Chemistry in silico

Computational Chemistry sandwich placement available

2011-12-28T15:26:00.000Z

It is that time of year again when I can announce my group at AstraZeneca has a new position available. We are looking for a Sandwich Student to join us in September 2012. We successfully rebooted our sandwich student program last year. The ideal candidate will currently be in the second year of their chemistry or computer science degree. No experience is required, but a willingness to learn is crucial as you will learn about cheminformatics and computational chemistry.

Unfortunately, I personally will not be involved with this student, apart from the recruitment process for reasons which are subject to another blog post.

If you are interested find out more here: http://www.ideas.astrazeneca.com/sandwich-and-summer-placements/ and search for reference: TRES DS 12. Closing date for applications is 25th Jan 2012. Good luck!

Photo courtesy of http://www.flickr.com/photos/53921113@N02/5645102295/

Computational Chemistry sandwich placement available

2011-01-15T18:30:00.002Z

I'm delighted to announce we have a 12 month placement available for a sandwich student. Typically the third year of a four year undergraduate degree. It has been a while since my department has had a placement student, but I firmly believe the experience is valuable for both the student and us. I did a placement during my undergraduate degree and thoroughly enjoyed it. Seemingly my employer agreed as they later sponsored my PhD.

The ideal candidate would be a chemist or computer scientist. The only skill you need to bring is a desire to learn. We don't expect you to know all about drug discovery or be an amazing programmer. During the placement you will have to the opportunity to pick up the skills required to make a meaningful contribution to our department.

If you are interested find out more here, http://www.ideas.astrazeneca.com/sandwich-and-summer-placements/ and search for reference: TRES DECS 11. Closing date for applications is 15th Feb 2011. Good luck!

Subversion Edge

2010-09-23T10:37:00.018+01:00

Subversion is an excellent version control system. It is mature enough to have all sorts of integration - with Apache and Python amongst others. This enables easy communication via the HTTP protocol and language bindings, such as python to form web interfaces for repositories.

With subversion being a server-client model the version of the server is the most important component as it determines what features you can actually use. No good having a 1.6 client if the server is 1.2 as only 1.2 features are available. Depressingly this was the situation I was in. Unsurprisingly, the good folk at CollabNet have added lots of useful new features, which I need to use.

Compiling subversion is actually dead easy (as I have discussed previously, plus lots of binaries are available). So what is Subversion Edge? Essentially a bundle of Apache, Subversion and ViewVC server in a convenient tarball. Then throw in a bonus admin web interface as well. Upgrading your server version becomes slightly more tricky when Apache and Python are tied to it. No worries with Subversion Edge as it has a built-in update mechanism. One of my pet peeves is multiple usernames/passwords. Another freebie from Subversion Edge is LDAP support so plug straight in your authentication system - nice. One less component to ensure you compile against.

I started using the beta over the summer and have had no problems. The 1.2.1 release is now happily serving many repositories for me. If you run a very large and complicated setup you may find Subversion Edge is too restricted for you, but for a large number of users it will meet your needs.

If you maintain subversion repositories I strongly recommend you give Subversion Edge a go today. Did I mention it was free as well?

Useful links:

iOS apps for Science

2010-09-21T00:11:00.000+01:00

I was going to list interesting iPhone/iPad apps months ago, but there is already an excellent list available here and I see no point in reinventing the wheel.

If you fancy hunting through the App Store, which isn't that great a search you'll generally find science apps under Books, Education, Reference or Utilities.

Now I have slightly more free time I might have a dabble with the iOS SDK.

Blog spring clean

2010-08-30T19:08:00.000+01:00

Admittedly this is late for a spring clean, but Blogger has introduced a host of updates since I last looked. One being this nifty new template.

Also, something I've wanted to try out is a decent syntax highlighter and this one looks good. See http://alexgorbatchev.com/SyntaxHighlighter/. The instructions I followed for Blogger can be found here.

So now I can easily publish code like this:

<html>
  <head>
    <title>Tutorial: HelloWorld</title>
  </head>
  <body>
    <h1>HelloWorld Tutorial</h1>
  </body>
</html>

(You have escape angular brackets)

print "Hello, World!"

// Outputs "Hello, world!" and then exits
public class HelloWorld {
   public static void main(String[] args) {
       System.out.println("Hello world!");
   }
}

Don't use the Blogger WYSIWYG editor for this, switch to HTML else it will get very confused. I have used the pre method over script. I imagine if you switch templates this may break, but a quick copy and paste should bring the functionality back.

Fingers crossed it comes out ok through RSS readers as well!

New content... part II

2010-04-03T17:58:00.001+01:00

I've finally submitted my PhD thesis! Therefore, I now have spare time, it might take a while to get used to. I've neglected this blog because of writing up but will start to post new content soon.

Eclipse Galileo

2009-06-28T19:07:00.002+01:00

Eclipse continues it's annual eclipse release, this year with Galileo. Available to download from here.

33 projects have released new updates, so something for everyone. Of particular note for Mac users, is the option for Cocoa, the successor to the Carbon API. (Pick when you download).

I've tried a handful of plugins and they all seem to work fine:

Subclipse
CDT (new release)
PyDev
Aptana Studio

You can find numerous reviews on the eclipse website.

Eclipse with Django

2009-06-14T19:29:00.001+01:00

Django is popular web framework written in Python. For Python users it is an obvious choice to deploy web applications. Once again I return to my favourite IDE to develop with Django - Eclipse.

Two plugins are needed to bring Django support to Eclipse. The second handles the Django template language. Grab the plugins:

PyDev (Python)
Aptana Studio (Python + Django)

Both plugins are from Aptana, PyDev is a plugin to their IDE. Thankfully, both work through Eclipse as well.

Eclipse with C++/OEChem

2009-06-01T15:10:00.005+01:00

The final post in this series, allowing you to develop your OpenEye applications using Eclipse.

First off you will need to ensure the CDT plugin is installed, or download Eclipse for C++ developers.

Now we are set to go. Create a new C++ Project (Executable > Hello World). Edit/Add C++ files to the source folder. Next we need to inform the project about OpenEye.

Open your project properties (Project > Properties).
Pick C/C++ Build > Settings
Edit [ All Configurations ] (by default Debug and Release)
Set include paths (-I) under GCC C++ Compiler > Directories > Include paths
Add $OE_DIR/toolkits/include
Set library paths (-L) under GCC C++ Linker > Libraries > Library search path
Add $OE_DIR/toolkits/lib
Set specific libraries (-l) under GCC C++ Linker > Libraries > Libraries
Add oeplatform, oesystem, oechem, m, z, pthread
You can set further Makefile details from this panel (optimisation etc)

If you have multiple versions of the toolkit you can create a configuration for each one.

Between C++/Java/Python you should be able to code away happily within Eclipse.

Eclipse with Java/OEChem

2009-05-01T16:49:00.001+01:00

Following up from a previous post, here I present the settings required to get Eclipse running with the OEChem Java wrapper.

Make sure you have Eclipse and and working OpenEye installation setup and running first.

Create a regular Java Project
Configure your build path to add:
a) Under sources add a linked source $OE_DIR/java/libs
b) Under libraries add external jars, $OE_DIR/java/*.jar (add them all)
Run your OEChem program, if you get license errors edit the run configuration; under environment add OE_LICENSE, with $OE_DIR/etc/oe_license.txt; OE_HOME with $OE_DIR and OEJAVA with $OE_DIR/java

Obviously substitute $OE_DIR with your actual absolute file path.

Now Eclipse's CDT can be used to use the C++ toolkit direct, so I'll post that - once I've started to use it!

Eclipse with Python/OEChem

2009-04-18T12:48:00.005+01:00

Eclipse is an excellent IDE. Alas it doesn't have support for Python - fear not the PyDev plugin comes to the rescue. (Installation information here).

While that now works like a charm, if you have an OpenEye license to hand (academics see this post) if would be great to use the Python toolkit through Eclipse.

Follow these steps to make your Python project OEChem ready:

Window > Preferences > Pydev > Interpreter - Python.
To Libraries add your $OE_DIR/python folder.
To Environment add OE_LICENSE and OE_DIR, with their respective locations.
Create a new PyDev project and it should have OE capability by default.

Java users don't worry, I'll cover OEChem/Java in my next post.

GCC 4.3 on RHEL4

2009-04-16T23:36:00.004+01:00

There comes a time when you'll need the latest (or newer compilers). Unfortunately they are not always easy to upgrade.

Here I've installed GCC 4.3 on RHEL4.4, but in principle should work for any distribution.

Download the latest version of these:

binutils 2.19.1
GMP 4.1+
MPFR 2.3+
GCC 4.3.3

Compile binutils first

./configure --prefix=/home/craigb/binutils

make

make install

Add your new binaries to your PATH (export PATH=/home/craigb/binutils/bin:$PATH) and libraries to LD_LIBRARY_PATH (export LD_LIBRARY_PATH=/home/craigb/binutils/lib:$LD_LIBRARY_PATH) next compile GMP

./configure --prefix=/home/craigb/gmp

make

make install

Add these libraries to your LD_LIBRARY_PATH (export LD_LIBRARY_PATH=/home/craigb/gmp/lib:$LD_LIBRARY_PATH), next compile MPFR

Download the latest patches first

./configure --prefix=/home/craigb/mpfr

make

make install

Add these libraries to your LD_LIBRARY_PATH (like above), now compile GCC

cd /home/craigb/gcc-build (Note not the same folder as the source)

/home/craigb/gcc-4.3.3/configure --prefix=/home/craigb/gcc --with-gmp=/home/craigb/gmp --with-mpfr=/home/craigb/mpfr

make

make install

You should find GCC in /home/craigb/gcc/bin!

It is good practise to read the INSTALL and/or README files for all the applications before running the generic configure, make, make install above. If make check or make test is available do that as well.

Install CPMD

2009-04-03T08:26:00.000+01:00

CPMD is massively parallel code. There is little point running it serially as it will literally take forever to do anything useful. I'm providing the instructions I used to compile the parallel version on our HPC facility, therefore they may need altering for your computer.

Some technical details:

CPMD 3.13.1
Intel compilers/MKL 10.1
openSUSE 10.3, 64-bit

cd SOURCE
./mkconfig.sh IFORT-AMD64-MPI > Makefile

# In Makefile alter
FFLAGS = -pc64 -O2 -unroll
LFLAGS = -L/opt/intel/mkl/10.0.3.020/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
CC = mpicc -cc=icc
FC = mpif90 -fc=ifort -c
LD = mpif90 -fc-ifort -i-static

Run make, hopefully it will compile happily, copy cpmd.x to somewhere on your $PATH.

It would be wise to test your binary. First download cpmd-test.tar.gz from the contrib section of the downloads (tests are not included with the source). Run as mpisub 5x2 cpmd.x inp-1 or similiar depending on your setup. This command would use 5 dual processor computers.

Python training

2009-04-01T14:43:00.000+01:00

Forgot to mention in my last post. If you are after Python/OEChem training and are not coming to EuroCUP, there is an alternative. Andrew Dalke is offering Python training for Cheminformatics. OEChem is just one part of this course, Django, SQL, R are also covered.

I've spoken to a previous attendee and he recommended it.

See Andrew's website for more details.

EuroCUP III

2009-04-01T12:47:00.001+01:00

I'm off to OpenEye's third annual EuroCUP next month. I've not been to a vendor organised conference before, so am looking forward to it.

Although I've previously posted about the free academic license; I wish I'd taken advantage of mine more. Alas time didn't permit. That's now changed and I've learning Python as quick as I can to take full advantage of the Python/OEChem training session offered at EuroCUP.

I can jump straight into OEChem via Java, but the Python wrapper lends itself better for web-based applications. I've no plans (yet) to use the C++ toolkit directly.

I've used Eclipse as my editor of preference and will post how to configure it to use the Java & Python wrappers. Any C++ users feel free to contribute!

New content... shortly

2009-03-13T13:15:00.004Z

Apologies for the lack of posts, moving home and job has made blogging a very low priority! I do have some topics lined up though, specifically:

Various installation howtos
Eclipse integration with OpenEye toolkits

Let me know if there is something specific, related to my previous posts that would be of interest and I'll try to blog on that too.

Chemistry on the iPhone

2009-02-20T09:52:00.003Z

The iPhone has had plenty of press since it's initial announcement. In my view, one of the best features is the App store. With some 15,000 applications currently available there is something for everyone - including Chemists! From straight reference to 3D visualisation with touch interface these applications demonstrate what scientists could do on a smartphone. This is by no means an extensive list, but some apps that have caught my eye:

Molecules (iTunes link)
iMoleBuilder (iTunes link)
The Chemical Touch (iTunes link)
miMol (iTunes link)
Atom in a box (iTunes link)
Solutions (iTunes link)
Wikipanion (iTunes link) - Not specifically for Chemistry, but lots of chemical data is now available on Wikipedia.

The App Store categories is the obvious way to find these, specifically in Education, Reference or Utilities. However, Solutions falls under Health & Fitness!

Anyone can write an App for the iPhone (and iPod Touch) using the SDK. It is Objective-C, not something I'm familiar with so that goes on my to do list for post-thesis!

Other smartphones are also introducing SDK's as well, e.g. Android. The mobile platform is becoming an increasingly important development arena. It is good to see that Chemistry has a presence there too.

Condor 7.2.0 success

2009-02-11T16:32:00.000Z

Condor 7.2.0 is successfully running on our condor pool. Using our own compiles for Mac/PPC, openSUSE 10.3 64-bit and openSUSE 10.3 32-bit (used on 10.2/10.3/11.0/11.1 computers). Mac/Intel binaries from the condor development team.

For reference the configure options I've used are:

Mac/PPC
./configure --without-classads --without-openssl

openSUSE 10.x/11.0
./configure --disable-glibc-version-check --disable-gcc-version-check --disable-full-port --without-classads --without-gsoap

openSUSE 11.1
./configure --disable-glibc-version-check --disable-gcc-version-check --disable-full-port --without-classads --without-gsoap --without-coredumper

Otherwise compile as per my previous posts.

Make Java look native on Mac

2009-02-04T22:43:00.000Z

Java is excellent as it just works on so many platforms. My Java software is used on Windows, Linux & Mac. Mac users will notice that the behaviour of Java applications doesn't follow that of the native applications (unlike on Windows/Linux). This is a bit annoying to be honest, however, there are several steps you can take to give a more Mac "feel" to your application.

This link was recently forwarded to me, some of it is certainly useful, although some outdated, but it will give you an idea of what you can alter to add that Mac feel.

MAMP on Leopard part III

2009-01-28T10:54:00.004Z

The final part to MAMP is PHP. PHP is already installed but not configured.

Apache needs to be told how to handle .php files (otherwise they are shown as plain text source in the browser). This handler needs to be added to /etc/apache2/httpd.conf, add near similar commands towards the end of the file.

AddType application/x-httpd-php .php

Also check whether the PHP module line is not commented, remove a # if present.

LoadModule php5_module libexec/apache2/libphp5.so

The PHP config file is not active by default, you will want to do this:

sudo cp /etc/php.ini.default /etc/php.ini

As you have installed MySQL, you will want PHP to be able to talk to it you need to edit two lines to ensure it actually works:

mysql.default_socket = /tmp/mysql.sock
mysqli.default_socket = /tmp/mysql.sock

(Add the bold values) Then restart apache for the changes to take affect.

That completes this 3 part installation guide for MAMP on Leopard. P can also be Perl or Python, if you need those languages.

MAMP on Leopard part II

2009-01-20T17:54:00.003Z

MySQL is the hugely popular SQL database server. It is the only part of MAMP that isn't installed by default with Leopard. No problem, a quick visit to mysql.com will let you download it, select Mac OS X package format. (N.B. Pick the 32-bit version, the 64-bit will cause a headache later if you plan to use Perl's MySQL DBI, see my previous post).

Run all 3 applications within the download: mysql-5.1.X-osx10.5-x86.pkg, MySQLStartupItem.pkg and MySQL.prefPane.

MySQL can be started/stopped via the the MySQL panel in System preferences, or via the command-line:

sudo /Library/StartupItems/MySQLCOM/MySQLCOM {start|stop|restart}

Now it is installed you should remove the anonymous login accounts and add a password to the root account. There is plenty of information on securing MySQL available here.

Configure PHP in part III.

MAMP on Leopard part I

2009-01-12T10:38:00.002Z

In this three part tutorial I'll detail how to take Mac OS X 10.5 Leopard (client version) from no MAMP to MAMP.

MAMP being a twist on the more common LAMP.

Mac OS X
Apache
MySQL
PHP (or Python or Perl)

MAMP is key for using modern web services and software, e.g. phpMyAdmin, MediaWiki, the list is almost endless. Each part of this tutorial will address one element. I assume you have Mac OS X Leopard installed, if not go buy yourself a Mac!

Apache2 comes with Leopard (and is periodically updated too). All you need to do is switch it on. Jump to System Preferences > Sharing, tick "Web sharing" from the list and apache is now running!

Find your configuration file at /etc/apache2/httpd.conf. Files for the default location can be found in /Library/WebServer/Documents and CGI scripts in /Library/WebServer/CGI-Executables. User websites (http://localhost/~username) can be found in the Sites folder of the specified user. Note the location of any of these can be altered using your httpd.conf. I recommend reading up on the manual before editing your .conf files first.

You can also stop/start apache via the command-line using:

sudo apachectl {start|stop|restart}

MySQL will be covered in part II.

Condor 7.2.0

2009-01-09T19:54:00.001Z

After not much luck with 7.1.x, I've successfully compiled 7.2.0 on Mac/PPC, openSUSE 10.3 64-bit & openSUSE 11.0 32-bit.

All using the following configure options:

./configure --disable-glibc-version-check --disable-gcc-version-check --disable-full-port --without-classads --without-gsoap

All I need to do now is test it on my pool, but looks promising so far!

MySQL & Perl on Leopard

2008-12-18T19:38:00.000Z

Mac OS X Leopard comes with Apache2 and PHP pre-installed, but no MySQL. This is the missing link in the very useful MAMP setup. The kind people at mysql.com offer it ready packaged for mac users. When picking your version, MacIntel users pick the 32-bit version, unless you want problems installing Perl's DBD::mysql. What is DBD::mysql? the very useful module that allows Perl scripts to access your MySQL databases. If you install the 64-bit version of MySQL you will hit errors when you install DBD::mysql as a 32-bit installation of Perl is not interested in compiling against 64-bit MySQL libraries.

If you need 64-bit MySQL you could install both versions and compile against the 32-bit libraries.

MacPorts on Leopard with a proxy

2008-12-18T19:26:00.000Z

MacPorts is an excellent tool for Mac users to grab extra software without having to worry about working out the compile options and read endless instructions etc. As of today there are 5253 ports available for everything from apache2 to iphone apps. The beauty of installing anything from MP is it will install any dependancies as well. I've just upgraded one of our servers to Leopard, but MP didn't want to play anymore. Turns out there is a bug in handling the proxy settings. We have to use a proxy, so this is a show stopper. It looks like they will fix for the 1.8 release, but I can't wait!

Thankfully a simple workaround exists, that requires you to edit /etc/sudoers.

sudo visudo (Don't use vim direct on /etc/sudoers)

in the Default specification section add:


Defaults        env_keep += "http_proxy HTTP_PROXY HTTPS_PROXY FTP_PROXY"
Defaults        env_keep += "ALL_PROXY NO_PROXY"

Essentially when you sudo port install apache2 sudo only takes a stripped down version of current environment variables, so even though you have set your all important $http_proxy, macports doesn't get it. Adding those two lines will fix that. Now install software galore!