SureshKumar's Bioinformatics Blog

I am Suresh Kumar Sampathrajan. I have completed my PhD degree in bioinformatics from the University of Vienna, Austria in the year 2010. If you want to know more about me and my research,please click the menus at the top.

I have started this bioinformatics blog mainly for undegraduate and postgraduate students of bioinformatics. This blog will serve as an open resource material for the students and for those who wish to know about bionformatics. This blog contains video tutorials, tips, bioinformatics software downloads, articles on bioinformatics and career opportunities.

What is Bioinformatics?-Video tutorial-Watch Online

What is Bioinformatics?-Video tutorial-Watch Online
A general introduction to bioinformatics- Need for biological database,defintion of bioinformatics,what we can do with the sequence database? -
Thanks Sandra Porter

Proteopedia-3D encyclopedia of proteins & other molecules

Proteopedia is a resource that presents protein structure/function & other molecules information in a user friendly manner. It is a interactive, wiki web-resource whose pages have embedded three-dimensional structures surrounded by descriptive text containing hyperlinks that change the appearance (view, representations, colors, labels) of the adjacent three-dimensional structure to reflect the concept explained in the text.

Proteopedia is a wiki-based web-resource serves as a mechanism for making three-dimensional structures easier to understand, a linking of function to interactive three-dimensional structure visualization, and a simplified sharing of structural and functional knowledge

VISIT PROTEOPEDIA

Proteopedia in action - Video


Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L. Sussman: Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Genome Biology 2008
VIEW FULL PAPER

Machine Learning for Bioinformatics-Video Lecture-Watch Online

Hidden Connections: Learning from data
General Introductory video lecture how to use machine learning methods for vast amount of data created.
One of the most intractable problems facing us all is how to understand the vast quantities of data that surround us. As we measure more and faster, as we create more digital content, as we search ever broader fields, we have a greater need for help in finding useful information from data.

In his inaugural lecture, Professor Professor Ian Nabney from Aston's school of Engineering & Applied Science, discusses how machine learning - the computer-based extraction of underlying models - can be used to uncover the hidden meanings of data and provide users with the information they need in a form that they can use.

These ideas will be illustrated with applications in many domains, including biomedical engineering, bioinformatics and pharmaceutical discovery, and meteorology.

RNA to Protein - Video Lecture-Watch Online for free

RNA to Protein - Video Lecture-Watch Online for free

Part 1


Part 2


Part 3

Cell Biology Animations-Interact & Learn


Cell Biology Animations Created by John Kyrk it includes animation of
  • Aminoacids and Protein
  • Cell Function Overview
  • Cell Anatomy
  • Cell membranes
  • Chromosome Structure
  • DNA structure,replication,transcription,translation
  • Glycolysis
  • Krebs cycle
  • Virus etc

Visit the website

http://www.johnkyrk.com/index.html

Current Issues in Computational Biology and Bioinformatics-Video Lecture-Watch Online

Current Issues in Computational Biology and Bioinformatics
A brief overview of bioinformatics computational problem landscape followed by a detailed look at one of the areas: multiple perturbation analysis of cells using reverse engineering principles.
Speaker: Gary Bader
Gary is Assistant Professor at the Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) at the University of Toronto. http://baderlab.org/

Bioinformatics-Beginning Perl for Nonprogrammers-Video Tutorial

In computer programming, Perl is a high-level, general-purpose, interpreted, dynamic programming language. Perl was originally developed by Larry Wall.Perl borrows features from other programming languages including C, shell scripting (sh), AWK, and sed. The language provides powerful text processing facilities without the arbitrary data length limits of many contemporary Unix tools,facilitating easy manipulation of text files. It is also used for graphics programming, system administration, network programming, applications that require database access and CGI programming on the Web(Wikipedia).


Beginning Perl for Nonprogrammers 1 of 2


This is an instructional video outlining the basics of the Perl scripting language.


VIEWFULLSCREEN



Beginning Perl for Nonprogrammers 2 of 2


This is an instructional video covering the basics of the Perl scripting language from Medquist Inc.


VIEWFULLSCREEN

Structure hierarchy of proteins -Video-Watch Online



Protein structure-Video


Based on Structure hierarchy proteins are classified as primary, secondary, tertiary, and quaternary structure.

  • Primary Structure refers to the linear sequence of amino acids that make up the polypeptide chain.
  • The secondary structure of protein molecules refers to the formation of a regular pattern of twists or kinks of the polypeptide chain. The regularity is due to hydrogen bonds forming between the atoms of the amino acid backbone of the polypeptide chain. The two most common types of secondary structure are called the alpha helix and ß pleated sheet.
  • Tertiary structure refers to the three dimensional globular structure formed by bending and twisting of the polypeptide chain. This process often means that the linear sequence of amino acids is folded into a compact globular structure. The folding of the polypeptide chain is stabilized by multiple weak, noncovalent interactions.
  • Quaternary structure refers that proteins contain more than one polypeptide chain. Each polypeptide chain in the protein is called a subunit. The subunits can be the same polypeptide chain or different ones.

Free Virtual Training Workshop on Bioinformatics


This 3rd Virtual Training Workshop on Bioinformatics is being organized by Asian Bioinformatics Research and Education Network (ABREN), a non-profit organization to promote research and education in this rapidly growing interdisciplinary field of science. This is an online training workshop with multimedia lectures being provided on demand through the Internet. This workshop covers various topics in Bioinformatics and the lectures are classified into basic, intermediate and advanced levels. Thus, the participants can go through the workshop lectures at their pace and convenience, and ask teachers questions and get answers any time during the workshop period. This workshop is now open for online registration. The registration is free but the number of participants may be restricted. The deadline for the online registration is February 28th, 2009.

Register via this Link: http://www.abren.net/workshop/

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