BioVenn - Venn diagrams

BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

http://www.cmbi.ru.nl/cdd/biovenn/

Evaluating the Comparability of Gene Expression in Blood and Brain

Evaluating the Comparability of Gene  Expression in Blood and Brain

http://www.ncbi.nlm.nih.gov/pubmed/16526044

Abstract

The availability of an accessible tissue whose gene expression profile is similar to more inaccessible CNS tissues has the potential to advance research in neuropsychiatric disorders. We conducted secondary data analysis of transcriptional profiling of 79 human tissues for 33,698 genes using the Affymetrix U133A microarray augmented with a custom microarray (Affymetrix GNF1H), which were produced by the Genomics Institute of the Novartis Research Foundation (http://symatlas.gnf.org). Our analyses suggested that: (a) on a transcriptome level, whole blood shares significant gene expression similarities with multiple CNS tissues; (b) the median non-parametric correlation between transcripts present in both whole blood and CNS was around 0.5; (c) this correlation of 0.5 was intermediate relative to all tissues in the Novartis data set--less than for the maximum achievable value of 0.85, less than a set of immune tissues (0.64), comparable to a heterogeneous set of somatic tissues (0.57) but greater than muscle (0.48) and peripheral nervous system tissues (0.36); (d) about half of a set of candidate genes relevant to schizophrenia were expressed in both whole blood and prefrontal cortex; and (e) the expression levels of many classes of biologically relevant processes were not significantly different between whole blood and prefrontal cortex. These analyses suggest that gene expression in whole blood is neither perfectly correlated and useful nor perfectly uncorrelated and useless with gene expression in multiple brain tissues. This suggests that the cautious and thoughtful use of peripheral gene expression may be a useful surrogate for gene expression in the CNS when it has been determined that the relevant gene is expressed in both.

Autism: The Road Back

http://www.knowledge.ca/program/autism-the-road-back

Autism: The Road Back charts the personal journey of three BC families with children who have been diagnosed with Autism Spectrum Disorder. It talks to parents, service providers, and experts in the field about assessment, diagnosis, and options available for treatment, and provides guidance for families trying to navigate their way through the challenges of ASD in the first six years of their child's life.

Related Links:
Autism Society of British Columbia
F.E.A.T. of BC
Autism Society of Canada

The genetic essence of our brains

http://www.nature.com/nmeth/journal/v9/n11/full/nmeth.2236.html?WT.ec_id=NMETH-201211

Two complete normal brains from adult male donors were first imaged by magnetic resonance imaging, then cut into sections, analyzed using histological techniques and finally reduced to 900 samples

Despite the fact that the neocortex is composed of over 15 billion neurons, the genetic signature of its different regions proved to be relatively homogeneous.

The group found that genetic variation across the different neocortical areas followed a graded pattern: the closer two neighboring regions were, the more similar their transcriptomes.

calcium binding protein CALB1, with a profile that was unique to humans

Hawrylycz, M.J. et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489, 391–399 (2012).

Points of view: Pencil and paper

http://www.nature.com/nmeth/journal/v9/n11/full/nmeth.2223.html?WT.ec_id=NMETH-201211

Creating pictures is integral to scientific thinking. In the visualization process, putting pencil to paper is an essential act of inward reflection and outward expression.

Visualization is vital to the scientific process. Relying on the powerful connection between thinking, seeing and understanding, exploratory drawing is critical for creating frameworks for knowledge.

Installing Zend Server

http://informasjonsviteren.blogspot.ca/2011/05/setting-up-zend-server-ce-in-ubuntu.html

$ sudo /usr/local/zend/bin/zendctl.sh restart

http://localhost:1008

install oracle java on ubuntu

http://ubuntuforums.org/showthread.php?p=11889700

sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java7-installer

Systems Analyst

problem solver
person that communicates business problems to software developers
requirements gathering - business requirements vs technical requirements
systems design and implementation
continuous testing, updating documentation
draw flowcharts, ER diagrams
systems development life cycle
project scope
deals with software and hardware
prepare financial reports

http://programmers.stackexchange.com/questions/22983/is-it-easy-for-a-developer-to-become-a-system-business-analysts?rq=1

Institute for Systems Analysis
http://www.youtube.com/watch?v=swO4j05Bi-Q&list=UUrhD6R3KJM8bAhWvuGWr85A&index=17&feature=plcp
http://www.youtube.com/watch?v=VEZKftiSRbE
http://www.youtube.com/watch?v=FwUVeow0MyA&feature=related
http://www.youtube.com/watch?v=ScVvNuuHg2M
http://www.youtube.com/watch?v=nDOFAatCRak

http://jobs.phsa.ca/ca/vancouver/information-technology/jobid2890543-systems-analyst-_-designer-(community)-jobs

Systems Analyst / Designer (Community)

Reference # 18062 & 18063

Regular Full-Time

Wage: $34.36 per hour

555 W 12^th Ave

Vancouver, BC

Within the context of the Information Management/Information Systems (IMIS) shared services initiative between Vancouver Coastal Health (VCH) and Providence Health Care (PHC), this is a professional level job responsible for maintaining the functioning of Community clinical information system(s) within a multi-site environment. The Systems Analyst/Designer is responsible for system maintenance, enhancement, evaluation, and design with a focus to meet Community client business needs, identifying and planning for the impact(s) of change on client departments.  Prepares detailed specifications, including flowcharts showing Community system linkage, data movement and resource requirements, from which complete programs will be written.  Participates on project teams and undertakes tasks as assigned.  Works with vendors to ensure service levels meet corporate standards; tests and evaluates software in order to recommend products that will meet current and future needs.  Provides user support, training and consultation as well as other user liaison services.  Provides input into the development of policies and procedures for designated Community healthcare information systems.

Example of Duties & Responsibilities

• Develops and maintains application programs by creating logic specifications, coding, testing, evaluating and documenting programs in accordance with established standards; ensures adequate file space is maintained by identifying and archiving data according to established procedures; ensures security measures are in place by verifying and monitoring user security assignments and liaising with co-workers responsible for maintaining systems security. 


• Ensures errors/deficiencies are corrected as required by responding to the user complaint or Help Desk report, analyzing/troubleshooting the problem, taking corrective action and testing to ensure the system meets optimum efficiency, managing client expectations and providing the required documentation. 


• Develops system design of approved projects or enhancements to a system by identifying information components involved, detailing data flow, determining the nature of changes required to interface with existing systems and developing, writing comprehensive system and operating documentation and preparing system design documents for user sign-off. 


• Determines or participates in the determination of healthcare business needs and technology requirements by methods such as interviewing department management and staff, participating in planning committees, assessing information and defining/documenting user requirements, conducting feasibility/advisability studies on proposed plans, and leading the data and process modeling activities. 


• Develops project plan and implementation schedules by developing system proposals and compiling project work plans, monitoring and controlling project plans and initiating action where required. 


• Provides information technology direction to project team members by participating in the client's planning committee as required, producing Requests for Proposals (RFP) documentation to be sent to vendors, assessing cost/benefit and feasibility/advisability of various technological and software packages, preparing cost/benefit recommendations for acquisitions and keeping informed of new developments in the industry.

Qualifications

Education & Experience

• Graduation from a recognized degree or diploma program in Computer Science or Health Information Sciences, three years' recent related experience or an equivalent combination of education, training and experience.  

Knowledge & Abilities

• Ability to plan, organize, problem solve and prioritize work.
• Ability to work in a networked environment.
• Ability to communicate effectively both verbally and in writing.
• Ability to deal with others effectively.
• Ability to work in a healthcare environment.
• Physical ability to carry out the duties of the position.
• Ability to write programs in a variety of programming languages.
• Ability to utilize effectively related hardware and software.

 

We invite you to apply by clicking the "Apply Online Now" button where you can register for the first time or enter your Username and Password in order to re-access your profile on our system.

Genotype-Tissue Expression (GTEx)

GTEx moves from pilot to scale up – The GTEx program is creating a comprehensive data and sample resource of genetic variation and gene expression profiles in multiple tissues from post-mortem donors. This resource will aid in the interpretation of Genome Wide Association Studies and help prioritize therapeutic targets by identifying those that affect gene expression.

http://commonfund.nih.gov/GTEx/

Japan Hotel Accommodations

Tokyo
Hotel Toyo
Oak Hotel
Khaosan Tokyo Smile
Backpacker's Hostel K's House
http://yokohama.hostelvillage.com/en/
http://www.toukaisou.com/index-e.htm
khaosantokyo.com


Osaka
Hotel Taiyo
Guesthouse Ueno
Hotel Chuo

Kyoto
Econo-Inn
Hotel Gojo


http://www.guardian.co.uk/travel/2012/feb/01/10-best-budget-hotels-tokyo
http://www.tripadvisor.ca/TravelersChoice-Hotels-cBargain-g294232
http://hanahostel.com/e_link.html

Convert PDF to PS

tiff2pdf
tiff2ps

pdf2ps
ps2pdf

or use Gimp

http://ubuntuforums.org/showthread.php?t=1478710

Why You Should Reject the “Rejection Improves Impact” Meme

http://caseybergman.wordpress.com/2012/10/25/why-you-should-reject-the-rejection-improves-impact-meme/

Over the last two weeks, a meme has been making the rounds in the scientific twittersphere that goes something like “Rejection of a scientific manuscript improves its eventual impact”.  This idea is based a recent analysis of patterns of manuscript submissionreported in Science by Calcagno et al., which has been actively touted in the scientific press and seems to have touched a nerve with many scientists.

To be fair, Science Insider does acknowledge that the effect is weak: “previously rejected papers had a slight bump in the number of times they were cited by other papers”

Calcagno, V., Demoinet, E., Gollner, K., Guidi, L., Ruths, D., & de Mazancourt, C. (2012). Flows of Research Manuscripts Among Scientific Journals Reveal Hidden Submission Patterns Science DOI: 10.1126/science.1227833

Improbable Research

http://www.improbable.com/ig/winners/#ig2012
http://www.jsur.org/ - Journal of Serendipitous and Unexpected Results

The 2012 Ig Nobel Prize Winners

Winners were announced and awarded on Thursday night, September 20. The ceremony was webcast live. For more information, check the ceremony page.
PSYCHOLOGY PRIZE: Anita Eerland and Rolf Zwaan [THE NETHERLANDS] and Tulio Guadalupe [PERU, RUSSIA, and THE NETHERLANDS] for their study "Leaning to the Left Makes the Eiffel Tower Seem Smaller"
REFERENCE: "Leaning to the Left Makes the Eiffel Tower Seem Smaller: Posture-Modulated Estimation," Anita Eerland, Tulio M. Guadalupe and Rolf A. Zwaan, Psychological Science, vol. 22 no. 12, December 2011, pp. 1511-14.
ATTENDING THE CEREMONY: Tulio Guadalupe. [NOTE: Two days after the ceremony, Anita Eerland and Rolf Zwaan married each other, in the Netherlands.]

PEACE PRIZE: The SKN Company [RUSSIA], for converting old Russian ammunition into new diamonds.
ATTENDING THE CEREMONY: Igor Petrov

ACOUSTICS PRIZE: Kazutaka Kurihara and Koji Tsukada [JAPAN] for creating the SpeechJammer — a machine that disrupts a person's speech, by making them hear their own spoken words at a very slight delay.
REFERENCE: "SpeechJammer: A System Utilizing Artificial Speech Disturbance with Delayed Auditory Feedback", Kazutaka Kurihara, Koji Tsukada, arxiv.org/abs/1202.6106. February 28, 2012.
ATTENDING THE CEREMONY: Kazutaka Kurihara and Koji Tsukada

NEUROSCIENCE PRIZE: Craig Bennett, Abigail Baird, Michael Miller, and George Wolford [USA], for demonstrating that brain researchers, by using complicated instruments and simple statistics, can see meaningful brain activity anywhere — even in a dead salmon.
REFERENCE: "Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction," Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford, poster, 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco, CA, June 2009.
REFERENCE: "Neural Correlates of Interspecies Perspective Taking in the Post-Mortem Atlantic Salmon: An Argument For Multiple Comparisons Correction," Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford, Journal of Serendipitous and Unexpected Results, vol. 1, no. 1, 2010, pp. 1-5.
ATTENDING THE CEREMONY: Craig Bennett, Abigail Baird, Michael Miller, and George Wolford