Observations:

I was standing near the lift for going to the second floor in my training building @ NIOT .There were other people too and for some reason the lifts took a longer to reach our floor.As new people came near the lift, I noticed that each and everyone was invariably pressing the lift button as soon as they arrived. I was thinking to myself whether they dont realise that already there were so many people standing near the lift and atleast one among them would have pressed the button for the lift to stop in the floor? But then also i remembered doing it myself so many times. I wondered why we do that? Is it an involuntary action that one is programmed to press the button as soon as he comes to a lift? Is it that fear that may be others wouldnt have done it before us? Is it that feeling of security one gets pressing the button by himself?


Then, is everyone so absent minded that they dont know what they are doing? Personally speaking, for me it was an involuntary action. The mind may be preoccupied with so many peremptory things that the routine stuff which it has already done so many times runs in automatic mode.The body is kind of programmed to perform the actions even if your concious mind is not constantly monitoring the your own actions. I can even quote an example like a person driving through the busiest streets to his office but cannot remember a single thing in the journey because he was always thinking about the meeting which he was attend that morning.I wonder myself.It has happenned with me so many times. Wierd but true.It could have happenned with anyone.It does happen i am sure.May be some psychologist who reads this blog may be able to post the answer.

Bio Informatics

The genomic eraThe genomic era has seen a massive explosion in the amount of biological information available due to huge advances in the fields of molecular biology and genomics. Bioinformatics is the application of computer technology to the management and analysis of biological data. The result is that computers are being used to gather, store, analyse and merge biological data. Bioinformatics is an interdisciplinary research area that is the interface between the biological and computational sciences. The ultimate goal of bioinformatics is to uncover the wealth of biological information hidden in the mass of data and obtain a clearer insight into the fundamental biology of organisms. This new knowledge could have profound impacts on fields as varied as human health, agriculture, the environment, energy and biotechnology.

The greatest challenge facing the molecular biology community today is to make sense of the wealth of data that has been produced by the genome sequencing projects. Traditionally, molecular biology research was carried out entirely at the experimental laboratory bench but the huge increase in the scale of data being produced in this genomic era has seen a need to incorporate computers into this research process.

Sequence generation, and its subsequent storage, interpretation and analysis are entirely computer dependent tasks. However, the molecular biology of an organism is a very complex issue with research being carried out at different levels including the genome, proteome, transcriptome and metabalome levels. Following on from the explosion in volume of genomic data, similar increase in data have been observed in the fields of proteomics, transcriptomics and metabalomics. The first challenge facing the bioinformatics community today is the intelligent and efficient storage of this mass of data.

It is then their responsibility to provide easy and reliable access to this data. The data itself is meaningless before analysis and the sheer volume present makes it impossible for even a trained biologist to begin to interpret it manually. Therefore, incisive computer tools must be developed to allow the extraction of meaningful biological information. There are three central biological processes around which bioinformatics tools must be developed:

DNA sequence determines protein sequence
Protein sequence determines protein structure
Protein structure determines protein function The integration of information learned about these key biological processes should allow us to achieve the long term goal of the complete understanding of the biology of organisms.

Biological databases :

Biological databases are archives of consistent data that are stored in a uniform and efficient manner. These databases contain data from a broad spectrum of molecular biology areas. Primary or archived databases contain information and annotation of DNA and protein sequences, DNA and protein structures and DNA and protein expression profiles. Secondary or derived databases are so called because they contain the results of analysis on the primary resources including information on sequence patterns or motifs, variants and mutations and evolutionary relationships. Information from the literature is contained in bibliographic databases, such as Medline.

It is essential that these databases are easily accessible and that an intuitive query system is provided to allow researchers to obtain very specific information on a particular biological subject. The data should be provided in a clear, consistent manner with some visualisation tools to aid biological interpretation. Specialist databases for particular subjects have been set-up for example EMBL database for nucleotide sequence data, UniProtKB/Swiss-Prot protein database and PDB a 3D protein structure database.Scientists also need to be able to integrate the information obtained from the underlying heterogeneous databases in a sensible manner in order to be able to get a clear overview of their biological subject. SRS (Sequence Retrieval System) is a powerful, querying tool provided by the EBI that links information from more than 150 heterogeneous resources.

Biological applications

Once all of the biological data is stored consistently and is easily available to the scientific community, the requirement is then to provide methods for extracting the meaningful information from the mass of data. Bioinformatic tools are software programs that are designed to carry out this analysis step. Factors that must be taken into consideration when designing these tools are:
The end user (the biologist) may not be a frequent user of computer technology
These software tools must be made available over the internet given the global distribution of the scientific research community The EBI provides a wide range of biological data analysis tools that fall into the following four major categories:
Similarity Searching Tools
Protein Function Analysis
Structural Analysis
Sequence Analysis

Similarity Searching Tools Homologous sequences are sequences that are related by divergence from a common ancestor. Thus the degree of similarity between two sequences can be measured while their homology is a case of being either true of false. This set of tools can be used to identify similarities between novel query sequences of unknown structure and function and database sequences whose structure and function have been elucidated. Protein Function Analysis This group of programs allow you to compare your protein sequence to the secondary (or derived) protein databases that contain information on motifs, signatures and protein domains. Highly significant hits against these different pattern databases allow you to approximate the biochemical function of your query protein. Structural Analysis This set of tools allow you to compare structures with the known structure databases. The function of a protein is more directly a consequence of its structure rather than its sequence with structural homologs tending to share functions. The determination of a protein's 2D/3D structure is crucial in the study of its function.Sequence AnalysisThis set of tools allows you to carry out further, more detailed analysis on your query sequence including evolutionary analysis, identification of mutations, hydropathy regions, CpG islands and compositional biases. The identification of these and other biological properties are all clues that aid the search to elucidate the specific function of your sequence.