Thursday, June 30, 2011

Car Rankings: Affordable Small Cars

http://usnews.rankingsandreviews.com/cars-trucks/rankings/Affordable-Small-Cars/

Exome sequencing pipeline

http://biostar.stackexchange.com/questions/1269/what-is-the-best-pipeline-for-human-whole-exome-sequencing

Phylop vs Phastcons

PhastCons (region) (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns.

By contrast, phyloP (position) separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).

http://compgen.bscb.cornell.edu/phast/faq.php
http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=200695383&g=cons30way#a_cfg_phastcons 

Publishing in the web for free

Google Sites
https://www.google.com/accounts
The key feature of Google Sites is its collaboration abilities

Wordpress
http://wordpress.com/
Powerful design

http://productivewise.com/free-website-building-platforms-compared-wordpress-google-sites/

What Makes You Irresistible to Employers


In a tight market, every job seeker needs to find a way to stand out from the crowd. What separates the "great" from the "good" and makes a particular candidate just too irresistible to pass up?

Oftentimes, it is one of these three things:

  • Ability to Prove Worth, 
  • More than a Simple Knowledge of the Company, 
  • and Enthusiasm.

http://www.careerbuilder.ca/Article/CB-774-Job-Search-What-makes-you-irresistible-to-employers/?sc_extcmp=cbca_9774&cblang=CAEnglish&SiteId=cbca_9774

Tips for landing higher pay in a new role

Here's how to excel in the art of negotiation:
  • Know Your Benchmark
  • Set a Minimum Threshold
  • Don't Start Too Early
  • Demonstrate Your Value
  • Be Assertive

BGI to expand into clinical, drug-development services

Earlier this month, Adam Bonislawski at GenomeWeb’s Proteomonitor reported that China-based BGI intends to expand its proteomics offerings and buy 50 new mass spectrometers over the next two years. This diversification into clinical and drug-development services is a forward-thinking move for the genomics/bioinformatics giant and one that should be taken seriously by current proteomics service providers.

http://www.medcitynews.com/2011/06/bgi-to-expand-into-clinical-drug-development-services/

new generation of ExPASy

SIB Swiss Institute of Bioinformatics just launched the new generation of ExPASy, a web portal which offers a point of entry to more than 120 SIB bioinformatics resources


http://www.expasy.org/

Crows learning

Not so bird-brained: Clever crows recognise faces

http://www.google.com/hostednews/afp/article/ALeqM5gDb05xN18drPIMfucOK6FaDQqcog?docId=CNG.b543d6b84be023e079ab0236d9bba908.491

Wednesday, June 29, 2011

A New Bioinformatics System Improves Medical Diagnosis

http://www.sciencedaily.com/releases/2011/06/110628094833.htm

The algorithm, called CliDaPa (Clinical Data Partitioning), uses histological and clinical data and pharmacological treatments to partition patients by means of a tree representation for a particular disease (called clinical tree), used to cluster patients according to similar behaviour. It then uses data mining techniques to analyse each patient partition with the associated genetic information.

CliDaPa is a different method of DNA microarray analysis that aims to generate a model representing different patient behaviours (gathered from clinical data). These behaviours will then be examined separately and specifically by means of data mining. New learning methods were also proposed in the course of the research.

Literature mining, ontologies and information visualization for drug repurposing

http://bib.oxfordjournals.org/content/early/2011/06/28/bib.bbr005.abstract?papetoc


Abstract

The immense growth of MEDLINE coupled with the realization that a vast amount of biomedical knowledge is recorded in free-text format, has led to the appearance of a large number of literature mining techniques aiming to extract biomedical terms and their inter-relations from the scientific literature. Ontologies have been extensively utilized in the biomedical domain either as controlled vocabularies or to provide the framework for mapping relations between concepts in biology and medicine. Literature-based approaches and ontologies have been used in the past for the purpose of hypothesis generation in connection with drug discovery. Here, we review the application of literature mining and ontology modeling and traversal to the area of drug repurposing (DR). In recent years, DR has emerged as a noteworthy alternative to the traditional drug development process, in response to the decreased productivity of the biopharmaceutical industry. Thus, systematic approaches to DR have been developed, involving a variety of in silico, genomic and high-throughput screening technologies. Attempts to integrate literature mining with other types of data arising from the use of these technologies as well as visualization tools assisting in the discovery of novel associations between existing drugs and new indications will also be presented.                  

http://nar.oxfordjournals.org/content/39/suppl_2/W450.abstract?etoc

Prevent ssh connection from disconnecting

$ man ssh_config
$ cat /etc/ssh/ssh_config
...
#   ProxyCommand ssh -q -W %h:%p gateway.example.com
    SendEnv LANG LC_*
    HashKnownHosts yes
#   GSSAPIAuthentication yes
#   GSSAPIDelegateCredentials no

ServerAliveInterval 30
ServerAliveCountMax 4

Get list of unread e-mails in Gmail

Type in search

label:unread

https://mail.google.com/mail/?shva=1#search/label%3Aunread

Nucleic Acids Research

Articles

The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community

Michelle D. Brazas, David S. Yim, Joseph T. Yamada, and B. F. Francis Ouellette
Nucl. Acids Res. 2011 39:W3-W7.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W3

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences

Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon
Nucl. Acids Res. 2011 39:W8-W12.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W8

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

Paolo Di Tommaso, Sebastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, and Cedric Notredame
Nucl. Acids Res. 2011 39:W13-W17.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W13

iPBA: a tool for protein structure comparison using sequence alignment strategies

Jean-Christophe Gelly, Agnel Praveen Joseph, Narayanaswamy Srinivasan, and Alexandre G. de Brevern
Nucl. Acids Res. 2011 39:W18-W23.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W18

CLICK—topology-independent comparison of biomolecular 3D structures

M. N. Nguyen, K. P. Tan, and M. S. Madhusudhan
Nucl. Acids Res. 2011 39:W24-W28.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W24

HMMER web server: interactive sequence similarity searching

Robert D. Finn, Jody Clements, and Sean R. Eddy
Nucl. Acids Res. 2011 39:W29-W37.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W29

FFAS server: novel features and applications

Lukasz Jaroszewski, Zhanwen Li, Xiao-hui Cai, Christoph Weber, and Adam Godzik
Nucl. Acids Res. 2011 39:W38-W44.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W38

R3D-BLAST: a search tool for similar RNA 3D substructures

Yun-Chen Liu, Chung-Han Yang, Kun-Tze Chen, Jyun-Rong Wang, Mei-Ling Cheng, Jen-Chun Chung, Hsien-Tai Chiu, and Chin Lung Lu
Nucl. Acids Res. 2011 39:W45-W49.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W45

WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs

Anton I. Petrov, Craig L. Zirbel, and Neocles B. Leontis
Nucl. Acids Res. 2011 39:W50-W55.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W50

SLiMSearch 2.0: biological context for short linear motifs in proteins

Norman E. Davey, Niall J. Haslam, Denis C. Shields, and Richard J. Edwards
Nucl. Acids Res. 2011 39:W56-W60.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W56

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design

Lars Rønn Olsen, Niels Bjørn Hansen, Mads Tvillinggaard Bonde, Hans Jasper Genee, Dorte Koefoed Holm, Simon Carlsen, Bjarne Gram Hansen, Kiran Raosaheb Patil, Uffe Hasbro Mortensen, and Rasmus Wernersson
Nucl. Acids Res. 2011 39:W61-W67.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W61

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Christophe Blanchet, Marco Pasi, Krystyna Zakrzewska, and Richard Lavery
Nucl. Acids Res. 2011 39:W68-W73.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W68

ConTra v2: a tool to identify transcription factor binding sites across species, update 2011

Stefan Broos, Paco Hulpiau, Jeroen Galle, Bart Hooghe, Frans Van Roy, and Pieter De Bleser
Nucl. Acids Res. 2011 39:W74-W78.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W74

Genome surveyor 2.0: cis-regulatory analysis in Drosophila

Majid Kazemian, Michael H. Brodsky, and Saurabh Sinha
Nucl. Acids Res. 2011 39:W79-W85.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W79

RSAT 2011: regulatory sequence analysis tools

Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, and Jacques van Helden
Nucl. Acids Res. 2011 39:W86-W91.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W86

The RNAmute web server for the mutational analysis of RNA secondary structures

Alexander Churkin, Idan Gabdank, and Danny Barash
Nucl. Acids Res. 2011 39:W92-W99.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W92

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences

Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, and Kiyoshi Asai
Nucl. Acids Res. 2011 39:W100-W106.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W100

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

Stefan E. Seemann, Peter Menzel, Rolf Backofen, and Jan Gorodkin
Nucl. Acids Res. 2011 39:W107-W111.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W107

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, and Steve Hoffmann
Nucl. Acids Res. 2011 39:W112-W117.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W112

ncFANs: a web server for functional annotation of long non-coding RNAs

Qi Liao, Hui Xiao, Dechao Bu, Chaoyong Xie, Ruoyu Miao, Haitao Luo, Guoguang Zhao, Kuntao Yu, Haitao Zhao, Geir Skogerbø, Runsheng Chen, Zhongdao Wu, Changning Liu, and Yi Zhao
Nucl. Acids Res. 2011 39:W118-W124.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W118

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling

Christopher L. Plaisier, J. Christopher Bare, and Nitin S. Baliga
Nucl. Acids Res. 2011 39:W125-W131.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W125

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

Michael Hackenberg, Naiara Rodríguez-Ezpeleta, and Ana M. Aransay
Nucl. Acids Res. 2011 39:W132-W138.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W132

mirAct: a web tool for evaluating microRNA activity based on gene expression data

Zhi Liang, Hong Zhou, Zongxiao He, Haoran Zheng, and Jiarui Wu
Nucl. Acids Res. 2011 39:W139-W144.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W139

DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

Manolis Maragkakis, Thanasis Vergoulis, Panagiotis Alexiou, Martin Reczko, Kyriaki Plomaritou, Mixail Gousis, Kornilios Kourtis, Nectarios Koziris, Theodore Dalamagas, and Artemis G. Hatzigeorgiou
Nucl. Acids Res. 2011 39:W145-W148.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W145

RNApredator: fast accessibility-based prediction of sRNA targets

Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, and Ivo L. Hofacker
Nucl. Acids Res. 2011 39:W149-W154.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W149

psRNATarget: a plant small RNA target analysis server

Xinbin Dai and Patrick Xuechun Zhao
Nucl. Acids Res. 2011 39:W155-W159.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W155

corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs

Edmund Lam, Alfred Kam, and Jérôme Waldispühl
Nucl. Acids Res. 2011 39:W160-W166.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W160

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map

Elina Tjioe, Keren Lasker, Ben Webb, Haim J. Wolfson, and Andrej Sali
Nucl. Acids Res. 2011 39:W167-W170.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W167

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction

Daniel B. Roche, Maria T. Buenavista, Stuart J. Tetchner, and Liam J. McGuffin
Nucl. Acids Res. 2011 39:W171-W176.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W171

KINARI-Web: a server for protein rigidity analysis

Naomi Fox, Filip Jagodzinski, Yang Li, and Ileana Streinu
Nucl. Acids Res. 2011 39:W177-W183.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W177

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

Frédéric Poitevin, Henri Orland, Sebastian Doniach, Patrice Koehl, and Marc Delarue
Nucl. Acids Res. 2011 39:W184-W189.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W184

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs

Ian Walsh, Alberto J. M. Martin, Tomàs Di Domenico, Alessandro Vullo, Gianluca Pollastri, and Silvio C. E. Tosatto
Nucl. Acids Res. 2011 39:W190-W196.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W190

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, and Rita Casadio
Nucl. Acids Res. 2011 39:W197-W202.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W197

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

Leslie Regad, Adrien Saladin, Julien Maupetit, Colette Geneix, and Anne-Claude Camproux
Nucl. Acids Res. 2011 39:W203-W209.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W203

The FALC-Loop web server for protein loop modeling

Junsu Ko, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias, Julian Lee, and Chaok Seok
Nucl. Acids Res. 2011 39:W210-W214.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W210

SDM—a server for predicting effects of mutations on protein stability and malfunction

Catherine L. Worth, Robert Preissner, and Tom L. Blundell
Nucl. Acids Res. 2011 39:W215-W222.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W215

GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing

Alexander A. Kantardjiev
Nucl. Acids Res. 2011 39:W223-W228.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W223

PRUNE and PROBE—two modular web services for protein–protein docking

Pralay Mitra and Debnath Pal
Nucl. Acids Res. 2011 39:W229-W234.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W229

firestar—advances in the prediction of functionally important residues

Gonzalo Lopez, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, and Michael L. Tress
Nucl. Acids Res. 2011 39:W235-W241.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W235

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Kuan Pern Tan, Raghavan Varadarajan, and M. S. Madhusudhan
Nucl. Acids Res. 2011 39:W242-W248.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W242

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

Nir London, Barak Raveh, Eyal Cohen, Guy Fathi, and Ora Schueler-Furman
Nucl. Acids Res. 2011 39:W249-W253.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W249

PAComplex: a web server to infer peptide antigen families and binding models from TCR–pMHC complexes

I-Hsin Liu, Yu-Shu Lo, and Jinn-Moon Yang
Nucl. Acids Res. 2011 39:W254-W260.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W254

Swimming into peptidomimetic chemical space using pepMMsMIMIC

Matteo Floris, Joel Masciocchi, Marco Fanton, and Stefano Moro
Nucl. Acids Res. 2011 39:W261-W269.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W261

SwissDock, a protein-small molecule docking web service based on EADock DSS

Aurélien Grosdidier, Vincent Zoete, and Olivier Michielin
Nucl. Acids Res. 2011 39:W270-W277.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W270

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Luca Parca, Iolanda Mangone, Pier Federico Gherardini, Gabriele Ausiello, and Manuela Helmer-Citterich
Nucl. Acids Res. 2011 39:W278-W282.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W278

PredUs: a web server for predicting protein interfaces using structural neighbors

Qiangfeng Cliff Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, and Donald Petrey
Nucl. Acids Res. 2011 39:W283-W287.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W283

MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

Andrea Passerini, Marco Lippi, and Paolo Frasconi
Nucl. Acids Res. 2011 39:W288-W292.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W288

RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology

Aleksandra Gruca, Marek Sikora, and Andrzej Polanski
Nucl. Acids Res. 2011 39:W293-W301.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W293

ADGO 2.0: interpreting microarray data and list of genes using composite annotations

Sang-Mun Chi, Jin Kim, Seon-Young Kim, and Dougu Nam
Nucl. Acids Res. 2011 39:W302-W306.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W302

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

Jüri Reimand, Tambet Arak, and Jaak Vilo
Nucl. Acids Res. 2011 39:W307-W315.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W307

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, and Liping Wei
Nucl. Acids Res. 2011 39:W316-W322.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W316

BioProfiling.de: analytical web portal for high-throughput cell biology

Alexey V. Antonov
Nucl. Acids Res. 2011 39:W323-W327.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W323

AnnotQTL: a new tool to gather functional and comparative information on a genomic region

F. Lecerf, A. Bretaudeau, O. Sallou, C. Desert, Y. Blum, S. Lagarrigue, and O. Demeure
Nucl. Acids Res. 2011 39:W328-W333.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W328

PINTA: a web server for network-based gene prioritization from expression data

Daniela Nitsch, Léon-Charles Tranchevent, Joana P. Gonçalves, Josef Korbinian Vogt, Sara C. Madeira, and Yves Moreau
Nucl. Acids Res. 2011 39:W334-W338.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W334

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Eriko Takano, and Rainer Breitling
Nucl. Acids Res. 2011 39:W339-W346.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W339

PHAST: A Fast Phage Search Tool

You Zhou, Yongjie Liang, Karlene H. Lynch, Jonathan J. Dennis, and David S. Wishart
Nucl. Acids Res. 2011 39:W347-W352.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W347

GCView: the genomic context viewer for protein homology searches

Iwan Grin and Dirk Linke
Nucl. Acids Res. 2011 39:W353-W356.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W353

MarkUs: a server to navigate sequence–structure–function space

Markus Fischer, Qiangfeng Cliff Zhang, Fabian Dey, Brian Y. Chen, Barry Honig, and Donald Petrey
Nucl. Acids Res. 2011 39:W357-W361.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W357

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

Marc Röttig, Marnix H. Medema, Kai Blin, Tilmann Weber, Christian Rausch, and Oliver Kohlbacher
Nucl. Acids Res. 2011 39:W362-W367.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W362

PILGRM: an interactive data-driven discovery platform for expert biologists

Casey S. Greene and Olga G. Troyanskaya
Nucl. Acids Res. 2011 39:W368-W374.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W368

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

Andrea Pierleoni, Valentina Indio, Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio
Nucl. Acids Res. 2011 39:W375-W380.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W375

PepServe: a web server for peptide analysis, clustering and visualization

Anastasia Alexandridou, Nikolas Dovrolis, George Th. Tsangaris, Konstantina Nikita, and George Spyrou
Nucl. Acids Res. 2011 39:W381-W384.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W381

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

H. B. Rao, F. Zhu, G. B. Yang, Z. R. Li, and Y. Z. Chen
Nucl. Acids Res. 2011 39:W385-W390.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W385

CENTDIST: discovery of co-associated factors by motif distribution

Zhizhuo Zhang, Cheng Wei Chang, Wan Ling Goh, Wing-Kin Sung, and Edwin Cheung
Nucl. Acids Res. 2011 39:W391-W399.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W391

GLAMM: Genome-Linked Application for Metabolic Maps

John T. Bates, Dylan Chivian, and Adam P. Arkin
Nucl. Acids Res. 2011 39:W400-W405.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W400

The University of Minnesota Pathway Prediction System: multi-level prediction and visualization

Junfeng Gao, Lynda B. M. Ellis, and Lawrence P. Wackett
Nucl. Acids Res. 2011 39:W406-W411.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W406

iPath2.0: interactive pathway explorer

Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, and Peer Bork
Nucl. Acids Res. 2011 39:W412-W415.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W412

mirConnX: condition-specific mRNA-microRNA network integrator

Grace T. Huang, Charalambos Athanassiou, and Panayiotis V. Benos
Nucl. Acids Res. 2011 39:W416-W423.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W416

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

Alex Lan, Ilan Y. Smoly, Guy Rapaport, Susan Lindquist, Ernest Fraenkel, and Esti Yeger-Lotem
Nucl. Acids Res. 2011 39:W424-W429.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W424

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

Jing Qin, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, and Junwen Wang
Nucl. Acids Res. 2011 39:W430-W436.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W430

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

Kunlin Zhang, Suhua Chang, Sijia Cui, Liyuan Guo, Liuyan Zhang, and Jing Wang
Nucl. Acids Res. 2011 39:W437-W443.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W437

SNPsyn: detection and exploration of SNP–SNP interactions

Tomaz Curk, Gregor Rot, and Blaz Zupan
Nucl. Acids Res. 2011 39:W444-W449.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W444

CoPub update: CoPub 5.0 a text mining system to answer biological questions

Wilco W. M. Fleuren, Stefan Verhoeven, Raoul Frijters, Bart Heupers, Jan Polman, René van Schaik, Jacob de Vlieg, and Wynand Alkema
Nucl. Acids Res. 2011 39:W450-W454.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W450

Génie: literature-based gene prioritization at multi genomic scale

Jean-Fred Fontaine, Florian Priller, Adriano Barbosa-Silva, and Miguel A. Andrade-Navarro
Nucl. Acids Res. 2011 39:W455-W461.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W455

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature

Moushumi Sen Sarma, David Arcoleo, Radhika S. Khetani, Brant Chee, Xu Ling, Xin He, Jing Jiang, Qiaozhu Mei, ChengXiang Zhai, and Bruce Schatz
Nucl. Acids Res. 2011 39:W462-W469.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W462

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Rubén Sánchez, François Serra, Joaquín Tárraga, Ignacio Medina, José Carbonell, Luis Pulido, Alejandro de María, Salvador Capella-Gutíerrez, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, and Hernán Dopazo
Nucl. Acids Res. 2011 39:W470-W474.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W470

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Ivica Letunic and Peer Bork
Nucl. Acids Res. 2011 39:W475-W478.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W475

PhyleasProg: a user-oriented web server for wide evolutionary analyses

Joël Busset, Cédric Cabau, Camille Meslin, and Géraldine Pascal
Nucl. Acids Res. 2011 39:W479-W485.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W479

ChemMine tools: an online service for analyzing and clustering small molecules

Tyler W. H. Backman, Yiqun Cao, and Thomas Girke
Nucl. Acids Res. 2011 39:W486-W491.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W486

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome

Heng Luo, Jian Chen, Leming Shi, Mike Mikailov, Huang Zhu, Kejian Wang, Lin He, and Lun Yang
Nucl. Acids Res. 2011 39:W492-W498.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W492

Detecting selection in immunoglobulin sequences

Mohamed Uduman, Gur Yaari, Uri Hershberg, Jacob A. Stern, Mark J. Shlomchik, and Steven H. Kleinstein
Nucl. Acids Res. 2011 39:W499-W504.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W499

ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry

Manor Askenazi and Michal Linial
Nucl. Acids Res. 2011 39:W505-W510.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W505

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

Enguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, and François-Yves Dupradeau
Nucl. Acids Res. 2011 39:W511-W517.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W511

CoMet—a web server for comparative functional profiling of metagenomes

Thomas Lingner, Kathrin Petra Aßhauer, Fabian Schreiber, and Peter Meinicke
Nucl. Acids Res. 2011 39:W518-W523.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W518

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Jose M. Muiño, Marlous Hoogstraat, Roeland C. H. J. van Ham, and Aalt D. J. van Dijk
Nucl. Acids Res. 2011 39:W524-W527.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W524

The BioExtract Server: a web-based bioinformatic workflow platform

Carol M. Lushbough, Douglas M. Jennewein, and Volker P. Brendel
Nucl. Acids Res. 2011 39:W528-W532.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W528


Web Services

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

Norio Kobayashi, Manabu Ishii, Satoshi Takahashi, Yoshiki Mochizuki, Akihiro Matsushima, and Tetsuro Toyoda
Nucl. Acids Res. 2011 39:W533-W540.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W533

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Patricia L. Whetzel, Natalya F. Noy, Nigam H. Shah, Paul R. Alexander, Csongor Nyulas, Tania Tudorache, and Mark A. Musen
Nucl. Acids Res. 2011 39:W541-W545.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W541

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences

Corin Yeats, Jonathan Lees, Phil Carter, Ian Sillitoe, and Christine Orengo
Nucl. Acids Res. 2011 39:W546-W550.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W546


Stand Alone Programs

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

Pavlo Lutsik, Lars Feuerbach, Julia Arand, Thomas Lengauer, Jörn Walter, and Christoph Bock
Nucl. Acids Res. 2011 39:W551-W556.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W551

HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

Jong Hyun Kim, Woo-Cheol Kim, Lei M. Li, and Sanghyun Park
Nucl. Acids Res. 2011 39:W557-W561.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W557

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies

Hugo López-Fernández, Daniel Glez-Peña, Miguel Reboiro-Jato, Gonzalo Gómez-López, David G. Pisano, and Florentino Fdez-Riverola
Nucl. Acids Res. 2011 39:W562-W566.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W562

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

Ji Qi and Fangqing Zhao
Nucl. Acids Res. 2011 39:W567-W575.
http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_2/W567

Monday, June 27, 2011

Saturday, June 25, 2011

2011 Steveston Salmon Festival

http://www.richmond.ca/home.htm


Steveston Salmon Festival - 22nd Annual Bullhead DerbyDate:Jun 26, 2011Time:9:00 a.m. Registration 10:00 a.m. to 12:00 p.m. Derby Prizes awarded as soon as results are talliedPlace:Garry Point Park
12011 7th Avenue, Richmond 
Price:This event is FREE!
Kids ages 12yrs and under and Seniors 65+yrs.

2011 Steveston Salmon Festival Schedule of Events.

Main Events (subject to change)
6:30am - 11:30am - Pancake Breakfast
9:30am - Kid's Bicycle Parade
9:55am - Kajaks Salmon Run road race - DETAILS
10:00am - noon - Canada Day Parade
10:00am - 4:00pm - Japanese Cultural Displays
10:00am - 5:00pm - Art Show, Children's Festival, Craft Fair, Trade Show, Community Food Fair, Community Information Tables, Steveston RCMP Child ID Station
11:00am until sold out - Salmon Barbecue
11:00am - 6:00pm - Inflatables and Mini Midway
12:00pm - 5:00pm - Horticulture Show, Youth Rock Fest, Three on Three Hockey 

Vancouver events

http://vancouver.about.com/od/vancouverevents/a/juneevents.htm

Galaxy tools

https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies

https://bitbucket.org/galaxy/galaxy-central/wiki/Home

http://main.g2.bx.psu.edu/

http://screencast.g2.bx.psu.edu/galaxy/flash/Exons_SNP.html


Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 Aug 25;11(8):R86.

Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.

FASD - Fetal Alcohol Spectrum Disorder

Fetal alcohol spectrum disorders (FASDs) are a group of conditions that can occur in a person whose mother drank alcohol during pregnancy. These effects can include physical problems and problems with behavior and learning. Often, a person with an FASD has a mix of these problems.

Diagnosing FAS can be hard because there is no medical test, like a blood test, for it.

http://www.cdc.gov/ncbddd/fasd/facts.html

Friday, June 24, 2011

Dolphin-emu


Comment 3 by francesc...@gmail.com, Aug 28, 2010
Compile dolphin:

Install this:
http://orwell.fiit.stuba.sk/~nou/ati-opencl-dev_2.01.deb
http://orwell.fiit.stuba.sk/~nou/ati-opencl-runtime_2.01_amd64.deb


Then:
sudo apt-get install subversion scons g++ wx2.8-headers libwxbase2.8-0 libwxbase2.8-dbg libwxbase2.8-dev wx2.8-headers libwxgtk2.8-0 libwxgtk2.8-dbg libwxgtk2.8-dev libgtk2.0-dev libsdl1.2-dev g++ wx2.8-headers libwxbase2.8-0 libwxbase2.8-dbg libwxbase2.8-dev libwxgtk2.8-0 libwxgtk2.8-dbg libwxgtk2.8-dev libsdl1.2-dev nvidia-cg-toolkit libxxf86vm1-dbg libxxf86vm-dev libxext6-dbg libxext-dev libglew1.5-dev libcairo2-dbg libcairo2-dev libao2 libao-dev libbluetooth-dev libreadline5-dev nvidia-cg-toolkit libxrandr2-dbg libxrandr-dev libxext6-dbg libxext-dev libglew1.5-dev libcairo2-dbg libcairo2-dev libao2 libao-dev libbluetooth-dev libreadline5-dev libwxbase2.8-0 libwxbase2.8-dbg libwxbase2.8-dev libwxgtk2.8-0 libwxgtk2.8-dbg libwxgtk2.8-dev libgtk2.0-dev libsdl1.2-dev nvidia-cg-toolkit libbluetooth-dev libxrandr2-dbg libxrandr-dev libxext6-dbg libxext-dev libglew1.5-dev libcairo2-dbg libcairo2-dev libao2 libao-dev libreadline-dev
sudo svn checkout http://dolphin-emu.googlecode.com/svn/trunk/ dolphin-emu-read-only
cd dolphin-emu-read-only
sudo scons opencl=true flavor=release
sudo chmod -R 777 Binary/Linux-x86_64/

Find libraries in Ubuntu using the 'ldd' command

http://code.google.com/p/google-gadgets-for-linux/issues/detail?id=323
$ldd /usr/bin/ggl-gtk
linux-gate.so.1 =>  (0xb7f6a000)
libgtk-x11-2.0.so.0 => /usr/lib/libgtk-x11-2.0.so.0 (0xb7ba7000)
libatk-1.0.so.0 => /usr/lib/libatk-1.0.so.0 (0xb7b8c000)
libpangoft2-1.0.so.0 => /usr/lib/libpangoft2-1.0.so.0 (0xb7b62000)
libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb7aeb000)
libgdk-x11-2.0.so.0 => /usr/lib/libgdk-x11-2.0.so.0 (0xb7a5e000)
libgdk_pixbuf-2.0.so.0 => /usr/lib/libgdk_pixbuf-2.0.so.0 (0xb7a44000)
libpangocairo-1.0.so.0 => /usr/lib/libpangocairo-1.0.so.0 (0xb7a38000)
...
$ldd /usr/lib/google-gadgets/modules/libxml2-xml-parser.so
linux-gate.so.1 =>  (0xb7f71000)
libxml2.so.2 => /usr/lib/libxml2.so.2 (0xb7e19000)
libggadget-1.0.so.0 => /usr/local/lib/libggadget-1.0.so.0 (0xb7aa3000)
...

Thursday, June 23, 2011

Apple's Steve Wozniak preaches innovation to Concordia grads

“There’s always time for innovation, thinking about how can I do it a little better than I was taught,” Wozniak said. “If you are able to make things simpler, you’ll have done the world a great service.”

Neurodegenerative disease: the value of mouse models

Questions raised about the use of ‘ALS mice’ are prompting a
broad reappraisal of the way that drugs are tested in animal
models of neurodegenerative disease. Jim Schnabel reports.


Scott and his colleagues con-
cluded that the previous positive drug trials in
ALS mice were likely to have been so plagued
by non-drug-related variations in mouse
lifespan that this ‘noise’ was really all they had
measured. In the context of small sample sizes
and a bias against negative results, they noted,
a high degree of noise could easily have led to
the appearance of positive results even when
no drug effect had existed.


mouse was not excluded appropriately from
a study. Such an exclusion should have hap-
pened if, for example, an animal died young of
non-ALS causes — Scott came to believe that
mouse colonies in some academic labs were
“filthy” with infections — or failed to express
enough copies of the mutant SOD1 gene.


“People will do
an experiment once with ten animals and get
a result, and if it’s the right result it gets pub-
lished in a high-profile journal,” says Duff


The wrong model?

Mouse models could therefore end up being
not only more difficult and expensive to use
with acceptable rigour, but at the same time
more narrowly predictive of the human con-
dition.


http://www.nature.com/nature/journal/v454/n7205/edsumm/e080807-02.html


One of the newly identified genetic variants, SCARB2, is associated with a known Parkinson's disease pathway involving protein degradation.
The other, SREBF1, is not associated with any known Parkinson's pathway.

Wednesday, June 22, 2011

We can't change the cards we are dealt with, just how we play our hand. - Randy Pausch, Last Lecture

We can't change the cards we are dealt with, just how we play our hand. - Randy Pausch (Virtual Reality), Last Lecture

fundamentals in football

when you're screwing up and people stop saying anything, then they probably stopped caring

experience is what you get when you didn't get what you wanted

the brick walls are there for a reason: they let us prove how badly we want things,
they're there to stop the 'other' people

Find the best in everybody; wait long enough and people will surprise and impress you
when people are angry at you, you just haven't given them enough time

Disney Imagineering (R & D)
http://corporate.disney.go.com/careers/who_imagineering.html

Found something astounding that your students did?  What do you say?
That was amazing but I know you can do better.

respect authority while questioning it

Learning to Program with Alice
http://www.aliceprogramming.net/

Advice for Girls, "Only pay attention to what the guys do, and not what they say."

How to get people to help you.  You can't get there alone, and I believe in Karma
Tell the truth
Be earnest
Apologize when you screw up
Focus on others, not yourself

Don't bail; the best gold is at the bottom of barrels of crap

Get a feedback loop and listen to it

Show gratitude

Don't complain; just work harder

Be prepared: "luck" is where preparation meets opportunity

http://www.youtube.com/watch?v=ji5_MqicxSo

Randy Pausch Last Lecture: Achieving Your Childhood Dreams

www.youtube.com/watch?v=ji5_MqicxSo

Carnegie Mellon Professor Randy Pausch (Oct. 23, 1960 - July 25, 2008) gave his last lecture at the university Sept. 18, 2007,

http://www.cs.cmu.edu/~pausch/

The "Last Lecture"

I am flattered and embarassed by all the recent attention to my "Last Lecture." I am told that, including abridged versions, over six million people have viewed the lecture online. The lecture really was for my kids, but if others are finding value in it, that is wonderful. But rest assured; I'm hardly unique. Send your kids to Carnegie Mellon and the other professors here will teach them valuable life lessons long after I'm gone.
-- Randy

Fast interval intersection methodologies

http://biostar.stackexchange.com/questions/99/fast-interval-intersection-methodologies/101#101

Most genomic annotations are specified as intervals along the genome.

http://code.google.com/p/bedtools/#Brief_example

Quinlan, AR and Hall, IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.


The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.
  1. Intersecting two BED files in search of overlapping features.
  2. Culling/refining/computing coverage for BAM alignments based on genome features.
  3. Merging overlapping features.
  4. Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
  5. Calculating the depth and breadth of sequence coverage across defined "windows" in a genome.
  6. Screening for overlaps between "split" alignments and genomic features. 
But now you subsequently detect an artifact where false positives are enriched in SNPs having coverage > 100. You refine my original query accordingly. 
$ awk '$5 < 100' snps.bed | \
  egrep "A/G|C/T" | \
  intersectBed -a stdin -b exons.bed | \
  intersectBed -v -a stdin -b dbSnp130.bed \
  > bonafideNovelSnpsInExons.bed

MOODS: fast search for position weight matrix matches in DNA sequences

http://bioinformatics.oxfordjournals.org/content/25/23/3181.full
http://www.cs.helsinki.fi/group/pssmfind/
http://cs.helsinki.fi/u/prastas/pdf/BIRD-fullC.pdf

J. Korhonen, P. Martinmäki, C. Pizzi, P. Rastas and E. Ukkonen. MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics 25(23), pages 3181-3182. (2009)


Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library.

Availability: The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL).                

  • based on Pizzi et al. 2007, 2009, standard scoring based on PWM scores (log-odds against background (can be user-defined))
  • online algorithm, simple sequential search over target sequence using string matching with lookahead filtration 
    • "we know without seeing the remaining symbols that the m-segment cannot be a match as the total score will be less than k for any choice of the sequence beyond the location h."
  • written in C++, has bindings for BioPerl and BioPython
  • return log-odds score or absolute score thresholds
  • seems to be good for significant p-values for short-avg-length matrices (4-20 bases), DNA
Comments
  • doesn't look like it incorporates  any conservation information
  • even though it's significantly faster than TFBS and can handle more data, I wonder how similar the results are in terms of predicted positions
TFBS BioPerl extension (Lenhard and Wasserman, 2002) - uses naive algorithm


lookahead scoring search
algorithm of [30] already utilizes the filtering idea.

Bioinformatics workflow tools

Kepler https://kepler-project.org/
- With R functionality

Taverna http://bioinformatics.oxfordjournals.org/content/26/19/2486.full

Phenomics, Cognitive ontologies for neuropsychiatric phenomics research.

Several free web applications are available already to support examination and visualisation of cognitive concepts in the literature (PubGraph, PubAtlas, PubBrain) and to aid collaborative development of cognitive ontologies (Phenowiki and the Cognitive Atlas).


http://www.ncbi.nlm.nih.gov/pubmed?term=pubbrain

If the nodes have queries X and Y, the top number is the number of hits for(X AND Y), and the bottom number is the number of hits for (X OR Y). The ratio of these numbers is called theJaccard co-occurrence index; it measures the degree to which the two queries coincide among all publications. 


http://www.pubatlas.org/

Consortium for Neuropsychiatric Phenomics
http://phenomics.ucla.edu/projects.asp#wording

Monday, June 20, 2011

In Tiny Worm, Unlocking Secrets of the Brain

http://www.nytimes.com/pages/science/index.html

http://www.nytimes.com/2011/06/21/science/21brain.html?ref=science

APBC2012

APBC2012: The Tenth Asia Pacific Bioinformatics Conference, Melbourne Australia

Deadline Approaching: APBC2012 – The Tenth Asia Pacific Bioinformatics Conference

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



The Tenth Asia Pacific Bioinformatics Conference

Melbourne, Australia, 17-19 January 2012

http://homepage.cs.latrobe.edu.au/ypchen/APBC2012/



Important Dates

Paper submission: 20th July 2011 *******

Author Notification: 20th Aug 2011

Final Version due on: 1st Oct 2011

Tutorial submission open: 1st July 2011

Poster submission open: 3rd Oct 2011

Registration open: 22nd Aug 2011

Cell graphics images animations

http://cellimagelibrary.org/

http://mgl.scripps.edu/people/goodsell


http://sbarrows.com/Home.html


http://www.xvivo.net/


http://www.invivo.ca/


http://www.hybridmedicalanimation.com/


http://www.hurdstudios.com/


http://multimedia.mcb.harvard.edu/

Sunday, June 19, 2011

Maryann Martone - The possibility and probability of a global neuroscience information framework

http://www.neuroinformatics2010.org/speakers/maryann-martone
http://neuinfo.org/  NIF (Neuroscience Information Framework)
http://wholebraincatalog.org/

Betcha by Golly, Wow

"Betcha by Golly, Wow" is a song written by Linda Creed and Thom Bell in 1970, and most notably recorded by the Philadelphia soul group The Stylistics in 1971.

Google Gadgets for Linux


Install Google Gadgets from Ubuntu Software Centre


"Program can't start because it failed to load the following
module(s):

js-script-runtime"

http://code.google.com/p/google-gadgets-for-linux/issues/detail?id=323

Comment 7 by project member james...@gmail.com, Jul 25, 2009
That's the problem: you have another copy of ggl installed in /usr/local. You need
remove all related files in /usr/local:
/usr/local/lib/libggadget*
/usr/local/lib/google-gadgets
/usr/local/bin/ggl*
/usr/local/share/google-gadgets


http://code.google.com/p/google-gadgets-for-linux/
http://tombuntu.com/index.php/2008/06/16/install-google-gadgets-for-linux-on-ubuntu/

Google Gadgets for Linux provides a platform for running desktop gadgets under Linux, catering to the unique needs of Linux users. It's compatible with the gadgets written for Google Desktop for Windows as well as the Universal Gadgets on iGoogle. Following Linux norms, this project is open-sourced under the Apache License.

Start Google Gadgets Automatically
To start Google Gadgets when you log in, open System->Preferences->Sessions. Click Add and create a new item for Google Gadgets with the command ggl-gtk.

Discoveries in Mitochondria Open New Field of Cancer Research

http://www.healthcanal.com/cancers/18176-Discoveries-Mitochondria-Open-New-Field-Cancer-Research.html

Leo Buscaglia - Love and differences

"Find the person who will love you because of your differences and not in spite of them and you have found a lover for life."

Saturday, June 18, 2011

Mitochondria - Microsopic Structures Found Inside Cells

http://www.parkinson.bc.ca/Research---Dr-Gordon-Rintoul


Parkinson's disease involves the loss of a select population of brain cells (neurons). My research, funded by Parkinson Society British Columbia, focuses on the involvement of "mitochondria" in this neurodegeneration.
 
Mitochondria are microscopic structures found within cells. They are often described as the "powerhouses" of cells, as they provide energy for all cellular processes. Recent studies have revealed that mitochondria are very mobile structures within many cells, including neurons. It is thought that the function of this mitochondrial motility is to deliver energy to regions of neurons that require it. In other words, mitochondria act as microscopic "meals on wheels" within neurons. We hypothesize that as neurons age, this energy delivery process is compromised, making neurons in older brains more susceptible to Parkinson's disease.
Our research is directed toward understanding the processes that control mitochondrial motility and determining the contribution of mitochondria to the Parkinson's disease process.

Seqlab

http://sequilab.org/pages/aboutUs.jsf


Sequilab is a leap forward for genetic researchers using online bioinformatics tools.  Sequilab is home to a rapidly growing community of researchers working with sequence data, with a wet lab focus, across the breadth of the life sciences field. 
The Sequilab research portal presents a simple, seamlessly-integrated interface that combines sequence analysis and manipulation, lab work management (custom notes and projects), and a personal work space with access to social media, personal profiles, community collaboration, as well as information on news, careers, and upcoming conferences. All research on Sequilab can be saved for later use, modified as the research focus changes, printed for sharing with peers, and is accessible via the web from home or on the go.  It is also iPhone and Android compatible!
The portal is free and can be accessed at http://www.sequilab.org.

Richard Dawkins - The Selfish Gene

Dawkins came to prominence with his 1976 book The Selfish Gene, which popularised the gene-centered view of evolution and introduced the term meme.

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

A meme (play /ˈmm/[1]) is an idea, behavior or style that spreads from person to person within a culture.[2] While genes transmit biological information, memes are said to transmit ideas and belief information.

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

Weeds, dandellions

http://www3.botany.ubc.ca/rieseberglab/people/nolan_kane.html

The Asteraceae (Compositae), with nearly 25,000 named species, is the largest plant family, with numerous important crops (sunflower, safflower, lettuce, artichoke, endive, chicory and many more), noxious weeds (e.g. knapweeds, thistles, dandelions) and ecologically important wild species (silverswords, Artemisia, Senecio), yet has no sequenced genome due to the prohibitively large genome sizes of most Asteraceae species.  This lack of genomic information has limited our ability to understand the roles of natural selection, artificial selection and gene flow in shaping both wild and domesticated members of the Asteraceae, and to better characterize the enzymes responsible for the diverse secondary metabolites in medicinally important species.

http://www3.botany.ubc.ca/rieseberglab/research.html

Invasive plants represent a major threat to the economy and environment, with annual economic costs to North America of $35-40 billion. In collaboration with laboratories at UBC (S. Otto, J. Whitton, and K. Adams) and Indiana University (Z. Lao, Jim Bever, and K. Clay), we are using common garden experiments, microarray analyses (Genetics 179:1881-1890), and hitchhiking and association mapping with next generation sequence data to identify specific genetic changes associated with invasiveness. By targeting Compositae weeds for this work – diffuse knapweed, starthistle, Canada thistle, ragweed, and common sunflower – we can exploit the genomic tools and resources developed by the Compositae Genome Project (see below).

Genome BC Bioinformatics Experts

http://gchelpdesk.ualberta.ca/bioinfo_directory/ViewDirectory.php?centre=British_Columbia

Friday, June 17, 2011

Neuroinformatics projects

http://www.anc.ed.ac.uk/dtc/index.php?option=com_projects&completed=-1

Beep code timer

$ alsamixer
enable beep, press m to unmute

$ for v in {1..100} ; do sleep 5; echo $v; beep; done;

500 Days of Summer (2009)

it was that you can't ascribe
great cosmic significance...

to a simple earthly event.


Coincidence.  That's all anything ever is.

Nothing more than coincidence.

Tom had finally learned there are no miracles.

There's no such thing as fate.

Nothing is meant to be.

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.

Prateek Kumar, Steven Henikoff, and Pauline C Ng, “Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm,” Nature Protocols 4, no. 7 (2009): 1073-1081.


The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). 


An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5-20 min, depending on the input. 

Allen Brain Atlas Symposium videos

http://www.alleninstitute.org/events/symposium/index.html

8 Ways to negotiate for job perks

8 Ways to negotiate for job perks

Rachel Farrell, Special to CareerBuilder.com


http://www.careerbuilder.ca/Article/CB-754-Interviewing-8-Ways-to-negotiate-for-job-perks/?sc_extcmp=cbca_9754&cblang=CAEnglish&SiteId=cbca_9754

Atul Gawande -- "A Townie Speaks"


Excerpts from Atul Gawande -- "A Townie Speaks"

core American idea: Anything is possible in people’s lives. No one should be counted out.

 But I think what I really liked was just the idea of being someone important. And you know where that gets you: nowhere.


But over time I learned that there are two very different satisfactions that you can have in your life.

A) One is the satisfaction of becoming skilled at something. It almost doesn’t matter what the terrain is.

Developing a skill is painful, though. It is difficult. And that’s part of the satisfaction. You will only find meaning in what you struggle with.

B) It comes from human connection. It comes from making others happy, understanding them, loving them.

People have layers. You must take the time to find them.

Your strengths as human beings come from both the abilities and the relationships you invest in nurturing. The trick you have had to learn to get through college, that you will have to carry with you for life, is how to turn the distractions away, how to focus at least a little bit every day on stuff that will take awhile. 

But somehow they never let themselves be completely defined by the institutions or the way they did things. They were insiders and yet poked at the customs, looking for better ways.


The Checklist Manifesto

well-designed check lists can improve outcomes