area 39 portion of Einstein’s brain has higher proportion of glial cells versus neurons

http://www.creativitypost.com/science/science/creative_innovation_possible_brain_mechanisms1

Thirty years later, the Brodmann’s area 39 portion of Einstein’s brain was analyzed histologically by Marian C. Diamond, PhD, and colleagues. They reported that this area of Einstein’s brain contained a higher proportion of glial cells versus neurons, compared with the brains of control subjects. Assuming that the paucity of cortical neurons was not the result of aging (the control subjects were significantly younger than Einstein at the time of his death), how did the loss of neurons relate to Einstein’s creative genius?

"If you have something going on in one side of the brain, [could] that ‘disinhibit’ the other side of the brain [into] developing even greater ability?" Dr. Heilman asked. "Could Einstein’s dyslexia and lack of development of his left hemisphere have allowed his right hemisphere to grow and be well connected and to have excellent modules?... People who have tremendous creativity also have tremendous connectivity."

"To be creative, people need to break away from what they have been taught to believe, and thus divergent thinking is a critical element of creativity," he said. "Patients who have their frontal lobe[s] removed or injured cannot perform divergent thinking…. The major hypothesis of this talk is that creativity is dependent upon the ability to diverge and then form innovative solutions.

To arrive at a creative solution to a persistently unsolvable problem, an individual must often change the method by which he or she has already attempted to solve the problem—in other words, think outside the box.

Charles Spearman’s suggestion in 1931 that creativity results from bringing together two or more ideas that previously have been isolated

"The frontal lobes appear to be the part of the cortex that is most important for creativity, in that they are critical for divergent thinking and might modulate the coactivation of diverse cognitive networks so important in innovation. The means by which family and friends might be able to encourage the development of the frontal lobes is to encourage independent and divergent thinking."

Reality and imagination

"Everything you can imagine is real."
--Pablo Picasso

Tuesday, February 14, 2012

Metagenomics - a guide from sampling to data analysis

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.

Monday, February 13, 2012

Nervous tissue

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

supporting cells (glia) are small relative to neurons

Doctor's practice

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

Tuesday, February 7, 2012

BrainStars

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

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

  1. Sydney Brenner1,
  2. Terrence J. Sejnowski2,*

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

The idea is to:
1. Add the host's name to .ssh/config file
2. Create the id_rsa.pub file in the client machine using ssh-keygen
3. Copy the client's id_rsa.pub file to the host's .ssh/authorized_keys

~/.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


Offending key for IP in /home/jdoe/.ssh/known_hosts:13

get rid of line 13 in .ssh/known_hosts

Monday, February 6, 2012

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

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

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

"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

Sunday, February 5, 2012

Remote control (slide changer) for Powerpoint or for OpenOffice

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

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.

Saturday, February 4, 2012

Conditional Random Fields applied to protein fold recognition

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.

Friday, February 3, 2012

Mouse atlas

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

Synapses, Receptor Cells, and Brain

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

Immunology

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

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.

Thursday, February 2, 2012

Science is refinement thinking

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

Roche takeover bid poses challenge to Illumina

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

Wednesday, February 1, 2012

Covariance vs Correlation

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

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.