International Society for Complexity, Information, and Design (ISCID) Encyclopedia

http://www.iscid.org/encyclopedia/FRET

The International Society for Complexity, Information, and Design (ISCID) is a 501(c)(3) non-profit organization which provides a forum for free and uncensored inquiry into complex systems.

12 Useful FireFox Plugins For Safe Browsing

http://www.smashingdownloads.com/2009/07/13/12-useful-firefox-plugins-for-safe-browsing/

https://addons.mozilla.org/en-US/firefox/addon/9727/
https://addons.mozilla.org/en-US/firefox/addon/4429
https://addons.mozilla.org/en-US/firefox/addon/6623
https://addons.mozilla.org/en-US/firefox/addon/6718
https://addons.mozilla.org/en-US/firefox/addon/722/
http://noscript.net/

UBC Research Facilities

http://www.cellphys.ubc.ca/resfacilities.htm

HeLa cell - the "immortal cell"

A HeLa cell (also Hela or hela cell) is a cell type in an immortal cell line used in scientific research. It is one of the oldest and most commonly used human cell lines.[1] The line was derived from cervical cancer cells taken from Henrietta Lacks, a patient who eventually died of her cancer on October 4, 1951. The cell line was found to be remarkably durable and prolific as illustrated by its contamination of many other cell lines used in research.[2][3]

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

Transgenic / Knockout Mice

http://www.cellmigration.org/resource/komouse/komouse_approaches.shtml

Cre - conditional gene modifications in mice

n extensive collection of mice have been generated, each line expressing Cre from a promoter that is either tissue specific, cell specific, developmentally specific or responsive to an exogenous agent like tetracycline.

proteomic fingerprints

Disease states might be associated with distinctive configurations of circulating proteins: so-called ‘proteomic fingerprints’.

Proteomic fingerprinting for the diagnosis of human African trypanosomiasis
Dan Agranoffa, August Stichb, Paulo Abelc and Sanjeev Krishnaa
Trends in Parasitology
Volume 21, Issue 4, April 2005, Pages 154-157

Christmas 2011 - Overdrive

http://www.watchanimeon.com/overdrive-episode-11/

Blood, cells, muscles and everything that has been sleeping within me until now.

Give me ... Give me ... strength.

Deeds, not words.

Prosperity makes friends, adversity tries them.

Joy and sorrow are next door neighbours.

You never know what you can do till you try.

Save You - Simple Plan

http://www.youtube.com/watch?v=eXT7iY2DgVo&feature=artistob&playnext=1&list=TL-N8vir6oee8

Overdrive

http://www.watchanimeon.com/overdrive-episode-1/

Biking , Bike

The Palme d'Or (English: Golden Palm)

The Palme d'Or (English: Golden Palm) is the highest prize awarded to competing films at the Cannes Film Festival.

http://en.wikipedia.org/wiki/Palme_d%27Or

Dropbox - file sharing

https://www.dropbox.com/referrals/NTExMTYyOTY5OQ?src=referrals_fb_post

Firefox flv downloader - Karbon

https://addons.mozilla.org/en-US/firefox/addon/54453/

noSQL

Casandra
Mongo
Dynamo
Amazon Simple DB
Google BigTable
javaCC - Query graph model (QGM)

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

BioPartnering North America

http://www.techvision.com/bpn/participants/index.php?src=lsbc&pageid=261#present

AAIPharma Services
ACT Biotech
Agere Pharmaceuticals, Inc.
AliX
Alligator Bioscience AB
Allon Therapeutics, Inc.
Allostera Pharma Inc.
Allphase Clinical Research Inc.
Alphora Research Inc.
Alsace BioValley
AltheaDx
Ambit Biosciences Corporation
AngioChem Inc
Aquinox Pharmaceuticals Inc.
Araclon Biotech
Augurex Life Sciences Corp.
AVOGADRO
Bridge Consulting
Calistoga Pharmaceuticals, Inc.
Cellectis SA
Cellvax
CIRION BioPharma Research Inc.
Conformetrix
Congenix, LLP
Crown Bioscience Inc.
CYTOO cell architects
Daiichi Sankyo Co., Ltd.
Debiopharm S.A.
DSM
Elan Corporation
Emerald Biostructures
Emmaus Medical, Inc.
Eurand International S.p.A.
Eurofins-ADME BIOANALYSES
Forma Therapeutics, Inc.
French Consulate
GlobalTox
Globe Laboratories Inc
Groupe FORENAP
i3 CanReg, Inc.
i3 Global
ImmunoVaccine Inc.
INC Research
InCode BioPharmaceutics, Inc.
Inimex Pharmaceuticals, Inc.
Inovio Biomedical Corp.
Invest in France Agency
iPierian, Inc.
Italian Trade Commission
KAI Pharmaceuticals Inc.
LEO Pharma A/S
London Genetics Ltd
Metabolys
NDA Regulatory Service AB
NeuMedics Inc.
NFX - Nord France eXperts
NicOx S.A.
Novozymes A/S
Oncodesign
Oncolytics Biotech Inc.
ORA, Inc.
OxyPharma AB
PATH
Pearl Therapeutics, Inc.
Pharmatek Laboratories, Inc.
PhysioStim
Piramal Healthcare
Plant Advanced Technologies
PlantForm
PolyMedix Inc.
Porsolt & Partners Pharmacology
Prestwick Chemical, Inc.
PROOF Centre of Excellence
ProPharma Partners International Inc.
Protaffin Biotechnologie AG
PX'Therapeutics
Rose Pharma A/S
Sandoz International GmbH
Sernova Corp
Shanghai Medicilon Inc.
Silence Therapeutics AG
Sirona Biochem
Skunkwerks Software Ltd
SuperGen Inc.
Synergy Pharmaceuticals, Inc.
Teva Pharmaceutical Industries Ltd
TFChem
Topica Pharmaceuticals Inc.
UBIFrance
University of Manitoba
Valocor Therapeutics, Inc.
Vifor Pharma Aspreva
Vifor Pharma Aspreva
VIVALIS
XenTech
YM BioSciences Inc.
Zoomedia Inc.
Zymeworks Inc. Contract Organization



3M Drug Delivery Systems
3M Drug Delivery Systems
3P Biopharmaceuticals, S.L.
4SC AG
Abbott Laboratories
Abeome Corporation
Abmedix Biomedical
Actelion Pharmaceuticals Ltd.
Affymax, Inc.
Ahngook Pharamceutical Co Ltd
Alder BioPharmaceuticals
Allergan, Inc.
Alphalyse, Inc.
Alvogen
Amicus Therapeutics
Aminex Therapeutics, Inc.
Anacor Pharmaceuticals, Inc.
AnaptysBio, Inc.
Antisoma Research Ltd
Apex Healthcare
Ark Therapeutics
ASEBIO, Spanish Bioindustry Association
Aska Research
Astellas
Astellas
Astellas
aTyr Pharma Inc.
Australian Research Network
Axon Clinical Research
BASF
Bayer AG
BC Advantage Funds (VCC) Ltd.
BC Cancer Research Centre (BCCRC)
BC Genome Sciences Centre, UBC
BCN Peptides
BELTAS Ltd
BioAlberta
biOasis Technologies Inc.
BIOCODEX
BioEnsemble
Biogen Idec, Inc.
BioMS Medical Corporation
Bioniche Life Sciences, Inc.
BIOPOLIS
Biopta Ltd
Bio-Sino Biotechnology&Science Inc.
BioTechLogic, Inc.
BioUETIKON Ltd
Biovail Corporation (Biovail Contract Research)
BioXcel Corporation
BITA
BC Ministry of Small Bus., Tech. and Econ. Dev.
BC Ministry of Small Bus., Tech. and Econ. Dev.
BC Ministry of Small Bus., Tech. and Econ. Dev.
Broadreach BioSystems Inc.
Business in Vancouver
Campbell Alliance
Canada's Research-Based Pharma Companies
Canadian Consulate General
Canadian Consulate General
Canadian Consulate General
Canadian Embassy
Canadian Embassy
Canadian Embassy
Canadian German Chamber of Ind. and Com. Inc
Canadian High Commission
Canadian HIV Trials Network
Can-Am Pharmaceutical Services, LLC
Cardiome Pharma Corp.
Catalent Pharma Solutions, Inc.
CCL Pharmaceuticals
Ceapro Inc.
Celator Pharmaceuticals, Inc.
Cell Therapy News
CellSeed Inc.
Cephalon, Inc.
CFC Underwriting Limited
Chelsea Therapeutics Inc.
ChemoCentryx Inc.
Christie Consulting Services
Chuncheon Bioindustry Foundation
Cipher Pharmaceuticals Limited
Circassia Ltd
Clinical Network Services (CNS) PTY Ltd
Clinimetrics, Inc.
CNETE
CombinatoRx, Incorporated
Compugen
Confederation Of Indian Industry
Consulate General of the Republic of Korea
Cook Pharmica LLC
Copenhagen Capacity
CPQ Ingenieros SL
Cqua Research International Inc
Creechurch Int'l Underwriters
Critical Outcome Technologies Inc.
Critical Pharmaceuticals Ltd
CrystalGenomics, Inc. / CG Pharmaceuticals
CrystalGenomics, Inc. / CG Pharmaceuticals
CSL Limited (CSL Biotherapies)
CTI Life Sciences Fund
Cytochroma Inc.
Dabur India Limited (Dabur Research Foundation)
Dalhousie University
Dalton Pharma Services, Inc.
DCI
deCODE genetics
DepoMed, Inc.
Diteba Research Laboratories Inc.
Donald MacPherson Inc.
Dong Wha Pharm. Co., Ltd.
Dong-A Pharmaceutical Co., Ltd.
DURECT Corporation
Dyax Corp.
E3 Resources
Economic and Commercial Office of Spain
Ecron AcuNova (Manipal Acunova Ltd)
Elevation Pharmaceuticals
EOStrat, Strategies & Management
ERA Consulting Group
Essa Pharma
Evotec AG
Exelixis, Inc.
Exploit Technologies Pte. Ltd
Fasken Martineau DuMoulin LLP
Fate Therapeutics Inc.
Fenwick & West LLP
Forest Laboratories, Inc.
Freeman
Galderma Laboratories, L.P.
GE Healthcare
Genhelix
Genoma Espana
GenomeDx Biosciences Inc.
Genzyme Corporation
GES Exposition
GlaxoSmithKline plc
GMD PharmaSolutions
Government of British Columbia
Government of Canada
Government of India
GP Pharm
Greenstone Venture Partners
Griffith University
GyeongGi Bio-center
Halozyme Therapeutics, Inc.
Histocell
HumanAutoCell GmbH
iCo Therapeutics Inc.
Ie Sung International
Illetrop Ltd
ImmuPharma PLC
Imperial Life Sciences USA, Inc,
IMS Health Inc.
Industry Canada / Industrie Canada
INIS Biotech
Innocoll Inc.
Innovaderm Research
Innovation PEI
Innovotech Inc.
Inogent Laboratories
Insymbiosis
International Science and Tech. Partnerships
International Trade Canada
Intrexon Corporation
IO Informatics
iProgen
Irwin Maclaren Enterprises
Ischemix
Japan Tobacco, Inc.
Jeollanamdo Biopharmaceutical Research Center
Jeonbuk Institute for Bioindustry
Kaken Pharmaceutical Company Limited
KaloBios, Inc.
Kareus Therapeutics, LLC
Korea Biotechnology Industry Organization
Korea Trade Centre, Vancouver (KOTRA)
KPMG LLP
Kyorin Pharmaceutical Co. Ltd
Kyukyu Pharmaceutical Co., Ltd
La Jolla Institute for Allergy & Immunology
LAB Research Inc
Laboratorios Farmaceuticos Rovi, S.A.
Life Science Analytics, Inc.
Ligand Pharmaceuticals, Inc.
Lupin Limited
Lupin Limited
Malachite Management Inc.
Marsh & McLennan Companies
Master of Biomedical Technology
Mayo Clinic
McGill University
MDMI Technologies Inc
MedGenesis Therapeutix Inc.
Medical College of Georgia
Medicon Valley Alliance
Menarini Group
Merck Serono International S.A
MergerMarket (PharmaWire)
Metaara Medical Technologies Inc.
Michael Smith Foundation for Health Research
Microbion BioSciences Corporation
Micromet AG
Micromyx, LLC
MIGENIX Inc.
MP Healthcare Venture Management, Inc.
MPI Research
MSI Methylation Sciences Inc.
multimmune
Myocept Inc.
Myriad Pharmaceuticals, Inc.
Nano Pacific Holdings,Inc.
Nanogen, Inc.
National Research Council Canada (IRAP)
National University of Singapore
NeoPharm Co., Ltd.
NewLink Genetics Corporation
Nexigen Therapeutics
NexMed, Inc.
NextPharma Technologies
Nexus Oncology Ltd
Nomura International plc
North Carolina Department of Commerce
Norwich Pharmaceuticals
Novartis International AG
Novartis International AG
Novo Nordisk A/S
Novo Nordisk A/S
Noxxon Pharma AG
NS Pharma, Inc.
Nucro-Technics Incorporated
Nuon Therapeutics Inc.
Nycomed Holding A/S
Nycomed Holding A/S
OCRI Life Sciences
OncoGenex Pharmaceuticals Inc.
Ono Pharmaceutical Co. Ltd.
OptiNose
Orcrist Bio Inc.
Osaka University, Inst. of Scientific & Ind. Res.
Otsuka Pharmaceutical Co. Ltd.
Pacific Pharmaceutical Co., Ltd. (PacificPharma)
PacificGMP
PAREXEL International Corp.
Penwest Pharmaceuticals Co.
PEPSCAN Systems B.V.
Pfenex Inc
Pharma 2.0 Inc.
PharmaGap
PharmaLegacy Laboratories
Physiosonics, Inc
Polypeptide Laboratories A/S (Group)
PREMAS Biotech Pvt. Ltd.
Priaxon AG
ProBioGen AG
ProteoGen Bio
ProtoKinetix Inc
Protox Therapeutics
PSI CRO AG
Purdue Pharma
QLT Inc.
Radient Technologies Inc.
ReachBio LLC
Regional Centre for Biotechnology
Regis Technologies, Inc.
ReSolution Latin America
Reuters Limited (Thomson Reuters)
Richcore Lifesciences Private Limited
Royal Thai Consulate General
Russian Federation
SageKey Software
Salus Technology Inc.
Sanofi-Aventis (Sanofi Pasteur)
Sanofi-Aventis (Sanofi Pasteur)
SBW Ltd. (Systems Biology Worldwide)
Scale Venture Partners
Scimega Research Inc.
Scottish Devel. International
SemBioSys Genetics Inc.
Siegfried AG
SierraSil Health Inc
Simon Fraser University
Sirius Genomics Inc.
Snowdon & Associates
Somnus Therapeutics Inc.
StemCell Technologies
Stiris Research, Inc.
SunConsult ApS
Superna Life Sciences
SurModics Pharmaceuticals, Inc
Synageva BioPharma
SynCo Bio Partners B.V.
Taiga Biotechnologies, Inc.
Takeda Pharmaceutical Company Limited
Takeda Research Investment, Inc.
Tectra
TetraQ
Teva Innovative Ventures
Tgen Drug Devel. Services (TD2)
TGen Translation Genomics Research Institute
The Hospital for Sick Children Research Institute
The Jackson Laboratory
The James Hogg iCAPTURE Centre
The Pfizer Incubator
The Prostate Centre at VGH
The Stiller Centre
The Student Biotechnology Network
Theracarb Inc.
Therapure Biopharma Inc.
Third Security, LLC
TianChen Scientific Inc.
Times of India
Tissue Solutions Ltd
Transdel Pharmaceuticals, Inc.
Trifermed Group
UCB Group
United Paragon Associates Inc.
Univalor
University Health Network, UHN
University of Alberta
University of British Columbia
University of Calgary
University of Ottawa
University of Prince Edward Island
University of Toronto
University of Victoria Innovation and Devel. Corp.
University Technologies International
UVic Genome BC Proteomics Centre
Vakzine Projekt Management GmbH (VPM)
Variation Biotechnologies
Vectura Limited
Verona Pharma plc
Versartis, Inc.
VIB, the Flanders Institute for Biotechnology
Victory Pharma
ViroMed Co., Ltd.
Washington Research Foundation
Wax-it Histology Services Inc.
Wellgenex
WEX Pharmaceuticals Inc.
Wingwalker Holding Inc.,
WITS Interactive Pvt. Ltd
World Courier
Xcovery, Inc.
Xenon Pharmaceuticals Inc.
XOMA Ltd. Drug Delivery

Seattle Proteome Centre - http://www.proteomecenter.org/software.php

Seattle Proteome Centre - http://www.proteomecenter.org/software.php

http://www.systemsbiology.org/

NIPS - Neural Information Processing Systems

http://nips.cc/Conferences/2010/Program/schedule.php

http://nips.cc/Conferences/2010/Program/event.php?ID=2291

University of Edinburgh; ; WTCHG Oxford; University of Edinburgh

Poster: Sparse Instrumental Variables (SPIV) for Genome-Wide Studies

Felix Agakov, Paul McKeigue, Jon Krohn, Amos Storkey

M74

This paper describes a probabilistic framework for studying associations between multiple genotypes, biomarkers, and phenotypic traits in the presence of noise and unobserved confounders for large genetic studies. The framework builds on sparse linear methods developed for regression and modified here for inferring causal structures of richer networks with latent variables. The method is motivated by the use of genotypes as ``instruments'' to infer causal associations between phenotypic biomarkers and outcomes, without making the common restrictive assumptions of instrumental variable methods. The method may be used for an effective screening of potentially interesting genotype phenotype and biomarker-phenotype associations in genome-wide studies, which may have important implications for validating biomarkers as possible proxy endpoints for early stage clinical trials. Where the biomarkers are gene transcripts, the method can be used for fine mapping of quantitative trait loci (QTLs) detected in genetic linkage studies. The method is applied for examining effects of gene transcript levels in the liver on plasma HDL cholesterol levels for a sample of sequenced mice from a heterogeneous stock, with $\sim 10^5$ genetic instruments and $\sim 47 \times 10^3$ gene transcripts.

Rails

SELECT
Customer.find(:all, :conditions=>["name LIKE ?", @message.to])

INSERT
@customer = Customer.new(:name => @message.to)
@customer.save

Autocomplete
1. app/views/layouts/messages.html.erb (javascript in header)
<%= javascript_include_tag :defaults %>
2. app/views/messages/new.html.erb (html form)
Replace
<%= f.text_field :to %>
with
<%= text_field_with_auto_complete 'message', 'to',{}, :skip_style => false  %>
3.app/controllers/messages_controller.rb (SQL select)
  def auto_complete_for_message_to() 
    user_name = '%' + params[:message][:to] + '%' 
    @customers = Customer.find(:all , :conditions=> ["name like ?", user_name.downcase]) 
    render :partial => 'username' 
  end
4. app/views/messages/_username.html.erb (partial output that is generated)

<% for customer in @customers do %>
• <%=h customer.name %>
 <% end %>

Scale-free network

A scale-free network is a network whose degree distribution follows a power law, at least asymptotically. That is, the fraction P(k) of nodes in the network having k connections to other nodes goes for large values of k as

P(k) \ \sim \ ck^\boldsymbol{-\gamma}

where c is a constant and γ is a constant whose value is typically in the range 2 < γ < 3, although occasionally it may lie outside these bounds. Scale-free networks are noteworthy because many empirically observed networks appear to be scale-free, including the world wide web, the Internet, citation networks, and some social networks. http://en.wikipedia.org/wiki/Scale-free_network

Random vs Scale-free networks
Random network (a) and scale-free network (b). In the scale-free network, the larger hubs are highlighted.

Firebug - The most popular and powerful web development tool

http://getfirebug.com/

JQuery java scripting widgets

http://www.salzburg.com/nwas/scripts/jquery-ui/

http://jqueryui.com/home

What is jQuery UI?

jQuery UI is a widget and interaction library built on top of the jQuery JavaScript Library, that you can use to build highly interactive web applications. This guide is designed to get you up to speed on how jQuery UI works. Follow along below to get started.

http://jqueryui.com/demos/accordion/


Stylesheets
http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.7/themes/base/jquery-ui.css
http://static.jquery.com/ui/css/demo-docs-theme/ui.theme.css

Scripts
http://ajax.googleapis.com/ajax/libs/jquery/1.4.4/jquery.min.js
http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.7/jquery-ui.min.js
http://jquery-ui.googlecode.com/svn/tags/latest/external/jquery.bgiframe-2.1.2.js
http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.7/i18n/jquery-ui-i18n.min.js

Rails Autocomplete

http://railsforum.com/viewtopic.php?id=23188

http://share-facts.blogspot.com/2009/02/autocompleter-example-in-ruby-on-rails.html

http://railscasts.com/episodes/102

Git - http://whygitisbetterthanx.com

http://whygitisbetterthanx.com

3rd generation transcriptomics - CAGE

Monday Noon Seminar: Dr. Piero Carninci, RIKEN Yokohama Institute
12:00 PM-1:00 PM (Lecture Theatre)

3rd generation transcriptomics - CAGE

Breakthroughs in science depend on the development of novel technologies to solve outstanding biological problems. We have previously developed key technologies including the cap-trapper to comprehensively clone full-length cDNAs and the cap-analysis gene expression (CAGE). The mission of the Functional Genomics Technology Team is to develop novel original approaches to comprehensively study genes, their products and their interactions. The approaches should address biological questions that cannot be addressed with technologies that are the state of the art today. In contrast with classic approaches considering one gene at the time, our mission is to develop approaches that aim at targeting biological problem as systems. This requires to comprehensively analyzing various biological aspects.
The members of the laboratory are engaged in the development of original approaches and to design, propose and realize original genomics technologies and apply these to challenging biological problems. These include the discovery, validation and analysis of novel classes of non-coding RNAs; establishing single-cell CAGE methods and its application to reduced biological samples; and data mining, with particular interest at identifying biological patterns and rules, including genome-wise analysis of novel classes of RNAs and their network. To address these genomics approaches for samples derived from living cells in their biological context, particular emphasis consists in the miniaturization of these technologies, to analyze systematically the biology of few or single isolated cells, such as the characterization of the molecular networks of individual neurons, included in a larger cellular networks. Going beyond simple expression profiling, the ultimate mission is to understand the complex relationships between gene expression regulation, the non-coding RNA world, the epigenome and the biological output.


http://genome.gsc.riken.jp/osc/english/members/Piero_Carninci.html

http://fantom.gsc.riken.jp

The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4.

Rumbling Hearts - Kimi Ga Nozomu Eien

Rumbling Hearts

Genres: Drama, Psychological, Romance,

http://www.watchanimeon.com/anime/rumbling-hearts/

iText - Java PDF writer

http://itextpdf.com/

http://today.java.net/article/2007/06/21/generating-pdfs-fun-and-profit-flying-saucer-and-itext

iText is a library that allows you to create and manipulate PDF documents. It enables developers looking to enhance web- and other applications with dynamic PDF document generation and/or manipulation.

Developers can use iText to:

• Serve PDF to a browser
• Generate dynamic documents from XML files or databases
• Use PDF's many interactive features
• Add bookmarks, page numbers, watermarks, etc.
• Split, concatenate, and manipulate PDF pages
• Automate filling out of PDF forms
• Add digital signatures to a PDF file

Open Source PDF Libraries
http://java-source.net/open-source/pdf-libraries

Origami

http://www.chilloutpoint.com/featured/the-incredible-art-of-origami.html

Courses workshops

http://www.grantfacilitation.ubc.ca/continuing-education/courses-workshops/

ESI vs MALDI

http://www.biocompare.com/Articles/FeaturedArticle/921/ESI-Versus-MALDI-For-Protein-Characterization-By-Mass-Spec.html

Molecular biology glossary

http://tainano.com/chin/Molecular%20Biology%20Glossary.htm
http://www.sci.sdsu.edu/~smaloy/Glossary/H.html

Proteomics tools

http://www.psidev.info/index.php?q=node/95

http://www.geneinfinity.org/sp/sp_proteinptmodifs.html

http://www.thegpm.org/

http://www.brc.ubc.ca/drupal5/node/37

Ronald Beavis
Canada Research Chair in Bioinformatics
Professor, Medical Genetics
rbeavis@brc.ubc.ca
604-822-7805

http://www.ncbi.nlm.nih.gov/pubmed?term=%22Beavis%20RC%22[Author]

MGI - Mouse Genome Informatics

http://www.informatics.jax.org/

Mouse Genome Informatics

Mass spectrometry

http://www.21stcenturybio.com/mass_spec_analytical/ms_cid.shtml

One of the most powerful tools available to the mass spectrometrist is MS/MS. Whereas fragmentation is virtually absent in electrospray mass spectrometry, it can be deliberately induced by MS/MS techniques. Tandem MS employs collision-induced dissociation (CID) to fragment a precursor ion.

Similarly, various amino acid modifications can be determined due to the gentle nature of ESI (versus MALDI, which tends to remove some modifications, such as phosphates). These include phosphorylation, glycosylation, acylation, nitronation, and many others.

Ionization source Advantages Disadvantages
Matrix associated desorption Ionization
(MALDI)
Simple sample application and acquisition,
high-throughput capable, low down-time
Variable sample preparation for
different samples

Electrospray Ionization (ESI) Consistent sample ionization efficiency,
capable of ionizing complex mixtures
Rigid sample preparation
requirements, can have high
downtime

• Amino acid
sequence can be
determined by
examining the mass
of the nested
fragments.
• Powerful
technique, does not
require protein
information.
• Not suitable for
complex protein
mixtures.

Stars, ranking

aaaaaaddddd

adjust 30px to 50px to get 5 stars

aaaaaaddddd

Foreign Key Constraints

http://dev.mysql.com/doc/refman/5.0/en/innodb-foreign-key-constraints.html

mysql> SET foreign_key_checks = 0;
mysql> SOURCE dump_file_name;
mysql> SET foreign_key_checks = 1;

Pragmatic Bookshelf

Screencasts on coding, rails, xcode, git, etc.

http://www.pragprog.com/screencasts

xvidcap - screen capture, screen record, screencast

http://xvidcap.sourceforge.net/instruct-video1.mpeg

Rails: Couldn't find Product without an ID

Couldn't find Product without an ID

Couldn't find tablename without an ID

A possible reason is that the tablename, Product doesn't have a primary_key. So fix this by editing the model and add:

class Product < ActiveRecord::Base has_many :items, :as => :item_id

set_primary_key :item_id

end

Rename database column in Rails

llhttp://stackoverflow.com/questions/1992019/how-to-rename-a-database-column-in-rails-using-migration

$ script/generate migration FixColumnName

  def self.up
    rename_column :table_name, :old_column, :new_column
  end

$ rake db:migrate

Life Built With Toxic Chemical: First Known Microbe on Earth Able to Thrive and Reproduce Using Arsenic

http://www.sciencedaily.com/releases/2010/12/101202140622.htm

Too bad they haven't named it yet, but apparently, this organism uses arsenic (chemically similar to phosphorus) instead of phosphorous in it's DNA/RNA, etc.  It was discovered in Mono Lake in California.

CGH, Chromosomal Microarray Analysis (CMA), Copy number variation (CNV)

Comparative genomic hybridization (CGH) or Chromosomal Microarray Analysis (CMA) is a molecular-cytogenetic method for the analysis of copy number changes (gains/losses) in the DNA content of a given subject's DNA and often in tumor cells.

CGH will detect only unbalanced chromosomal changes. Structural chromosome aberrations such as balanced reciprocal translocations or inversions cannot be detected, as they do not change the copy number.

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

ncRNA.org - database of non-coding RNA tools and databases

http://www.ncrna.org/

Add comments to PDF files

http://www.afritz.org/freetools/adding_PDF_comments.pdf

Protocols JOVE - Large Insert Environmental Genomic Library Production

http://www.jove.com/index/Details.stp?ID=1387

Large Insert Environmental Genomic Library Production

Papers, 5 minute

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
http://bioinformatics.oxfordjournals.org/content/26/18/i460.full
- it's fast, uses threshold-cut to limit search space
CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals.
http://bioinformatics.oxfordjournals.org/content/26/21/2776.long
- compare many things at the same time, so better accuracy?
Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001007
- uses machine learning, lower false positive rate, compared with other methods, Match, MATRIX SEARCH, QPMEME, method of Berg and von Hippel, data from ChIP-chip assays to measure transcription binding on DNA sequences of Fis (TF), binding sites obtained from RegulonDB
-  A long-standing problem has been how to identify new TF binding sites given known binding sites.

SmashCommunity: a metagenomic annotation and analysis tool
http://bioinformatics.oxfordjournals.org/content/26/23/2977.full
- SmashCommunity (Simple Metagenomics Analysis SHell for microbial communities) to annotate shotgun metagenomes with inbuilt tools for quantitative and comparative analyses.
- Each task in metagenomic analysis, such as sequence assembly or gene prediction, is implemented as a module that is a wrapper around a software program that implements this task.

BigWig and BigBed: enabling browsing of large distributed datasets
http://bioinformatics.oxfordjournals.org/content/26/17/2204.full
- BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser
- BigBed and BigWig files are similar in many ways to BAM files (Li et al., 2009), which are commonly used to store mappings of short reads to the genome.
- http://samtools.sourceforge.net/ SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data
http://gvi.seas.harvard.edu/paper/multeesum-tool-comparative-spatial-and-temporal-gene-expression-data
- Comparision of different Drosophila embryos (for morphological studies) from different Drosophila species, eg. Dmel, Dpse (Drosophila pseudoobscura, second species to be sequenced)
- Developed using the Processing language (Processing.org), based on PointCloudXplor
- http://multeesum.org/

Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths.
http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=21059789
- Using a minimal lateral network approach, we compared LGT rates at different phylogenetic depths.
- Hence our results indicate that the rate of gene acquisition per protein family are similar at the level of species (by recombination) and at the level of classes (by LGT).
is-rSNP: a novel technique for in silico regulatory SNP detection
http://bioinformatics.oxfordjournals.org/content/26/18/i524.short
- Determining the functional impact of non-coding disease-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) is challenging. Many of these SNPs are likely to be regulatory SNPs (rSNPs): variations which affect the ability of a transcription factor (TF) to bind to DNA.

Modeling associations between genetic markers using Bayesian networks
http://bioinformatics.oxfordjournals.org/content/26/18/i632.short
- Many coefficients were proposed for measuring the degree of LD, but they provide only a static view of the current LD structure. Generative models (GMs) were proposed to go beyond these measures, giving not only a description of the actual LD structure but also a tool to help understanding the process that generated such structure.
- method is based on learning optimal BN structures (weighted) from haplotype data, extracting equivalence structure classes (PDAGs) and using them to model LD.
- HapMap database
- These plots provide a nice visualization of how single nucleotide polymorphisms (SNPs) travel together in human subpopulations and samples due to linkage disequilibrium (LD).
- http://www.goldenhelix.com/SNP_Variation/Manual/svs7/using_ld_plots.html
- http://bioinformatics.oxfordjournals.org/content/23/6/774/F1.medium.gif
- snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package

Peripheral blood - circulating blood,

Peripheral blood is the flowing, circulating blood of the body. It is composed of erythrocytes, leukocytes and thrombocytes. These blood cells are suspended in blood plasma, through which the blood cells are circulated through the body. Peripheral blood is different from the blood whose circulation is enclosed within the liver, spleen, bone marrow and the lymphatic system. These areas contain their own specialized blood.

Read more: What is Peripheral Blood? | eHow.com http://www.ehow.com/about_4672930_what-peripheral-blood.html#ixzz16sx3Wl5v

http://www.ehow.com/about_4672930_what-peripheral-blood.html

----------

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

Lymph nodes also have clinical significance. They become inflamed or enlarged in various conditions, which may range from trivial, such as a throat infection, to life-threatening such as cancers. In the latter, the condition of lymph nodes is so significant that it is used for cancer staging, which decides the treatment to be employed, and for determining the prognosis.

Lymphoma is a cancer in the lymphatic of the immune system and presents as a solid tumor of lymphoid cells. It is treatable with chemotherapy, and in some cases radiotherapy and/or bone marrow transplantation, and can be curable depending on the histology, type, and stage of the disease.[1]

Thomas Hodgkin published the first description of lymphoma in 1832, specifically of the form named after him, Hodgkin's lymphoma.[2]

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

Non-hodgkin Lymphoma (Follicular lymphoma)
http://lymphoma.about.com/od/nonhodgkinlymphoma/p/follicularnhl.htm
Slow-growing cancer

Zombie Ants, Cat loving mice

Zombie ants
http://news.nationalgeographic.com/news/2009/05/photogalleries/zombie-ants/

Cat-loving mice
http://en.wikipedia.org/wiki/Toxoplasma_gondii
T. gondii infections have the ability to change the behavior of rats and mice, making them drawn to, rather than fearful of, the scent of cats. This effect is advantageous to the parasite, which will be able to sexually reproduce if its host is eaten by a cat.[11] The infection is highly precise, as it does not affect a rat's other fears such as the fear of open spaces or of unfamiliar smelling food.

Studies have also shown behavioral changes in humans, including slower reaction times and a sixfold increased risk of traffic accidents among infected males[12], as well as links to schizophrenia including hallucinations and reckless behavior[13]. A study of 191 young women in 1999 reported higher intelligence and lower guilt proneness in Toxoplasma-positive subjects[14].

from Robert Holt
http://www.bccrc.ca/dept/cmsgsc/faculty/rholt

Rene Warren
SSAKE - short read sequence aligner
http://www.renewarren.ca/main/Rene.html

Processing: A programming language for visual designers and artists

http://www.processing.org/
http://processing.org/learning/gettingstarted/

Processing is an open source programming language and environment for people who want to create images, animations, and interactions. Initially developed to serve as a software sketchbook and to teach fundamentals of computer programming within a visual context, Processing also has evolved into a tool for generating finished professional work. Today, there are tens of thousands of students, artists, designers, researchers, and hobbyists who use Processing for learning, prototyping, and production.