Vivek Rai


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Bioinformatics, computational biology, systems biology, computational neuroscience, data analysis and visualization, molecular biophysics.



  • Priyam et al: Sequenceserver: rapid creation of assistive graphical BLAST frontends for custom sequence databases (submitted)

Research Experience

B.Tech Thesis, IIT Kharagpur

Prof. Amit Kumar Das, August 2015 - ongoing

The existence of knots in proteins is an curious event and has aroused interest in researchers for over a decade. They are rarely found in nature (<1%), and their folding process is described to be slow and energetically unfavorable. The knots are not known to perform quite an useful function across all knot examples, which otherwise cannot be done with an unknotted structure. Despite significant advancement in our understanding of the underlying mechanism, much remains elusive to our notebooks. In this study, I set up a two-dimensional objective to investigate the sequence and structure-related properties of a protein knot and build upon our previous understanding of the related questions.

More details in my shorts post.

BEST Fellow, Indian Institute of Science

Prof. Sandya S. Visweswariah, May - July 2015

Extraction, verification and purification of Cytolysin A pore forming toxin of E. coli and its mutant (ClyA Q56C) from expression constructs. Several experiments for verifying the activity and kinetic efficacy of the toxins were examined using hemolytic assay and calcein leakage assay. The mutant protein was further labeled using appropriate fluorescent dye and after assuring activity, was used for imaging studies.

We also investigated the lipid phase dependent kinetic behavior of Cytolysin A, and observed that ClyA behaved distinctly in a two component and three component systems (double exponential versus single exponential curve).

More details (including links to my data, presentation and report) in my shorts series.

Open Source

Wikpedia Gender Indicators

May 2015 - Present

WIGI is a project producing a open data set about the gender, date of birth, place of birth, ethnicity, occupation, and language of biography articles in all Wikipedias. Our data set comes from Wikidata, the database the feeds Wikipedia, and is updated weekly. I'm a co-developer and reseracher on the project. I have worked on creating interactive analysis graphs using the data we have collected as a demo, contributed to the research paper review, and formulation of problem statements for further analysis.

This project started as a personal research interest by Maximilian Klein (, and is now funded by a Wikimedia Foundation Grant.

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More details in my shorts post.


May 2014 - Present

SequenceServer allows users to easily set up a BLAST+ server to be used locally or over the web with a nice and intuitive user interface. It is an elegant alternative to many other similar projects that are often an overkill or too complex to set up. My important contribution includes (but not limited to) - Creating graphical overview with D3, Understanding BLAST Output and creating the data layer, maintaining code compatibility with previous versions etc.,

A list of my merged and unmerged changes can be found at gh:vivekiitkgp/sequenceserver.


Dec 2014 - Jan 2015

Afra is a gene annotation platform inspired by crowdsourcing approaches and platforms including Foldit, Galaxy Zoo and Crowdflower to recruit additional gene feature curators. It aims to simply and provide an easy learning curve so that even a complicated task like quality gene curation can be performed by general public.

I have mainly worked with the user interface of the program improving the overall look and experience. While these changes may seem insignificant in general, they play a very important role in a client-side heavy application (such as this one) where user is highly reliant on visual feedback.

A list of my merge commits can be found at Afra - Contributers.

Other Projects


A collaborative effort to promote Wikipedia style open content culture, collect, curate and archive the unfathomable amount of regularly generated information in the college.

The efforts of project are live at MetaKGP.

Sign Language Interpreter

Prof. P. Patnaik, Apr 2014

  • Conceived and designed a gesture to text (or speech) application to interpret sign language gestures (non-motion) with a team of 4 people for aiding deaf and dumb people;
  • Implemented image processing techniques to obtain noise free information from real time video; classified data into relevant clusters and predicted unknown information using k-means clustering;
  • Exploring further possibility of providing service through chat applications or online widget/web based services.

Jigsaw Puzzle Solver

Prof. S. K. Barai, March 2014

  • Evaluated different techniques based on genetic algorithm to solve large piece jigsaw puzzle (randomly shuffled pieces of an image); implemented mutation strategies; came up with an approach to use this technique to solve images with non unique components;
  • Programmed the algorithm entirely from scratch in C++ using OpenCV image processing libraries; could solve up to 1000 pieces.

Term Paper

Comparison of Fuzzy Guided Gene Prediction Methods

  • Reviewed different state-of-art techniques to analyze and annotate whole organism genome in an automated way to predict genes and other regions of interest;
  • Critiqued the future prospects and application strategies of SVM, NN learning with emphasis on heuristic techniques (GA, Fuzzy Logic) as hybrid methods for better annotation of raw genomic data.


A small script that allows one to quickly create GitHub gists of outputs received from many terminal commands. Often helpful in scenarios where we want to create a log of a command output for pasting somewhere or showing to someone. License and installation instructions are on GitHub page.


Positions of Responsibility

Team Member, iGEM

A core team member of college team participating in iGEM 2015 held at MIT. Involved in conceptualization and executation of participation idea and experiments.

Captain, Opensoft

Led a team of 6 people for participation in Inter Hall Opensoft competition, an annual software design competition

Core Team Member, Google Students Club

Co-organized multiple hackathons, online coding competitions, a Google blogger challenge, and other activities as a core team member under student ambassador of IIT Kharagpur.

Writer, Technology Literary Society

Contributed articles to in-campus magazines, newsletters and relevant articles as English writer with official literary body of students Gymkhana.

Online Profiles

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