Interesting databases in the 2010 NAR issue

NAR 2010 databases

• Daniel Glez-Peña, Daniel Gómez-Blanco, Miguel Reboiro-Jato, Florentino Fdez-Riverola, and David Posada

            ALTER: program-oriented conversion of DNA and protein alignments

          Nucl. Acids Res. (2010) 38(suppl 2): W14-W18 doi:10.1093/nar/gkq321

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF Supplementary Data

• Alexey V. Antonov, Esther E. Schmidt, Sabine Dietmann, Maria Krestyaninova, and Henning Hermjakob

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases

          Nucl. Acids Res. (2010) 38(suppl 2): W78-W83 doi:10.1093/nar/gkq482

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• Kunlin Zhang, Sijia Cui, Suhua Chang, Liuyan Zhang, and Jing Wang

i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study

Nucl. Acids Res. (2010) 38(suppl 2): W90-W95 doi:10.1093/nar/gkq324

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• Vivek Kaimal, Eric E. Bardes, Scott C. Tabar, Anil G. Jegga, and Bruce J. Aronow

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

Nucl. Acids Res. (2010) 38(suppl 2): W96-W102 doi:10.1093/nar/gkq418

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• Jignesh R. Parikh, Bertram Klinger, Yu Xia, Jarrod A. Marto, and Nils Blüthgen

Discovering causal signaling pathways through gene-expression patterns

Nucl. Acids Res. (2010) 38(suppl 2): W109-W117 doi:10.1093/nar/gkq424

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• Y.-T. Wang, Y.-H. Huang, Y.-C. Chen, C.-L. Hsu, and U.-C. Yang

PINT: Pathways INtegration Tool

Nucl. Acids Res. (2010) 38(suppl 2): W124-W131 doi:10.1093/nar/gkq499

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF Supplementary Data

• Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Hubert Charles, Marie-France Sagot, and Fabien Jourdan

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

Nucl. Acids Res. (2010) 38(suppl 2): W132-W137 doi:10.1093/nar/gkq312

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

• Marija Cvijovic, Roberto Olivares-Hernández, Rasmus Agren, Niklas Dahr, Wanwipa Vongsangnak, Intawat Nookaew, Kiran Raosaheb Patil, and Jens Nielsen

BioMet Toolbox: genome-wide analysis of metabolism

Nucl. Acids Res. (2010) 38(suppl 2): W144-W149 doi:10.1093/nar/gkq404

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• Richard Côté, Florian Reisinger, Lennart Martens, Harald Barsnes, Juan Antonio Vizcaino, and Henning Hermjakob

The Ontology Lookup Service: bigger and better

Nucl. Acids Res. (2010) 38(suppl 2): W155-W160 doi:10.1093/nar/gkq331

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

• Xin He, Yanen Li, Radhika Khetani, Barry Sanders, Yue Lu, Xu Ling, ChengXiang Zhai, and Bruce Schatz

BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects

Nucl. Acids Res. (2010) 38(suppl 2): W175-W181 doi:10.1093/nar/gkq544

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

• Scott F. Saccone, Raphael Bolze, Prasanth Thomas, Jiaxi Quan, Gaurang Mehta, Ewa Deelman, Jay A. Tischfield, and John P. Rice

SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study

Nucl. Acids Res. (2010) 38(suppl 2): W201-W209 doi:10.1093/nar/gkq513

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

• Ignacio Medina, José Carbonell, Luis Pulido, Sara C. Madeira, Stefan Goetz, Ana Conesa, Joaquín Tárraga, Alberto Pascual-Montano, Ruben Nogales-Cadenas, Javier Santoyo, Francisco García, Martina Marbà, David Montaner, and Joaquín Dopazo

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

Nucl. Acids Res. (2010) 38(suppl 2): W210-W213 doi:10.1093/nar/gkq388

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF Supplementary Data

• Miguel Vazquez, Ruben Nogales-Cadenas, Javier Arroyo, Pedro Botías, Raul García, Jose M. Carazo, Francisco Tirado, Alberto Pascual-Montano, and Pedro Carmona-Saez

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures

Nucl. Acids Res. (2010) 38(suppl 2): W228-W232 doi:10.1093/nar/gkq476

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF Supplementary Data

• Maria José Nueda, José Carbonell, Ignacio Medina, Joaquín Dopazo, and Ana Conesa

Serial Expression Analysis: a web tool for the analysis of serial gene expression data

Nucl. Acids Res. (2010) 38(suppl 2): W239-W245 doi:10.1093/nar/gkq488

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF Supplementary Data

• Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, and Nir Ben-Tal

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Nucl. Acids Res. (2010) 38(suppl 2): W529-W533 doi:10.1093/nar/gkq399

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• Gilad Wainreb, Haim Ashkenazy, Yana Bromberg, Alina Starovolsky-Shitrit, Turkan Haliloglu, Eytan Ruppin, Karen B. Avraham, Burkhard Rost, and Nir Ben-Tal

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

Nucl. Acids Res. (2010) 38(suppl 2): W523-W528 doi:10.1093/nar/gkq528

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF Supplementary Data

• Jiten Bhagat, Franck Tanoh, Eric Nzuobontane, Thomas Laurent, Jerzy Orlowski, Marco Roos, Katy Wolstencroft, Sergejs Aleksejevs, Robert Stevens, Steve Pettifer, Rodrigo Lopez, and Carole A. Goble

BioCatalogue: a universal catalogue of web services for the life sciences

Nucl. Acids Res. (2010) 38(suppl 2): W689-W694 doi:10.1093/nar/gkq394

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

• Mickael Goujon, Hamish McWilliam, Weizhong Li, Franck Valentin, Silvano Squizzato, Juri Paern, and Rodrigo Lopez

A new bioinformatics analysis tools framework at EMBL–EBI

Nucl. Acids Res. (2010) 38(suppl 2): W695-W699 doi:10.1093/nar/gkq313

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

• Huabin Hou, Fangqing Zhao, LingLin Zhou, Erle Zhu, Huajing Teng, Xiaokun Li, Qiyu Bao, Jinyu Wu, and Zhongsheng Sun

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

Nucl. Acids Res. (2010) 38(suppl 2): W732-W736 doi:10.1093/nar/gkq302

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

• Dougu Nam, Jin Kim, Seon-Young Kim, and Sangsoo Kim

GSA-SNP: a general approach for gene set analysis of polymorphisms

Nucl. Acids Res. (2010) 38(suppl 2): W749-W754 doi:10.1093/nar/gkq428

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF Supplementary Data

• Zefeng Zhang, Hao Lin, and Bin Ma

ZOOM Lite: next-generation sequencing data mapping and visualization software

Nucl. Acids Res. (2010) 38(suppl 2): W743-W748 doi:10.1093/nar/gkq538

Abstract FREE Full Text (HTML) Full Text (PDF) Screen PDF

Tell emacs to use git instead svn or cvs when a file is managed by both versions systems.

Stack overflow is wonderfull, I posted a question and it was answered in less than a minute. Was so quick that I needed to wait for 4 minutes before being able to accept it!.

http://stackoverflow.com/questions/5059804/howt-to-tell-emacs-vc-that-i-want-a-file-to-be-managed-by-git-not-by-svn-when-the/5059848#5059848

In short: if you have a file managed by Git and several other versions systems and you want to use emacs VC shortcuts with Git, you need to edit vc-handled-backends and move Git the first one.

'(vc-handled-backends (quote (Git CVS SVN SCCS Bzr Hg Arch MCVS)))

I have also added git.el to my site-lisp

$ cp /usr/share/doc/git/contrib/emacs/git* ~/.emacs.d/site-lisp/

And then added to my .emacs

;; from git.el (complement to vc-git.el)
(require 'git)
(require 'git-blame)

then creating a keybinding (from http://www.michael-hammer.at/blog/emacs_git/)

;keybindindings for git
(global-set-key "\C-xgs" 'git-status)

git.el shortcuts
m - mark the file the cursor is on ATM
M - mark all files in buffer
u/DEL - unmark file below/above
R - resolve conflicts during merge
a - add file to repository
r - remove file
i - add file to ignore list
c - commit
U - Undo -> revert file
l - see log file
g - refresh the status buffer
q - quit status buffer
? - get help!

Managing script options: Getopt-Long-Descriptive

I use GetOpt::Long for all my scripts, and as many other people I have my own methods to handle some logic for many of the standard options that my scripts have (-verbose -debug -test -run -in_file -out_file -bsub, etc...). Things get complicated when you check if your script has the right options, some times there are incompatible options, or alternative ones, or if you pass -test, many mandatory options are not mandatory anymore. And also you need to provide the right message for each scenario and write the usage message.

Today reading the code of the WWW::PivotalTracker::Command Perl module I have seen that it uses Getopt::Long::Descriptive. This is right away the module that I was looking for. It implements the 'one of these', 'required', etc.., and also writes the usage automatically for you. I have not tried it yet but I will give it a try this week. Any comments about other users experiences would be welcome.

PivotalTracker perl module

I like XP and Agile programming style. And I am very fond of day and week to-do lists to mark project goals achievements. I have recently started to use PivotalTraker for managing my projects tasks and recod completion velocity and I am very happy with it. I use it as a companion to the workplace Jira (old version with no extensions so a very handicaped Jira.). Therefore I am using PivotalTraker as a pseudo jira extension ( when I finish a week I export the stories to CSV and paste into Jira).

I love the approach of PivotalTraker and also is good that it is easy to import/export data. Also it has perl bindings to its API: WWW-PivotalTracker . I will try it soon.

firefox 4.0

the beta5 is working fairly well, and my favorite plugins like no-script, foxy-proxy and firebug work well. Firebug seems to have some documented minor issues but this does not affect to me.

FF4 has two big visible changes, the tabs on top (like google's chrome) and panorama view for grouping tabs (upper-right corner). This is a nice feature, but when you create several groups I have not found how to cycle between them without the mouse. For me is easier to put tabs in different windows and in my mac I can F10 to see the windows and select one (like in panorama when selecting between groups) but I can also alt-` to cycle between ff4 windows, so I can change swiftly between conceptualy grouped tabs, for example from the journals window to the bloger-mail window when writing an entry in my blog.

What I miss is an option to list all windows and tabs opened and be able to select the wanted one. This is just the opposit of when you start firefox from a stored session and an error occur and gives you the list of all the windows and tabs so you can deselect the unwanted one. This options should be somewhere but I have not discovered yet.

firefox 4.0 beta 6 (how to use it along firefox 3)

The firefox 4.0 beta is in the 6th release. This is the first ff4 release that I have tested.

Firefox uses only one process for all windows, so you can not open two different firefox at the same time. Well, you can but not with the same profile. So in order to use ff4 without losing my ff3 plugins and usability I need to create first a new profile and then a symlink to launch ff4.

1.  first of all install ff4 with another name

• I tried to raname ff4 in the dmg installer but was not possible, so used the terminal in my mac
• cp -r firefox.app /Volumes/Macintosh\ HD/Applications/Firefox-4.0.app

2.  Create a new profile

• In my macOS (change your path for  linux or windows), open the terminal and type:
• /Volumes/Macintosh\ HD/Applications/Firefox-4.0.app/Contents/MacOS/firefox-bin -profilemanager -no-remote
• Then add a new profile "ff4"

3. Create an alias in your .bashrc
• alias ff4='/Volumes/Macintosh\ HD/Applications/Firefox-4.0.app/Contents/MacOS/firefox-bin -P ff4 -no-remote'
• -no-remote tells firefox not to use the running instance but create a new one. You can use only one profile at a time though.

Note: you can copy your data from the older profile to the new one if you wish, or create a backup:

• rsync -av ~/Library/Application\ Support/Firefox/Profiles/n6jajvmu.default  ~/personal/firefox_backup

[perl%dbi] find available drivers

I have found a nice script to find out which are your available DBI drivers, in this page:

http://defindit.com/readme_files/sqlite.html

#!/usr/bin/perl
use DBI;
@driver_names = DBI->available_drivers();
print "driver_names (apparently installed, available):\n";
foreach my $dn (@driver_names)
{
print "$dn\n";
}

I have create a script with it and this is the output:

$ perl find_dbi_drivers_installed.pl
driver_names (apparently installed, available):
DBM
ExampleP
File
Gofer
Proxy
SQLite
Sponge
mysql

EDITED[2010-10-08]:
The previous script is a copy-paste from the web. Obviously I will add the use strict and will go inside a Utils module instead of a script.

For single uses I will use a one-liner as the comments suggest. I like the perl 5.10 one-liner

$ perl -MDBI -E 'say for DBI->available_drivers'

especially the say for...

perl debugger and perl >5.10 features

I have been using perl >5.10 for a long time and I use give/when and ~~ a lot. But when I try to debug my programs I get annoyed by the fact that I can not use this features in the debugger command line: Why I can not use these features directly in the debugger?? The debugger handle them very well when they are in the code but not in the command line.

This is annoying because I am also get used to use the debugger as a REPL (yes, I know Devel::REPL but I have not installed it everywhere and I usually have a perl debugger already open in my emacs).

After a lot of time avoiding the issue I asked it in stack overflow:

How to use perl 5.10 features inside the debugger?

and eldarerathis explained to me why

perl -dEbug

is not working:

[ eldarerathis]
I found a reference to the issue here, but it's about a year old. However, the relevant portion of the perl source hasn't changed since, and can be seen here.
[...]
Basically, the debugger is loaded before the -E flag is processed, so the features aren't yet enabled when the debugger gets loaded. The gist of this is that you can't currently use -E with the -d command. If you want to use say, switch, or any other feature from the debug prompt, you have to do it like this:

  DB<1> use feature 'say'; say "x"
  x

Also seems that feature is lexically scoped so this does not work:

DB<19> use feature 'say'
DB<20> say 1
Number found where operator expected at (eval 41)[/homes/pmg/pmg-soft/local-perl/lib/5.12.1/perl5db.pl:638] line 2, near "say 1"

but this does:

DB<21> use feature 'say';say 1
1

This is annoying because when debuggin perl >5.10 scripts, sometimes I need to fix a given/when, or a line with ~~ or copy-paste a line with say and it does not work :-(.

If someone has any idea how to use new Perl code features in the debugger command line please let me know or answer in stack overflow.

[perl] Rakudo Star will be available at the end of July

Hopefully, Rakudo Star will be released at the end of the month.
http://rakudo.org/node/73

There is also a inline-rakudo (nice!)
http://search.cpan.org/dist/Inline-Rakudo/lib/Inline/Rakudo.pm


A nice excuse to play with perl6 during holidays

nice blog entries about GWAS QC checks

Three very nice blog entries from campus coworkers to read:

First two about how to scrutinize GWAS, and one about the sociological, ethical and political issues of giving feedback to the DNA donors:

* [Daniel MacArthur] Serious flaws revealed in "longevity genes" study
* [Jeff Barret] How to read a genome-wide association study
* [Vincent Plagnol] Communicating genetic data to DNA donors


The points of the two first blog entries are relevant to the recent Nature paper
Prepublication data sharing where one of the recommendations of the Toronto International Data Release Workshop is:

Editors and reviewers

As reviewers of manuscripts submitted for publication, scientists should be mindful that prepublication data sets are likely to have been released before extensive quality control is performed, and any unnoticed errors may cause problems in the analyses performed by third parties. Where the use of prepublication data is limited or not crucial to a study's conclusions, the reviewers should only expect the normal scientific practice of clear citation and interpretation. However, when the main conclusions of a study rely on a prepublication data set, reviewers should be satisfied that the quality of the data is described and taken into account in the analysis.

Participants at the Toronto meeting recommended that journals play an active part in the dialogue about rapid prepublication data release (both in their formal guide to authors and informal instructions to reviewers). Journal editors should remind reviewers that large-scale data sets may be subject to specific policies regarding how to cite and use the data. Ultimately, journal editors must rely on their reviewers' recommendations for reaching decisions about publication. However, encouraging reviewers to carefully check the conditions for using data that authors have not created themselves can help to raise both the quality of analysis and fairness in citation of published studies.

If the reviewers start to ask for these checks, studies using big consortium data (WTCCC etc) would be fine but studies would face serious problems if using data from small labs without web page or metadata information availability other than the supplementary information (if any) in a low impact paper. I wonder if would it be possible that resources like EGA , dbGAP or Gen2Phen would have tools to facilitate this checks to the users, referees and readers in the public metadata area (as the data is expected to be in any of these repositories) and have a very 'proactive attitude' asking for this kind of data as complete as possible to the submitter and backing this request with this nature or similar paper.


Finally the image of the Daniel's entry comparing the science longevity paper Manhattan plot vs WTCCC Manhattan plots