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.

Introduction to R-Video tutorial

R-statistical analysis program-Video tutorial-Introduction
R is a programming language and software environment for statistical computing and graphics. R is widely used for statistical software development and data analysis.R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, and others) and graphical techniques.R is a pen source statistical analysis program which is widely used in bioinformatics.

Source:Virgina Tech

First tutorial on the statistical software R covers: How to get R Variables Simple data types Operations Functions How to get help

Second tutorial on the statistical software R covers: Vectors Lists Data Frames Tables Basic creation and modification

Third tutorial on the statistical software R covers: Index vectors Index lists Index data frames Index tables Index by conditions

Fourth tutorial on the statistical software R covers: Read vectors from file Write vectors to file Read data frames from clipboard Read data frames from file Write data frames to file

Paperless Ph.D workflow-Video tutorial

Paperless Ph.D
This work flow includes RSS feeds from PubMed, reading abstracts in NetNewsWire, and finally downloading and archiving the article PDF, using journal Papers as an example how to cope up with the large volume of research in the field of neurophysiology.

Ph.D student Mike Pascoe demonstrating his paperless Ph.D workflow using a series of screen-casts.

In the first of his screen-casts Mike demonstrates how he uses a combination of medical journal site PubMed, clever custom RSS feeds (to inform him when articles of possible interest are submitted) and an interesting MAC-only app called Papers which provides him with a 'bells and whistles' front-end for the PubMed articles he needs to process and store.

In his second screen-cast Mike moves on to the business of dealing with Illiad sourced e-journal articles and the process he uses to firstly e-print to Papers before utilising PubMed to append the correct meta-data to his 'imported' articles

In the third of his screencast Mike begins with a brief explanation of how he use a copy machine to scan an article into a PDF and then he explains how to retrieve the PDF from the webspace and then add it to the Papers library.

Introduction to Multiple sequence alignment

Introduction to Multiple sequence alignment

A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.

Python Programming-Video Tutorials for Bioinformatics-Watch Online

Python Programming-Video Tutorials for Bioinformatics-Watch Online for free
pythontutorialsPython is a general-purpose high-level programming language. Its design philosophy emphasizes code readability.Python's core syntax and semantics are minimalistic, while the standard library is large and comprehensive. Its use of indentation as block delimiters is unusual among popular programming languages.

Structural Bioinformatics: Shortcuts and Pitfalls-Video Lecture

Structural Bioinformatics: Shortcuts and Pitfalls
3rd ISCB Student Council Symposium 2007 (SCS3) held during ISMB/ECCB 2007, Vienna. Keynote - "Structural Bioinformatics: Shortcuts and Pitfalls" by Anna Tramontano, Professor of Biocomputing, University of Rome "La Sapienza", Rome, Italy

Introduction to Rasmol- Free video tutorial

Introduction to Rasmol
by Dr Robert Sbaglia

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations.

In this tutorial Dr Robert Sbaglia teaches use of Rasmol to display and manipulate amino acids, peptides and proteins, examining structures of drug-protein complexes, and the investigation of interactions between the drugs and proteins.

-Download full tutorial booklet (right click & save as)

-The PDB files that are used in the workshop can be found in this zip file (right click & save as)

Chapter 1

Chapter 2

Chapter 3

chapter 4

Chapter 5

Chapter 5 v2.0

Getting Started with R and S-Plus- Free video tutorial

R-statistical analysis program-Video tutorial-Introduction
R is a programming language and software environment for statistical computing and graphics. R is widely used for statistical software development and data analysis.R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, and others) and graphical techniques.R is a pen source statistical analysis program which is widely used in bioinformatics.

Getting Started with R and S-Plus
by Mohammad Ehsanul Karim

- Download full tutorial as pdf (right click & save as)

Part 1:Vector arithmetic's tutorial

Part 2:Help search commands tutorial

Part 3:Plot and history tutorial

Part 4:R CRAN web tutorial

Part 5:External files tutorial

Part 6:Matrix operations tutorial

Part 7:Large dataset tutorial

A brief introduction to computational problems in haplotype Inference

A brief introduction to computational problems in haplotype Inference-Video Talk-Watch Online
Daniel G.Brown

Haplotype inference is a field that results from a technological limitation: it is expensive to separate the paternal and maternal chromosomes of an organism. However, being able to do so would be useful, particuarly when one tries to identify genetic variations partly responsible for common diseases. Haplotype inference is the computation problem of inferring these different chromosome sequences, by optimizing some combinatorial or statistical requirement. What makes haplotype inference attractive to computer scientists is that one can very quickly abstract away many biological details, and focus on the underlying mathematical structure of the various problems in the field. Moreover, in many cases, this structure is attractive, making this an appealing area in which to do research. We will discuss a few of these different problems and their properties, and for one problem, the Haplotype Inference by Pure Parsimony problem, focus on some of the mathematical structure that we have discovered.

Introduction to Bioinformatics-Video Lecture-Watch Online

Introduction to Bioinformatics-Video Lecture-Watch Online
This course will cover bioinformatics concepts and methodologies. It seeks to emphasize the concepts behind the rapid development of the field, both to give conceptual understanding of these very new areas, and to give students a foundation for how to do innovative work in these fields. The course aims to teach the conceptual foundations for the student to be able to invent new kinds of bioinformatics. It seeks to teach this material through real problems and examples of solutions. The course emphasizes statistical inference and algorithmic complexity as the two foundations of bioinformatics. Bioinformatics can be described broadly as the study of the inherent structure of biological information. In practice this means that bioinformatics problems can be considered to reduce to the problem of discovering whatever patterns are present in the data. This has two components: algorithms for finding a given kind of pattern (and the inherent computational difficulty of finding that pattern), and ways to measure the strength of the evidence that a given pattern is statistically significant (i.e. not just “random noise”). We will consider both components in detail, and their inter-relationships on various problems. The course will cover bioinformatics algorithms, their foundations in genomics data, and their use for analysis and interpretation of genomics data. We’ll examine sequence analysis and comparative genomics algorithms to get an understanding of the fundamental computational issues for biological data search and analysis

PhD Position in Evolutionary Genomics, Canada

PhD Position in Evolutionary Genomics, Canada

Applications are sought from outstanding candidates for a PhD position in evolutionary genomics of antibiotic resistance. This work is part of a Canadian Institutes of Health Research funded study to investigate the persistence of resistance to fluoroquinolone antibiotics in Pseudomonas aueruginosa infections associated with cystic fibrosis. The project demands a combination of skills including genome resequencing and bioinformatics, experimental evolution, and molecular microbiology. Experience in at least one of these fields is an asset. The successful candidate will work under the supervision of Rees Kassen ( ) in partnership with researchers at the Ottawa Hospital and will join a growing community of evolutionary biologists at the University of Ottawa ( ).

The University is also host to the 2012 meeting of the Society for the Study of Evolution held in conjunction for the first time with the European Society of Evolutionary Biology.

Applications should include a cover letter and curriculum vitae, as well as the names and contact information (including e-mail) of at least two referees. All application materials must be submitted as a PDF in a single email to Rees Kassen (, to whom queries may also be addressed. The closing date for applications is March 10, 2009. It is anticipated that the successful candidate would take up the position as early as May 01, 2009 and no later than September 01, 2009.

Located at the confluence of English and French Canada, Ottawa is a vibrant national capital of approximately1 million inhabitants ( ). The city offers a wide range of cultural activities in the visual and performing arts, as well as easy access to green spaces and wilderness. The University of Ottawa is located next to the historic Rideau Canal, steps from Parliament and within easy access to a wide range of research facilities of interest to evolutionary biologists including the Canadian Museum of Nature,
the National Wildlife Research Center, Health Canada, and Environment Canada.

R-statistical analysis program-Video tutorial-Introduction

R-statistical analysis program-Video tutorial-Introduction
R is a programming language and software environment for statistical computing and graphics. R is widely used for statistical software development and data analysis.R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, and others) and graphical techniques.R is a pen source statistical analysis program which is widely used in bioinformatics.

A tutorial on how to download and install R - a highly sophisticated open source statistical analysis program and environment.

A brief tutorial on how to install and update new packages in R.

The Cell Cycle-Video tutorial

The Cell Cycle-Video tutorial
The cell cycle, or cell-division cycle, is the series of events that take place in a cell leading to its replication. In prokaryotes, the cell cycle occurs via a process termed binary fission. In eukaryotes, the cell cycle can be divided in two brief periods: interphase—during which the cell grows, accumulating nutrients needed for mitosis and duplicating its DNA—and the mitotis (M) phase, during which the cell splits itself into two distinct cells, often called "daughter cells". The cell-division cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed.

Cell Division cycle: Prokaryotes-Binary fission
Binary fission is the form of asexual reproduction and cell division used by prokaryotic organisms (such as bacteria or archaea). This process results in the reproduction of a living prokaryotic cell by division into two parts which each have the potential to grow to the size of the original cell.

Cell cycle: Eukaryotes
The cell cycle is an ordered set of events, culminating in cell growth and division into two daughter cells. Non-dividing cells not considered to be in the cell cycle. The stages, pictured to the left, are G1-S-G2-M. The G1 stage stands for "GAP 1". The S stage stands for "Synthesis". This is the stage when DNA replication occurs. The G2 stage stands for "GAP 2". The M stage stands for "mitosis", and is when nuclear (chromosomes separate) and cytoplasmic (cytokinesis) division occur. Mitosis is further divided into four phases.

Chromosome structure-Video tutorial

Chromosome structure-Video tutorial
A chromosome is composed of two identical chromatids attached by a centromere. Each chromatid is made up of tightly wound DNA wrapped around histones. During cell division, spindle fibers attach to the kinetichore.

Cell Division:Mitosis & Meiosis - Video tutorial-Watch Online

Cell Division:Mitosis & Meiosis - Video tutorial-Watch Online
Mitosis and Meiosis describes the process by which the body prepares cells to participate in either asexual or sexual reproduction to make an entire organism.
Examples of Mitosis and Meiosis
Mitosis is the reproduction of skin, heart, stomach, cheek, hair etc. cells. These cells are "Autosomal" cells. This is also a form of "Asexual" reproduction, where one organism or cell reproduces itself. Some organisms that reproduce asexually are hydra, bacteria, and single celled organisms.

Meiosis is the production of sperm and egg cells. These cells are "Gamete" or "Sex" cells. Each cell has to go through the division process twice in order for the cell to end up with half the number of chromosomes. The cells pass on genetic information to the offspring. This is a form of "Sexual" reproduction, where one organism or cells reproduces by crossing with another organism or cell. Types of organisms that reproduce sexually are; plants, animals, and insects.



Comparison of Mitosis and Meiosis-Animation

Computational Molecular Biology - Free Video Course

Computational Molecular Biology - Free Video Course
Douglas L. Brutlag
Professor of Biochemistry & Medicine
Stanford University School of Medicine

Computational Molecular Biology is a practical, hands-on approach to the field of computational molecular biology. The course is recommended for both molecular biologists and computer scientists desiring to understand the major issues concerning representation and analysis of genomes, sequences and proteins. Various existing methods will be critically described and the strengths and limitations of each will be discussed. There will be practical assignments utilizing the tools described.

1.Require Quick time Installed in your computer
2.Requires Broadband internet

Video Lectures List

  • Genomics & Bioinformatics -Video

  • Bibliographic and Full Text Journal Access-Video

  • Genome Databases-Video

  • Molecular Biology Databases on the Web-Video

  • Pattern Matching with Consensus Sequences-Video

  • Quantitative & Probabilistic Pattern Matching-Video

  • Sequence Alignment-Video

  • Rapid Sequence Similarity Search-Video

  • Near-Optimal Sequence Alignments-Video

  • Multiple Sequence Alignment-Video

  • Distance Based Phylogenies-Video

  • Sequence Blocks & Profiles-Video

  • Protein Sequence Motifs-Video

  • Protein Structural Motifs-Video

  • Clustering and Functional Analysis of Coordinately Regulated Genes-Video

  • Discovering Transcriptional Regulatory Signals-Video

  • Ultraconservation in the Human Genome-Video

  • Pathway Bioinformatics-Video


DNA structure-Video tutorial

DNA structure-Video tutorial
The structure of DNA is illustrated by a right handed double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C).

Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three.

DNA structure-Video tutorial

DNA structure animation-Video

Useful resource
DNA structure-Interactive tutorial-Click here

Personal Genome Computing: Breakthroughs, Risks and Opportunities-Video

Personal Genome Computing: Breakthroughs, Risks and Opportunities-Video
"Technology breakthroughs are making DNA sequencing faster and cheaper than ever. In its top ten list of 2008 scientific breakthroughs that broke through with the potential for lasting impact, Science magazine included technology that has blown the doors off genome sequencing. In Nature magazines list of the top news stories of 2008, "Personal genomics goes mainstream" came in second. With the cost of DNA sequencing plummeting, the emergence of "molecular sequencing" platforms has forever changed the field of genetics.

A new paradigm appears on the horizon. Personal genome information will be used not just for health maintenance, disease diagnosis, and treatment, but will also be the foundation for lifestyle applications from shopping for food, to buying cosmetics, to assessing ones environment and making choices about fabrics, places - even friends.

The panel of Silicon Valley players and innovators of new business models examines the dynamic business and investment opportunities as well as the risks, global competition, regulatory and legal challenges, new individual contributor roles, and leading alliances emerging from Silicon Valley and beyond.

Personalized genomes at your doorstep

Personalized genomes at your doorstep

Three giants of the personal genomics industry are Linda Avey's 23andMe , Kari Stephansson's deCODEme and Dietrich Stephan's Navigenics.

They will genotype millions of regions in customers' genomes, called single nucleotide polymorphisms or SNPs, which have

been linked to a handful of diseases and nonmedical traits. They then sell that information

back to the customer.

Navigenics will use information from scientific studies to estimate composite risk factors for diseases based on each customer's SNPs. It also plans to provide genetic counselling to help customers interpret these risk factors. The firm will conduct long-term studies on how well those predictors work.

23andMe will analyse not just medical information, but also traits not necessarily linked to disease. The firm will introduce a social networking component to genomics by allowing customers to link their data with others', such as family members. It is also considering providing researchers with access to the data.

deCODEme will also analyse genetic risk factors,complete Ancestry Scan,provide tools to compare your results to those of friends and family.

All three of the company interests in developing whole-genome sequencing capabilities, sequencing has always been the Holy Grail of personal genomics, with the current SNP chip technology really little more than a crude place-holder until sequencing prices drop.

The first African Virtual Conference on Bioinformatics

The first African Virtual Conference on Bioinformatics (Afbix '09), Online at Bioinformatics.Org, February 19-20, 2009.

Graduate students and researchers in computational biology, molecular biology and medicine. The conference theme is "Tropical Bioinformatics." While most of the presenters are either in Africa or studying African species, attendance is open to everyone.

In addition to research on tropical diseases, pathogenesis and their vectors, the field of bioinformatics has become an important part of life science studies in Africa. But, with the great geographical expanse of the continent, it is often impractical or uneconomical for African researchers to come together for conferences. That is, in person. The Bioinformatics Organization (Bioinformatics.Org) has therefore collaborated with the African Society of Bioinformatics & Computational Biology (ASBCB) and Regional Student Groups (RSGs) in Africa to develop a bioinformatics conference that utilizes local institutions in Africa as "virtual hubs."

Participating African RSGs and the hub institutions:

- RSG East Africa (ILRI)
- RSG East Africa (ICIPE)
- RSG South Africa (SANBI)
- RSG Morocco (SMBI)
- RSG West Africa (Covenant University, Ota)

Other hub institutions:

- Notre Dame University, Indiana, USA

Individual registrations cost only $10-30, depending on location. Please see the conference description page (URL below).

For more information about attending this conference via one of the aforementioned hubs, please contact

Please visit the conference description page:

Primer-BLAST-New Primer Design Tool-Tutorial

Primer-BLAST was developed at NCBI to help users make primers that are specific to the input PCR template. It uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. The BLAST results are then automatically analyzed to avoid primer pairs that can cause amplification of targets other than the input template.

How to use Primer-BLAST

1.Go to
2.Enter your FASTA sequence, an accession or a GI into the PCR Template box or you can upload fasta file
3.Provide forward prime & Reverse primer parameters
4.By default it searches human sequence database, but you can change your specific organism by typing in the organism section of primer pair specificity checking parameters
5.Use the "Get Primers" button at the bottom of the page to submit your search.

Bioinformatics-Short Introduction-Multimedia kit-Download for free

Mining the Genome using Bioinformatics-Short Introduction-Multimedia learning kit-Download for free
This tutorial demonstrates finding genes, finding functions, and examining variation through the use of bioinformatics. Bioinformatics is the branch of biology that is concerned with the acquisition, storage, display, and analysis of the information found in nucleic acid and protein sequence data.

Note for Windows users: After installation, locate the shortcut on your desktop named Launch Bioinformatics and click it to begin playing.

-Right click save target as

Windows Download Windows Download (22.6 MB)
Apple Download Mac OS X Download (27.1 MB)

Biobar-Bioinformatics toolbar-Video Demo tutorial-Watch Online

The biobar project is a bioinformatics power-browsing toolbar for Mozilla-based browsers including Firefox/Flock/Mozilla/Netscape and Seamonkey. This toolbar provides access to major biological data resources. The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases. In addition to the browsing features, biobar also provides links to important bioinformatics sites and services including services at the European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ). The tool also provides links to major data deposition sites for nucleotide, protein and 3D-structure data. Finally, the menu also contains links to many Sequence, Structure alignment and analysis tools.

Biobar toolbar for bioinformatics-visit site

This video shows how to install and use the BioBar toolbar on Firefox. This is a nifty addition to the browser that makes accessing many of the usual online databases and tools very easy. It also allows you to easily run a search at these databases without having to navigate to the website first. BioBar can be found at and was written by Jawahar Swaminathan at the EBI.

How Not to Use BLAST-Tutorial

How Not to Use BLAST-Tutorial
Chris Dwan gave this “common BLAST mistakes” talk at the 2003 ORA Bioinformatics Technology Conference.

Right click-Save target as
Download Pdf version-How Not to Use BLAST

Free Course-Bioinformatics and Proteomics

Free Course-Bioinformatics and Proteomics: MIT OpenCourseWare

Course Description
Proteomic analysis is an emerging field that utilizes algorithms, statistics, databases and other tools of bioinfomatics for analyzing large amounts of data for the purpose of improving the knowledge base in the study of genomics and proteins. 'Bioinformatics and Proteomics' is a free course provided by the MIT Department of Electrical Engineering and Computer Science and Professors Gil Alterovitz, Manoli Kellis and Marco Ramoni. Students are taught practical methods and techniques that will prepare them for the variety of tasks associated with the analysis, evaluation and interpretation of proteomic data. The lectures include a review of modern biology, sequence analysis and microarray expression data analysis. Bayesian methodologies and bioinformatics applications in the biotech industry are also discussed. Students investigate statistical models and stochastic processes in proteomics, signal processing for proteomics, biological methods, automation and robotics.

The materials for this course include downloadable lecture notes and lab assignments. There is also a reading list and an extensive collection of related resources.

Visit Bioinformatics & Proteomics Opencourseware Page

Introduction to GeneGo Pathway Analysis-Video Seminar-Watch Online

Introduction to GeneGo Pathway Analysis-Video Seminar-Watch Online
Demonstration of data analysis using the GeneGO data analysis tool. In general the audience has very little background in bioinformatics and pathway analysis. The level is non-specialist.Visit GeneGo site

Ingenuity Systems for Pathway Analysis-Video Seminar-Watch Online

Ingenuity Systems for Pathway Analysis-Video Seminar-Watch Online
Dr Chris Kirchber
Dr Chris Kirchberg of Ingenuity hosts a Q&A session on the Ingenuity Pathway Analysis tool. Topics covered include finding information on drugs and dealing with replicate data sets.Visit Ingenuity Systems site

Nextbio Biological Sciences Data Search Engine-Video Seminar-Watch Online

Nextbio Biological Sciences Data Search Engine:oVerview and Worked Examples-Video Seminar-Watch Online
Ilya Kupershmidt
Overview and guide to using the Nextbio database tool. Contains a lot of information which is not obvious from the documentation of the system.

The search engine searches through and correlates highly complex experiments, literature and clinical data to aid researchers in making new discoveries. It provides a unified interface for researchers to easily formulate and test new hypotheses across vast collections of experimental data. [1]The NextBio platform enables biologists, clinicians and biomedical researchers to examine a gene, protein, compound or disease of interest in a global, biological, or clinical context.Visit Nextbio interactive life-science search engine website

Introduction to ACCELRYS DiscoveryStudio-Video Seminar-Watch Online

Introduction to ACCELRYS DiscoveryStudio-Demo-Video Seminar-Watch Online
Drs F. G. Hernandez-Guzman and Tedman J. Ehlers

Introduction to Accelyrs Discovery Studio Discovery Studio 2.0 includes a profusion of new science aimed to deliver the most complete package of modeling and simulation tools for drug discovery available. Included are innovative algorithms for rational flexible docking, fragment-based design and activity profiling, providing ground breaking capabilities

Using NCBI e-tools-Video Seminar-Watch Online

Overview, shortened version of a 4 day workshop to learn e-Utils, as offered by NCBI. Everything you ever wanted to know about Medline, NCBI blast, GEO, plus others, and how to glue them all together.

Part 1

Part 2

Introduction to Microarray Data Analysis-Video Seminar-Watch Online

Introduction to Microarray Data Analysis for Stem Cell Biologists-Video Seminar-Watch Online

Seminar given to Stem Cell biologists on Microarray technology. The audience had very little background in the field so the material is basic. Tutorial on basic microarray analysis. Data normalisation, filtering, P-values and clustering

Part 1

Part 2

Introduction and Data Analysis--Seminar Video - Watch Online

Introduction and Data Analysis-GeneGo -Seminar Video - Watch Online

Whole Genome Association in Inbred Mouse Strains-Video Seminar-Watch Online

Computational Challenges in Discovering the Genetic Basis of Complex Traites in Inbred Mouse Strains-Video Seminar-Watch Online
Christopher Lee

Insights Into Origins of Spliceosomal Introns-Video Seminar-Watch Online

Insights Into Origins of Spliceosomal Introns-Video Seminar-Watch Online
Stella Veretnik, Ph.D.
Computational Molecular Biology, National Laboratory for Computational Science and Engineering
University of California - San Diego

Accelerating Biology with Bioinformatics-Video Seminar-Watch Online

Accelerating Biology with Bioinformatics: Collaborations with Lab Scientists-Video Seminar-Watch Online
Fran Lewitter, Ph.D. Director of the Bioinformatics and Research Computing Department, Whitehead Institute, MIT

Challenges in Automated Assignment of Function for Proteins From the Genome Projects-Video Seminar-Watch Online

Challenges in Automated Assignment of Function for Proteins From the Genome Projects-Video Seminar-Watch Online
Patricia Babbitt, Ph.D. Professor of Biopharmaceutical Sciences and Pharmaceutical Chemistry,University of California - San Francisco

Phylogenomics: New algorithms and genome-scale classification-Video Seminar-Watch Online

Phylogenomics: New algorithms and genome-scale classification-Video Seminar-Watch Online
Kimmen Sjolander, Ph.D. Associate Professor, Department of Bioengineering
University of California - Berkeley

Predicting structural disorder and induced folding-Video Seminar-Watch Online

Predicting structural disorder and induced folding: From theoretical principles to practical applications
Sonia Longhi, Ph.D. Permanent Senior Scientist, Architecture et Fonction des Macromolécules Biologiques, Centre National De La Recherche Scientifique (CNRS), Marseille, France

Predicting Protein Interactions-Video Seminar-Watch Online

Predicting Protein Interactions-Video Seminar-Watch Online
Soshana Wodak, Ph.D. Scientific Director, Centre for Computational Biology (CCB), The Hospital for Sick Children
Professor, Biochemistry and Medical Genetics, University of Toronto Canada Research Chair, Computational Biology and Bioinformatics

Bioinformatics Comes of Age-Video Seminar-Watch Online

Bioinformatics Comes of Age-Video Seminar-Watch Online
Janet Thornton, Ph.D. Head of European Bioinformatics Institute (EBI)
Dr. Thornton is a leading expert in relating protein sequence to structure and function. She has worked extensively in knowledge-based approaches to sequence analysis. Dr. Thornton is a member of the Royal Society

The Past, Present and Future of the Protein Data Bank

The Past, Present and Future of the Protein Data Bank-Video Seminar-Watch Online
Dr. Helen M. Berman, Director of the Protein Database (PDB), Rutgers University.
Dr. Berman is internationally renowned for her development of protein and nucleic acid databases. Her research interest is in the application of Bioinformatics to protein structure.

Evolution of High-Throughput Data-Video Seminar-Watch Online

Evolution of High-Throughput Data-Video Seminar-Watch Online
Tina M. Hernandez-Boussard, Ph.D.
Scientific Curator, Computational Biologist, Department of Genetics, School of Medicine. PharmGKB
University of Stanford

Bioinformatic Insights Into Mammalian Gene Regulation-Video Seminar-Watach Online

Bioinformatic Insights Into Mammalian Gene Regulation: Can Keystrokes Confront Cancer?-Video Seminar-Watch Online
Dr. Laura Elnitski, Head of the Genomic Functional Analysis Section, Genome Technology Branch NHGRI/NIH. Dr. Elnitski uses experimental and Bioinformatic methods to discover non-coding functional elements in the human genome.

Protein Structure Prediction-Video Lecture-Watch Online

Protein Structure Prediction-Video Lecture-Watch Online
An introduction to basic protein structure, structure determination and problems which motivate the development of computational approaches to structure prediction, including secondary structure prediction, ab initio structure prediction, fold family recognition or threading approaches and homology modeling. Some of problems with computational prediction methods are discussed briefly.

Craig Venter: A voyage of DNA, genes and the sea -Video

Craig Venter: A voyage of DNA, genes and the sea-Video-Watch Online
Genomics pioneer Craig Venter takes a break from his epic round-the-world expedition to talk about the millions of genes his team has discovered so far in its quest to map the oceans biodiversity.

The New Genomics - Software Development at Petabyte Scale-Video

The New Genomics - Software Development at Petabyte Scale-Video-Watch Online

The Personal Genome Project-Video-Watch Online

The Personal Genome Project (PGP) aims to publish the complete genomes and medical records of several volunteers, in order to enable research into personalized medicine. It was initiated by Harvard University's George Church and announced in January 2006.For more information - Visit Personal Genome Project website.The project will publish the genotype (the full DNA sequence of all 46 chromosomes) of the volunteers, along with extensive information about their phenotype: medical records, various measurements, MRI images, etc. All data will be freely available over the Internet, so that researchers can test various hypotheses about the relationships among genotype, environment and phenotype.

Information-Based Personalized Medicine-Video Lecture-Watch Online

Information-Based Personalized Medicine-Video Lecture-Watch Online
Personalized medicine the concept that information about a patient's genotype or gene expression profile could be used to further tailor medical care to an individual's needs. Such information could be used to help stratify disease status, select between different medications and/or tailor their dosage, provide a specific therapy for an individual's disease, or initiate a preventative measure that is particularly suited to that patient at the time of administration. Several examples of approaches to personalized medicine have been established in medical practice, but in general the genotype-centered approach is not yet in widespread use clinically. It is currently debated whether such "personalized medicine" offers significant advantages over traditional clinical approaches that combine an individual's personal medical history, family history, and data from imaging, laboratory, and other tests.

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


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

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

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.

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.


Beginning Perl for Nonprogrammers 2 of 2

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


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:

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