I am Vivek Rai, a biotechnology graduate student from Indian Institute of Technology Kharagpur, India. My research interests lie at the intersection of biology, computer science and engineering.

I will be joining Program in Biomedical Sciences (PIBS) at University of Michigan, Ann Arbor this fall as a PhD student.

This blog (fondly called shorts) is a personal destination to satisfy my cravings for writing, science, code, and books.

My older blog is retired and all previous posts are now archived. Shorts takes over the previous blog as a more active version with focus on concise and frequent spurts of writing. A few useful posts from my older blog are:

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Science provides intellectual freedom. It enables us to explore and understand the nature of reality around us — from tiny atoms, living cells and organisms, to the magnanimous universe.

Doing science, however, requires a careful and systematic investigation, perseverance, and an unshakable curiosity to seek knowledge. However, it is not a lone journey. It cannot be. To do science, is to participate in the largest collective experience of mankind.

Thus, all my efforts – internships, projects, term papers, conferences – are a desperate reflection of my desire to become a useful member of this community, to develop and explore own niche.

I am interested in understanding the structure of genome and its evolution at molecular and as well as systems level, how it alters the cell phenotype and leads to anthropological diversity in a population or complex genetic diseases. Focusing more on the methods development, I wish to work in omics driven areas that draw heavily from integrated experimental, quantitative, and computational approaches.

Previously, I have worked in Dr. Gustavo Glusman in Dr. Leroy Hood’s lab at Institute for Systems Biology, and Prof Sandhya S Vishweswariah at Indian Institute of Science, Bangalore.

As this blog develops, I plan to write several primer articles on my topics of interest.

Lastly, a (tiny) list of published, public, or in progress work where I have made non-trivial contributions:

O’Neill, Rai, Kilpatrick; The International Society for Computational Biology and WikiProject Computational Biology: Celebrating Ten Years of Collaboration Towards Open Access. Bioinformatics 2017. (abstract, pdf)

Priyam, Woodcroft, Rai et al; Sequenceserver: A modern graphical user interface for custom BLAST databases. Biorxiv 2015. (abstract, pdf)

Klein, Gupta, Rai et al; Monitoring the Gender Gap with Wikidata Human Gender Indicators. Opensym 2016. (abstract, pdf)


I am hooked to open-source software development — an ambitious outgrowth of my personal interest to create free (as in free speech!) and open-source content. During summer 2016, I was selected for Google Summer of Code program, where I contributed to OpenSNP.org under umbrella of Open Bioinformatics Foundation.

I am also one of the founding members of metaKGP.

Few projects with my significant contributions are:

I use GNU/Linux, keep files under version control and edit using Vim.

I have used Python, R, Ruby, JavaScript, MATLAB, BASH in my works.


I am interested in the ideas of quantified self, getting things done, lateral thinking, language and learning, history of humans, open communities, free knowledge, and societal issues like gender biases.

I speak English, Hindi (native), and I am learning Esperanto in my free time.


I enjoy hiking, playing table tennis, long no-purpose walks, camping, open-spaces, and a delicious coffee.

blog by Vivek Rai