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Need some code for actual work flows

Tue, 31 Aug 2010 06:02:01 +0100

I read the book, the book is nice and would be happy if the authors and readers make available code for workflows, Samuel, Bangalore, India

Perl CGI query

Tue, 20 Apr 2010 00:37:52 +0100

Hi there,

Anyone have a preferred way to query a website like NCBI/Pubmed using CGI?

For example, using the gene_query.html form given in the book:

"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<br /> Basic Web Form<br />

Basic Web Form Example

Please enter a gene name and click 'Search' to get a report of information for a gene.

In gene_query.pl what is the best technique to search Pubmed for all articles involving this gene?

Thanks,
Shuraski

R won't write output file

Thu, 18 Mar 2010 00:36:10 +0000

Greetings,
I took a screen shot of the situation: modified r-test.pl for my local server. Set permissions to the tempfiles dir to 777, the perl seems to work, and CGI.pm, but R doesnt' seem to want to write the file. When I run the perl generated R script "by hand" R.app, it works fine. I can't seem to find the problem. Suggestions greatly appreciated.

dyld: lazy symbol binding failed: Symbol not found: _mysql_init

Thu, 11 Mar 2010 21:49:01 +0000

Greetings,
Just installed MySQL-5.1.44-osx10.6-x86 via the dmg (package). Seemed to work fine. I also installed DBD::mysql, but had to use force to get it to install.
When I run the cgi programming script on p.202-3 I get this error:
dyld: lazy symbol binding failed: Symbol not found: _mysql_init
Referenced from: /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle
Expected in: flat namespace

dyld: Symbol not found: _mysql_init
Referenced from: /Library/Perl/5.10.0/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle
Expected in: flat namespace

Trace/BPT trap

The mysql package was the 32 bit version, not the 64 bit version.
Suggestions?

thanks,

Enabling CGI in Mac OS X with Apache

Sat, 13 Feb 2010 20:37:11 +0000

Is anyone experienced at enabling CGI using XAMPP for Mac OS X? I would like to use perl to execute scripts from cgi-bin/ -- for example, those contained in this bioinformatics book. However, after reading and rereading the on-line manuals, I continue to get:

Error 403 Access forbidden! You don't have permission to access the requested object. It is either read-protected or not readable by the server.

Which tells me this is a permissions issue.

I believe my permissions are correct:

In cgi-bin/

-rwxr-xr-x 1 root admin 43 Jan 28 07:06 form_query.pl

In the error_log:

in error_log: Options ExecCGI is off in this directory/Applications/XAMPP/xamppfiles/cgi-bin/form_query.pl

So, I go to httpd.conf to turn ExecCGI on:

Lines from httpd.conf file:

ScriptAliasMatch ^/cgi-bin/((?!(?i:webobjects)).*$) "/Library/WebServe +r/CGI-Executables/$1"

AddHandler cgi-script .cgi .pl
# "/Library/WebServer/CGI-Executables" should be changed to whatever y +our ScriptAliased # CGI directory exists, if you have that configured. # AllowOverride None Options ExecCGI Order allow,deny Allow from all

That did not work, so I tried enabling CGI in the directory that my cgi executable files are in:

AllowOverride None
Options Indexes FollowSymLinks MultiViews ExecCGI
Order allow,deny
Allow from all

But still the 403 error persists

Could the problem be here? When calling ls -l in the XAMPP directory:

drwxr-xr-x 3 user admin 102 Aug 16 07:35 XAMPP Control.app
lrwxr-xr-x 1 user admin 18 Sep 27 09:49 cgi-bin -> xamppfiles/cgi-bin
lrwxr-xr-x@ 1 user admin 14 Sep 27 09:49 etc -> xamppfiles/etc
lrwxr-xr-x 1 user admin 17 Sep 27 09:49 htdocs -> xamppfiles/htdocs
lrwxr-xr-x@ 1 user admin 15 Sep 27 09:49 logs -> xamppfiles/logs
drwxr-xr-x@ 23 root admin 782 Aug 16 07:36 xamppfiles

Is there a problem with the Symlinks? Any help would be very much appreciated.

Has anyone else had this problem, and successfully solved it?

I am running Mac OS X 10.5.7, with XAMPP for Mac OS X (Apache 2.0, Perl5, mod_perl 2.0.4)

Thank you!

Erratum for GROUP BY section (page 61)

Fri, 31 Jul 2009 11:13:52 +0100

In the first print run of the book, the description of GROUP BY on page 61 is potentially misleading as the ordering of results described may not be repeatable for other data.

To fix this, in the second print run we replaced the section that starts with "If we wanted to ..." and ends with "... the cost of that kit." (just before the "JOIN" heading) with the following:

Quote:However, if we wanted to know the maximum kit cost from each manufacturer, this method could require a lot of manual inspection of the table. Instead, we would use:

SELECT manufacturer, MAX(kit_cost)
FROM Kit
GROUP BY manufacturer;

This will return a two-column table; the first column containing the name of each manufacturer and the second the cost of their most expensive kit.

Unfortunately we cannot simply get the name of the most expensive kit from that manufacturer by entering the following:

SELECT manufacturer, name, MAX(kit_cost)
FROM Kit
GROUP BY manufacturer;

expecting that it will return a three-column table; the first column containing the manufacturer, the second the name of their most expensive kit and the third the cost of that kit. This does not necessarily return the correct result as the kit name retrieved and shown is not logically linked to the result of the MAX(kit_cost) operation.

To ensure that we do get the name of the most expensive kit we can first create a temporary table ordered by kit_cost and then apply the above selection to this temporary table:

CREATE TEMPORARY TABLE Ordered_kit
SELECT manufacturer, name, kit_cost
FROM Kit
ORDER BY kit_cost DESC;

SELECT manufacturer, name, MAX(kit_cost)
FROM Ordered_kit
GROUP BY manufacturer;

As this is a temporary table, it will disappear when the database session is ended.

'R' Guide (pdf).

Sun, 19 Apr 2009 02:02:02 +0100

Hi.

I thought the following document might be beneficial for those of us learning R:

http://heather.cs.ucdavis.edu/~matloff/R/RProg.pdf

Thanks,

Caitlin

Apache & mod_perl on Mac OS X Leopard

Wed, 18 Feb 2009 19:13:11 +0000

I am trying to install Ensembl on an Intel Core 2 Duo iMac which runs OS X 10.5.6. I notice that Ensembl require Apache 2 and mod_perl 2. I wonder does OS X 10.5.6 come with mod_perl 2, and if it does not, how can I install it?

Bioinformatician (Genomic Profiling) Position at Pfizer

Wed, 11 Feb 2009 10:26:53 +0000

Quote:Bioinformatician: Genomic Profiling

An exciting opportunity has arisen within the new Pfizer Regenerative Medicine unit in Cambridge, UK for a skilled computational scientist to assist in the analysis and interpretation of large-scale molecular profiling data. Our goal is to understand the molecular events concerning stem-cell differentiation and identify novel mechanisms to promote the generation of specific cell types. As part of this work we will be performing extensive molecular profiling studies and are seeking a computational biologist with experience in this area. The successful candidate will be working on a diverse range of projects investigating the pathways controlling the generation of therapeutically-relevant cell types and the identification of potential therapeutic targets.

We are specifically interested in anyone candidates with knowledge of techniques such as micro-RNA, microarray, ChIP-ChIP, ChIP-Seq, next generation sequencing and epigenetic profiling analyses. The ideal candidate would be able to demonstrate previous experience in processing and downstream analysis of such data, ideally using multiple different datasets. The candidate will also need to demonstrate an understanding of good experimental design, considering the issues with regards to replicates, time-studies and use of appropriate controls. A solid background in statistical analysis of molecular profiling is essential and candidates should be proficient in the use of systems such as R/Bioconductor. Awareness of the issues and practical steps concerning integration of multiple datasets would also be desirable, as would previous use of integration and analysis tools. An ability to communicate findings to group is essential, as is an interest in the biological application of such data such as pathway and systems analysis.

Pfizer Regenerative Medicine is a new research unit working at the forefront of science using the latest developments in stem cell biology to bring novel treatments straight to patients to prevent disability, repair failing organs, treat degenerative diseases and even slow down parts of the ageing process. We work within the Guidelines developed by the National Academy of Sciences in the USA and equivalent organisations around the world. Pfizer Regenerative Medicine, has been set up as an entrepreneurial business unit in the UK and US to focus on delivering a new generation of innovative medicinal products. For us, this is the start of a new era of medicine â€“ and Pfizer Regenerative Medicine will not only be part of it, but shape it.

Key Skills: Molecular Profiling/â€™omics/high-throughput technologies; Microarray/Epigenetics/Next generation sequencing; bioinformatics; computational biology; statistical analysis; R/Bioconductor; Ensembl; GO/GSEA; Solexa/Illumina/Affymetrix/454.

To find out more and to apply visit http://www.pfizer.co.uk/careers and enter the job opening I.D. 929568

Closing date: 26th February 2009.

Weâ€™re proud to be an equal opportunity employer and welcome applications from people with different experiences, backgrounds and ethnic origins.

Research Associate (Bioinformatician) Position at UCL

Thu, 05 Feb 2009 18:44:55 +0000

I got forwarded this by a friend today:

Quote:Research Associate (Bioinformatician)

Applications are invited for a Research Associate (Bioinformatician) to join a Wellcome Trust funded collaboration between laboratories from University College London (Linda Partridge, Dominic Withers, David Gems) and the European Bioinformatics Institute (Janet Thornton). The position will be based at the European Bioinformatics Institute, near Cambridge.

The goals of the programme are to understand how single gene mutations in the insulin/Igf-like signalling pathway extend healthy lifespan and ameliorate ageing-related disease. A variety of approaches, including functional genomic, are used, and experimental systems include nematode worms, fruit flies and mice. Working with two colleagues in the bioinformatics team, the appointee will have the opportunity to be fully involved in the research programme, to develop individual research projects and to develop methods for addressing new technologies.

The successful applicant will have some combination of the following:

A post-graduate degree (MSc or PhD) Experience in bioinformatics, especially microarray analysis String programming skills in at least one of Perl, Python, Java or C/C++ Knowledge of statistics and experience in using statistical software, such as R or an equivalent Experience of working in a Unix environment Good communication skills and an ability to work in an inter-disciplinary research environment

The position will require regular day trips to London to attend meetings with UCL-based project members.

The post is at Grade 7: Â£28,839 - Â£35,469 per annum plus Â£2,781 per annum London Allowance. The position is available immediately. The appointment is funded until July 2013.

Application Process:

It is essential that candidates first read the Job Description and Person Specification. Please ensure that your skills and experience meet the criteria outlined before applying.

Visit http://www.ucl.ac.uk/iha where you can view the Job Description and Person Specification, and download the UCL Application Form and Equal Opportunities Monitoring Form. These two forms must be completed and sent - accompanied by a covering letter, a current CV and details of three referees - either via email to Julie Black at ucbhlof@ucl.ac.uk or by post to Prof. Linda Partridge, c/o Julie Black, Institute for Healthy Ageing, Department of Genetics, Evolution and Environment, Darwin Building, University College London, Gower Street, London WC1E 6BT.

Please note that the closing date for applications is Monday 23 February 2009 with interviews scheduled to take place in Cambridge on Friday 20 March 2009.

UCL Taking Action For Equality.

The closing date for applications is Monday, 23rd February 2009.

Install MySQL and DBD::MySQL on Mac OS X

Mon, 02 Feb 2009 23:38:34 +0000

(16 March 2010) Edit - it seems that installing MySQL and DBD::MySQL got a little more complicated in Snow Leopard... (Mac OS X 10.6) I'll put up some new instructions in the next week or so specific to Snow Leopard.

In chapter 3 we promised to keep a guide to installing DBD::MySQL on Mac OS X up to date on the website as in the past (on older versions of Mac OS X) this has been at best a tricky operation, and at other times a down right pain. Sorry it has taken a while to materialize (the book has been out several months already), but we hope this should do the trick.

All of the following was carried out on Mac OS X 10.5 (Leopard), if you have an older version of OS X the instructions should still work but if you get any problems let me know in your reply what version of OS X you are using.

Right, onto the information that you need. Getting DBD::MySQL set-up and ready for use is a two step process, first we must install MySQL itself as this is needed to compile the DBD drivers against, then second we shall build and install the DBD drivers.

Installing MySQL

There are several ways that you can install MySQL on Mac OS X:

Install binary packages from MySQL
Build it from source
Build and install it using MacPorts
Install it using Fink

All have their merits and different people have their preferences for which option they would choose, but for simplicity we're going to go with the binary package install from MySQL. If you would prefer instructions for the other methods, let me know (by replying to the thread) and I'll put something together.

First head on over to the MySQL 5.1 download page (the most recent version at the time of writing), and download the 'Mac OS X (package format)' installer for the type of processor you have in your Mac.

Once you have the image, it's a simple Mac .pkg installer to install MySQL and all of its tools. In the image file you will also notice two other files: 'MySQL.prefpane' and 'MySQLStartupitem.pkg'. Double-click the first file 'MySQL.prefpane' - this will install an entry in your System Preferences to allow you to stop and start your new MySQL server. Once you have installed this preference pane, start your MySQl server.

The other package (MySQLStartupitem.pkg) is for if you would like MySQL to start on system boot - I personally prefer to leave MySQL off and only start it when I need it, but if you want to install this please go ahead.

Now we just need to do a small bit of set-up before moving on with the Perl side of things...

First we need to give the MySQL root user a password. Open up the terminal and issue the following command (ignore the '$' - that is there to signify the bash prompt) and substitute in the password you would like to use:

Code:

$ mysqladmin -u root password NEW_ROOT_PASSWORD

Now log into MySQL with the root user and your new password to check that it has worked.

Code:

$ mysql -u root -p

Finally, I prefer to use a separate account to the root user to admin my databases, if you'd like to do the same, set up your account with something like the following (ignore the 'mysql>' - that's to signify we're at the MySQL prompt):

Code:

mysql> grant all privileges on *.* to 'daz'@'localhost' identified by 'YOUR_PASSWORD';

That's MySQL set-up and running, now let's move onto the Perl!

Install DBD::MySQL

We're going to use Cpan (Cpan.pm to be exact) to do most of the hard work for us, so let's fire up cpan by typing the following in the Terminal:

Code:

$ perl -MCPAN -e 'shell'

If this is the first time you've used the Cpan module on your Mac you will be asked about configuring your Cpan set-up, something like the following will be in front of you:

Code:

Are you ready for manual configuration? [yes]

At this point what you do is up to you - you can try to configure all of your settings manually, (there's quite a lot to configure), but I normally just answer 'no' and hit return. The Cpan module does a pretty good job of auto-configuring itself.

Next we shall fetch the packages we need (ignore the 'cpan>' - it's there to signify we're at the cpan prompt):

Code:

cpan> get DBI

cpan> get DBD::mysql

cpan> exit

All we have done so far is fetch our packages, there is a reason for this - you need admin privileges to install, so let's do this now. First install DBI:

Code:

$ sudo perl -MCPAN -e 'install DBI'

Unfortunately, this is where things are not as straight-forward, DBD::mysql will not install if we try the same trick as it needs to connect to a MySQL database and perform tests to confirm things will work, but the Cpan module does not know about your connection details. So instead we are going to use the files Cpan downloaded and build DBD::mysql ourselves.

First cd into the directory that the Cpan module created when we told it to 'get DBD::mysql'.

Code:

$ cd ~/.cpan/build/DBD-mysql-4.010/

If this doesn't work for you cd into '~/.cpan/build' and have a look for the directory - your version numbers may be different.

Next we shall configure the build - in the next command substitute in your login details for your MySQL server that you have just set-up:

Code:

$ perl Makefile.PL --testuser='daz' --testpassword='YOUR_PASSWORD'

Now follow up with the next three commands:

Code:

$ make

$ make test

$ sudo make install

This completes the build and install of DBD::mysql! Not too bad in the end was it?!? Finally, let's just confirm that things are working copy the code below into a Perl script, change the login details to the details for your server and run it. If things have gone okay you should have a series of user names (mostly 'root') printed in front of you.

Code:

#! /usr/bin/perl

use strict;

use warnings;

use DBI;

use DBD::MySQL;

my $dbh=DBI->connect(

  "DBI:mysql:database=mysql;host=localhost",

  "daz",

  "YOUR_PASSWORD"

) || die "Error connecting to database: $!\n";

my $sth = $dbh->prepare("SELECT * FROM user");

$sth->execute();

while (my $ref = $sth->fetchrow_arrayref) {

  print $ref->[1] . "\n";

}

exit;

Biocep

Thu, 18 Dec 2008 18:13:28 +0000

I posted this on my blog, but thought it would be good to post the info here too:

Quote:I went to an event called Cloudcamb last night (I love working in Cambridge) organised by Matt (ta very muchly), the evening was very good an informative, but the one thing that really stood out for me was a very interesting presentation on the Biocep project that anyone who uses R (or would like to use R) should be interested in.

Here's my take on the basics of it and why you would want this - there's really LOTS more there!!!

The first thing Biocep is (that's not really advertised much on the site) is that it offers a vastly improved interface to R that has the following tools:

Built-in spreadsheet like functionallity

Built-in code editor (jEdit)

Plug-in architecture for creating custom interfaces to things (similar potential to Matlab's GUIDE)

There are other R gui's out there (i.e. Mac and Windows R spring to mind) - but they are not as slick as this.

The second thing biocep gives is that it allows you to run R instances on remote machines (i.e. up in the "cloud", or on clusters or grid systems in your work place / institute), from your desktop and be able to work collaboratively with other people using fully shared sessions (i.e. both of you can play with shared data, talk and see all of the visuals the other person is seeing all in real-time - it's really impressive to watch).

Seriously, if you work with R, check it out!

BBS is at number 1!!!

Mon, 24 Nov 2008 21:31:48 +0000

Thought I'd better post this screenshot for posterity - BBS is currently the number 1 selling Perl book on Amazon! How weird is that?!?!?

Either our book is doing well, or it's a slow sales day... (I'm hoping for the first option being the case!)

http://www.amazon.co.uk/gp/bestsellers/b...b_1_5_last