My profile gives a more professional account of my expertise.

My Research Interests:

  1. Biological programming, Bio-software and web application solutions
  2. Developing and implementing novel algorithms, methodologies, discovering & formulating new biological rules in the areas of Systems Biology, Pathway Engineering, HT Transcriptomics, Structural Genomics & Proteomics
  3. Drug Discovery, Designing, Docking and Analysis
  4. Macromolecule and Bio-Nanomachine Design, Engineering, Modeling & Simulation

Check out My Blogs @ BioIT - Growth and Prospects


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Prasad (Shiva/Subbu)

My Professional Expertise - to list a few:

  1. Typical Algorithm Implementations:
    1. DPA : Dynamic Programming Algorithm - for sequence Alignments
    2. SVD : Singular Value Decomposition - as a Refinement Problem
    3. Protein Structure Alignment as an Eigen value problem
    4. Multi - pattern sequence alignment algorithm
    5. Repetitive sequence pattern discovery
    6. UPGMA - for phylogenetic tree construction
    7. Protein Secondary structure prediction and assignment algorithm
  2. Core Programming:
    1. C++ - ~ 300,000 lines of Code for developing BOS & BioBhasha
    2. OpenGL - Graphics programming language
  3. Core Web Programming:
    1. Javascript, PHP, Ajax, MySQL
  4. Web technologies:
    1. HTML, XHTML, DHTML, CSS, XML; Wikis: SGMP Wiki, Confluence, PmWiki
  5. Miscellaneous Programming APIs:
    1. BioBhasha: A Biological programming Language
    2. Back end DBMS Programming: MySql, TCP/IP
    3. Mootools: An Object Oriented Javascript Framework for Web Application Development
  6. Miscellaneous Software:
    1. Numerous biological software: ccp4,gcg,clustalw,O,vmd,molscript,InsightII etc.
    2. Povray, Modeller, Blender, graphviz, vtk

Check out My Blogs @ BioIT - Growth and Prospects


Thanks for stopping by!!
Best Wishes
Prasad (Shiva/Subbu)

A historical account of my decade long Research Journey in Bioinformatics

I enjoy Algorithms, Analysis and Automation and my passion is working in varied areas of computational biology.

In the past, during my MS, I was involved in Sequence and Genome Analysis, that was just 1 year of entry into biology. Earlier I was engineer. I was lucky to publish that work, one of the first computational biology papers from the University.

During my PhD, I thoroughly enjoyed XRay crystallography, Structural Biology and Structural Bioinformatics. I realized that X-Ray crystallography has reached the stationary phase and definitely crossed the 'log' phase of the sigmoid curve. So decided to concentrate on Computational biology, especially, Algorithms, Analysis and Automation. Though it was a struggle for 3.5 years, later, I could publish 2 good quality(personal assessment) articles, initiated Biobhasha development on the spare time, developed another novel design algorithm/methodology for efficient protein engineering and design.

Learnt lot of lessons about Life/Society/Relationships/Hypocricy/Politics in Science during PhD (Doctor of Philosophy, though it should mean Doctor of Science). One bitter truth I realized after observing the Bosses/Scientists/Students around for 5.5 years is:

Today Science and Research have become alternative means of Survival, definitely not for the passion and motivation to discover, learn about the external and internal being/NATURE.

Finally, truely recieved a doctorate degree of Philosophy, not just a doctorate for science.

Later as an entrepreneur,CTO, I enjoyed the Software Development cycle, polishing my expertise in Programming and transcending to a project designer. That company, because of early greed and egocentric & unprofessional investors, is closed in principle.

Now I am a PDF (Post-Doctoral Research Associate) @UCSD in Prof. Shankar Subramaniam Lab, working in Systems Biology & Pathway modeling. In the past 2 years, added Web Designing skills - PHP, Javascript, MySQL - together AJAX.

I try to occupy myself with algorithms , analysis ,automation projects or web design and development projects. For all work, I tend to use my own creations: BioBhasha/BOS, since I created them with that purpose i.e.Biological Programming - to be a one stop solution for all biological queries.

Check out My Blogs @ BioIT - Growth and Prospects


Thanks for stopping by!!
Best Wishes
Prasad (Shiva/Subbu)