Tomcat server debug

Redeploy without re-starting server:

http://localhost:8080/manager

admin password in
conf/tomcat-users.xml

  <role rolename="manager"/>
  <role rolename="admin"/>
  <user username="admin" password="admin" roles="admin,manager"/>

 http://www.mkyong.com/tomcat/tomcat-default-administrator-password/

Limiting the number of records from mysqldump?

http://stackoverflow.com/questions/135835/limiting-the-number-of-records-from-mysqldump

mysqldump -h hostname -u user --quick --where="1 limit 1000000" myDatabase > out.sql


mysql --force -h hostname -u user --password=password myDatabase < out.sql

Chapter 16: Text Mining for Translational Bioinformatics

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003044

Abstract

Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research—translating basic science results into new interventions—and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

J2EE AndroMDA (Model driven Architecture)

http://myjeeva.com/how-to-create-java-j2ee-project-using-mda-tool-andromda.html

AndroMDA (pronounced as “Andromeda”) is an extensible generator framework that adheres to theModel Driven Architecture (MDA) paradigm.  It transforms UML models into deployable components forJava/J2EE & Microsoft .NET; using AndroMDA means one main thing:write less code.  Not only that, AndroMDA also lets you create better applications and maintain order on large projects.  AndroMDA enforces best practices and lets developers focus on high level problems.

Improving transcriptome assembly through error correction of high-throughput sequence reads

http://arxiv.org/abs/1304.0817

The study of functional genomics--particularly in non-model organisms has been dramatically improved over the last few years by use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure--the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on, and while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, by reducing assembly error by nearly 50%, and therefore should be applied to all datasets. 

Matthew D MacManes, Michael B Eisen

Best Places to Work Academia, 2012

http://www.the-scientist.com/?articles.view/articleNo/32392/title/Best-Places-to-Work-Academia--2012/

 Sage Bionetworks, Seattle Washington
Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences 

Autowiring in Spring

http://stackoverflow.com/questions/3153546/how-does-autowiring-work-in-spring

// tells the application context to inject an instance of UserService here
    @Autowired
    private UserService userService;

Free Web Hosting

• http://www.prchecker.info/web-hosting/top-10-free-web-hosting-sites/
• http://blogsuccessjournal.com/blog-tips-and-advice/web-hosting-reviews/10-free-web-hosting-services-to-consider-if-you-really-dont-want-to-pay-for-it/ 
• http://www.freehostingeu.com/web-hosting-page.php
• http://wiki.python.org/moin/FreeHosts  
• http://www.openshift.com/
• Google App Engine 

1. Biz.nf (PHP, MySQL, WordPress, Joomla, Free .co.nf domain, No ads)
2. Free Hosting EU (Blog / Site builder, No ads, Free .eu.pn domain)
3. AwardSpace.net (PHP, MySQL, Email Sending, No Ads, Free subdomain)
4. Biz.ly (Website & Blog builder, Photo album, Free .biz.ly domain)
5. FreeHostia.com (PHP, MySQL, 1-click Scripts, No Ads, Free subdomain)
6. Wix.com (Easy Flash website builder + mobile sites, blogs, etc.)
7. ByetHost.com (PHP, MySQL, PHPbb, SMF, Wiki, Free subdomain)
8. x10Hosting.com (Support cPanel, PHP, FTP, No ads, Free subdomain)
9. Yola.com (Visual website builder, add videos, photos, shopping cart)
10. Webs.com (Easy site builder, blog, forms, polls, Free subdomain)

Sophia Financial Group

Tracy Theemes

Financial adviser, investment, workshops

sophiafinancial.ca

How I did it: Ali Tehrani

Zymeworks took a radical approach to drug development with computer modelling that helps eliminate dead ends and focus research on leads that have the best chance of success

http://www.biv.com/article/20130416/BIV0201/304169958/how-i-did-it-ali-tehrani

Philosophy

Happiness Hypothesis
Eternal sunshine of the spotless mind

Associate Computational Biologist

Broad Institute
Cambridge, MA

http://www.genomeweb.com/node/1218816?hq_e=el&hq_m=1570572&hq_l=13&hq_v=283a2218e8

http://track.tmpservice.com/ApplyClick.aspx?id=1780974-2647-4121

Panel settings not appearing on right-click in gnome

http://askubuntu.com/questions/125891/panel-settings-not-appearing-on-right-click-in-gnome

Alt + Super (Windows Key) + Right-click

Ubuntu 12 weather indicator applet - my-weather-indicator

• sudo add-apt-repository ppa:atareao/atareao
• sudo apt-get update
• sudo apt-get install my-weather-indicator

http://askubuntu.com/questions/30334/what-application-indicators-are-available

If it fails to start

/opt/extras.ubuntu.com/my-weather-indicator/bin/my-weather-indicator

try
$ rm ~/.config/my-weather-indicator/my-weather-indicator.conf

http://www.webupd8.org/2013/02/how-to-use-your-own-weather-services.html

Annual events in Vancouver

April
Vancouver Cherry Blossom
Vaisakhi parade

Java books

• (Amazon, ISBN.nu) — Effective Java (2nd Edition)
• (Amazon, ISBN.nu) — Java Puzzlers: Traps, Pitfalls, and Corner Cases
• (Amazon, ISBN.nu) — Java Concurrency In Practice
• (Amazon, ISBN.nu) — The Java Programming Language (4th Edition)

5 Ways To Be an Exceptional Leader

http://www.openforum.com/infographics/5-ways-to-be-an-exceptional-leader/

What is GWAS?

http://ki.se/content/1/c6/02/50/96/applied-seminar_GWAS_20100128.pdf

Genome wide association studies

UAB day 4: analytical approaches

http://www.cureffi.org/2012/12/14/uab-day-4-analytical-approaches/

Speaker 1: Suzanne Leal – Methods to detect rare variant association

 

Aggregate tests

• Variously called aggregate tests, burden tests, or collapsing methods.
• Misclassification is a huge issue.  Causal variants may be excluded, neutral variants may be included.  Methods must be robust to misclassification.
• Frequency cutoffs are usually used to determine which variants to include in the analysis.

Brains as Clear as Jell-O for Scientists to Explore

http://www.nytimes.com/2013/04/11/science/brains-as-clear-as-jell-o-for-scientists-to-explore.html?_r=0

Scientists at Stanford University reported on Wednesday that they have made a whole mouse brain, and part of a human brain, transparent, so that networks of neurons that receive and send information can be highlighted in stunning color and viewed in all their three-dimensional complexity without slicing up the organ.

Two views of the same intact adult mouse brain, before, at left, and after a new technique developed by researchers at Stanford University was applied to it to make its tissue transparent. 

Even more important, experts say, is that unlike earlier methods for making the tissue of brains and other organs transparent, the new process, called Clarity by its inventors, preserves the biochemistry of the brain so well that researchers can test it over and over again with chemicals that highlight specific structures within a brain and provide clues to its past activity. The researchers say this process may help uncover the physical underpinnings of devastating mental disorders like schizophrenia, autism, post-traumatic stress disorder and others. 

There are several ways to make tissue transparent. The key to the new technique is a substance called a hydrogel, a material that is mostly water held together by larger molecules to give it some solidity. 

Dr. Chung said the hydrogel forms a kind of mesh that permeates the brain and connects to most of the molecules, but not to the lipids, which include fats and some other substances. The brain is then put in a soapy solution and an electric current is applied, which drives the solution through the brain, washing out the lipids. Once they are out, the brain is transparent, and its biochemistry is intact, so it may be infused with chemicals, like antibody molecules that also have a dye attached, that show fine details of its structure and previous activity. 

Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders

Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders
http://www.nature.com/jhg/journal/v57/n10/full/jhg201291a.html

Traditional approaches for gene mapping from candidate gene studies to positional cloning strategies have been applied for Mendelian disorders. Since 2005, next-generation sequencing (NGS) technologies are improving as rapid, high-throughput and cost-effective approaches to fulfill medical sciences and research demands. Using NGS, the underlying causative genes are directly distinguished via a systematic filtering, in which the identified gene variants are checked for novelty and functionality. During the past 2 years, the role of more than 100 genes has been distinguished in rare Mendelian disorders by means of whole-exome sequencing (WES). Combination of WES with traditional approaches, consistent with linkage analysis, has had the greatest impact on those disorders following autosomal mode of inheritance; in more than 60 identified genes, the causal variants have been transmitted at homozygous or compound heterozygous state. Recent literatures focusing on identified new causal genes in Mendelian disorders using WES are reviewed in the present survey.

Keywords: exome sequencing; mendelian disorder; mutation; next-generation sequencing; NGS; WES

Computational and statistical approaches to analyzing variants identified by exome sequencing

http://genomebiology.com/2011/12/9/227

New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged.

 

Consensus Rules in Variant Detection from Next-Generation Sequencing Data

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038470#s4
A critical step in detecting variants from next-generation sequencing data ispost hoc filtering of putative variants called or predicted by computational tools. Here, we highlight four critical parameters that could enhance the accuracy of called single nucleotide variants and insertions/deletions: quality and deepness, refinement and improvement of initial mapping, allele/strand balance, and examination of spurious genes. Use of these sequence features appropriately in variant filtering could greatly improve validation rates, thereby saving time and costs in next-generation sequencing projects.

Transcriptome profiling in neurodegenerative disease

http://www.sciencedirect.com/science/article/pii/S0165027010004784

Changes in gene expression and splicing patterns (that occur prior to the onset and during the progression of complex diseases) have become a major focus of neurodegenerative disease research. These signature patterns of gene expression provide clues about the mechanisms involved in the molecular pathogenesis of neurodegenerative disease and may facilitate the discovery of novel therapeutic drugs. With the development of array technologies and the very recent RNA-seq technique, our understanding of the pathogenesis of neurodegenerative disease is expanding exponentially. Here, we review the technologies involved in gene expression and splicing analysis and the related literature on three common neurodegenerative diseases: Alzheimer's disease, Parkinson's disease and Huntington's disease.