Village on the height: Mana (Uttarachal, India)

Mana, a tiny village near Badrinath (State Uttarachal, India), is located just few meters inside the Indo-Tibet border in the Himalayas. This village, referred to as the last village of India on the Indo-Tibet border, has been designated as a ‘tourism village’ by the Uttarakhand government.

With 10,248 ft above sea, Mana village holds a lot of mythological relevance and we can actually see traces of the Mahabharata scattered across this small village.

On the top of hill at Mana, the air is more rarified and it is difficult to breath as well. There is a board announcing ‘India’s last tea shop’, stands distinctly with a neat crowd of tourists mingling about. Chand, the owner of hotel, welcomes all with smile and a cup of tea. He always says “Take this tulsi tea. In the Himalayas tulsi is available in plenty”.

You can have a view of border road on the one side and Himalayas on the other side. From here, there is no other way to go!

H1N1 virus – What do H & N refer to ?

The influenza A virus is divided into subtypes, such as H1N1. The letters H and N refer to hemagglutinin and Neuraminidase. Hemagglutinin and neuraminidase are antigens, proteins that provoke an immune response in the human body.

There are 16 known hemagglutinin subtypes for influenza A (H1 to H16) and 9 known neuraminidase subtypes (N1 to N9). Each of these subtypes is vulnerable to a similar type of antibody.

There are three hemagglutinin subtypes that are known to attack human cells: H1, H2, and H3. These three subtypes bind with cells in the human respiratory tract. Other hemagglutinin subtypes target different mammals or birds. H5, for example, attacks the digestive tracts of birds. Of the nine neuraminidase subtypes, N1 and N2 are most commonly found in humans.

Attack of H and N:- Each viral particle is covered with hemagglutinin and neuraminidase. Hemagglutinin binds to the targeted host cell and injects the virus’s genetic material into it. After the virus has reproduced inside the host cell, neuraminidase releases the offspring. The host cell then dies

Microsoft Biology Foundation

The Microsoft Biology Foundation (MBF) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework, initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, and documentation are freely downloadable.

The source code and development of MBF is managed on CodePlex site, but all downloads are hosted on the Microsoft Research site here: http://research.microsoft.com/bio/mbf.aspx

GSL: GNU Scientific Library – An overview

Another wonderful project from GNU, the GSL library for mathematics !!!
GSL is a numerical library written in C that provides a wide range of mathematical routines, that the C/C++ developers can make use of, to implement or design a nice platform for mathematicians. There are many such libraries available in Python (NumPy or SciPy), Java (JMSL, JavaNumerics, JNL), Perl (PDL). But GSL comes with over 1000 functions and an extensive test suite for beginners.

My dream was to utilize this API to build all-in-one suite for mathematics world. That’s I’m with ScientificX, one of my dream project which is currently in progress.

More about GSL | Documentation | my ScientificX project

Create your own service in Linux

If you wish to create your service daemon in linux box, try the following tips:

1) The existing services are managed by shell scripts located in /etc/init.d directory. You can use any of this as a template file to build a service script.
2) You may notice “case” blocks in the script to handle start/stop/restart/status operations.

For Eg:

case "$1" in
start)
echo -n $"Starting name: "
echo

echo
;;


The above block will be executed when somebody try

$service start

command. Similarly you can put “stop” or “restart” blocks as well.

You can download this template file start building !!

MayaVi is now back !!

The Mayavi project includes two related packages for 3-dimensional visualization:

• Mayavi2: A tool for easy and interactive visualization of data, with seamless integration with Python scientific libraries.
• TVTK: A Traits-based wrapper for the Visualization Toolkit, a popular open-source visualization library.

These libraries operate at different levels of abstraction. TVTK manipulates visualization objects, while Mayavi2 lets you operate on your data, and then see the results. Most users either use the Mayavi user interface or program to its scripting interface; you probably don’t need to interact with TVTK unless you want to create a new Mayavi module.

Project homepage: http://code.enthought.com/projects/mayavi/

See some screen-shots

Galaxy server for Bioinformatics

Galaxy is a python based “framework” for bioinformatics, that enables communication between Experimental Biologists and Computational Biologists. It’s very easy to configure and set-up, also you can define the analysis tools to be incorporated, etc so that that it would act as a complete computational tool for biologists.

Galaxy aims to be a zero configuration entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files. more…

[ SCREEN CASTS ] [ DOWNLOAD ] [ SAMPLE DEMO ]

Have you heard about CDK ??

CDK is noting but “Chemistry Development Kit”, a Java library for Structural Chemo – and Bioinformatics. Latest version 1.2.3 is now available at sourceForge.net. You can use this java API for the following functionality in your application;

Calculation of molecular, atomic and bond descriptors
Interface to R and Weka for modeling
3D model builder
Isomorphism detection
Maximal common substructure search
Substructure searching (SMARTS like)
Ring searches (SSSR, all rings)
NMR prediction
Structure Generation
Active site detection
and more… [ CDK Home ] [ Documentation and Tutorials ] [ Download ]

Opensource in Bioinformatics

The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics – gene research software. The number of open source software kits are coming day by day with a lot of enhancements in terms of accuracy, better interpretation of results, one-step analysis workbench, design own experiment with pipeline concept, advanced graphical implementation and more. If you see an amazing collection of tools for Bioinformatics in sourceForge.net, which is one of the largest open source software repository available today. More than 2090 open source tools are available at this moment;
Just explore it and contribute

Draw Ramachandran Plot by yourself

Using suitable python libraries, its probably very easy to draw a (φ,ψ) scatter plot – but ideally we want to highlight the “allowed” and “favoured” regions in the background of the figure. This requires a definition of those regions in a format that python can understand… and a way of using this for a contour plot. [ Complete tutorial ]

Also if you are interested in R language, there are r libraries to compute the phi-psi angles and plot the graph. Read now, download sample code and try by yourself