☘☘☘ Letters by Vivek Rai
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Physics of Life 2017

Frans Johansson, in his popular bestseller book The Medici Effect, makes an argument: The intersection is the best place to innovate. These innovations change the world in leaps along new directions by opening up new fields, creating new information and allowing creators to become leaders. This intersection is the place where wildly different ideas from various areas bump into each other and build upon each other. He goes on to illustrate, with examples and appealing case studies, how starting from artists and painters in the ancient city of Florence to the Charles Darwin and modern day scientists, by working at the intersection, have pushed the boundaries of knowledge and technology beyond comprehension.

Overview of BOSC and ISMB, 2016

This year I attended the Intelligent Systems for Molecular Biology (ISMB) from July 8-12 in Orlando, Florida. But before I talk about my experience of the conference (and amazing Disney World!), let me roll back a bit and tell you about why I was there. ⊕ ISMB 2016. ISCB Competition Several months ago, I wrote a short describing my submission for ISCB Wikipedia article writing competition. For those who don’t know, the competition invited people to improve upon existing computational biology articles on Wikipedia by adding or improving upon existing resources.

A Letter in the Name of Science

Posted below is an email that I rediscovered in my mailbox a few days ago. I had no memory of it whatsoever, perhaps because I never received a reply from the intended recipient. Whatever be the reasons, looking back at it today feels like discovering a diamond in the rough. The letter was an outcome of my personal struggle. The conundrums of an aspiring researcher - Where do my moral and ethical standards of science?

Metabolic Network Analysis - I

In this short tutorial, we will explore the basic steps of a metabolic network analysis. For our convenience, we will avoid using full models or discuss their reconstruction methods, instead focus on simple reactions to create a theoretical background. However, the steps can be scaled without any loss of generality. The related exercises should help build a theoretical background along with necessary programming skills. ⊕ Metabolic network showing interactions between enzymes and metabolites in the Arabidopsis thaliana citric acid cycle.

WikiProject article submission

Almost an year ago, I had written a blog post about different Wikipedia WikiProjects and how one could contribute to them. In short, A WikiProject is simply an organized effort by the community of editors on the Wikipedia, where they try to curate and improve the quality of articles belonging to a particular genre or of specific interest to a group. In loose terms, WikiProjects to Wikipedia are what subreddits are to reddit.

Notes from Systems Biology Winter School

This winter, I attended the fourth session of Winter School on Quantitative Systems Biology at International Centre for Theoretical Sciences (ICTS), Bangalore. The school is organized by the ICTS, Bangalore and ICTP, Italy in jointly as a part of their ICTP-ICTS Programme in Biology since 2012. It was an extraordinarily fun-filled learning experience. I share below some impressions of the school hoping that it would be useful to some of you.

Notes from WMCB 2016

This weekend (Jan 9 - Jan 10), I participated in a workshop on mathematical and computational biology (WMCB-2016) organized at Indian Institute of Science Education and Research Kolkata (IISER-K). This annual workshop is co-sponsored by NNMCB, a group of multiple premier institutions in India that coordinate activities in the area of interest. The primary motivation for participating in this workshop was to present my ongoing work on the knotted proteins. It seemed like a reasonable place to attract further ideas and help.

A challenging course catalog

I’m very excited to talk about my course catalog for the fall semester, specially because it’s turning about to be pretty challenging and full of new information. Prologue: During my research internship at Indian Institute of Science, I had the opportunity to attend several lecture series by eminent professors, who introduced us to different fields (e.g., Biomechanics, Systems Biology) and relevant research they have done in their careers. While all of the lectures were insightful, one which caught my most attention were those delivered Dr.

Protein Knots: A tangled story

Journal Club is a weekly paper presentation session organized in our department by us, where one could present an remarkable research finding, discuss a new experimental technique or simply introduce everyone to a new or less explored field in the area of biology. I have mentioned about this initiative in my earlier posts, and it is something that I really feel excited to talk about. The audience size is pretty decent (around 15-20 people) consisting of professors, research scholar, graduates and undergraduate students.

Working with pore forming toxin-2

Give a man a fish and you feed him for a day. Teach a man to fish and you feed him for a lifetime. Chinese Proverb The quote above quite vividly describes the experience I had at Indian Institute of Science. Finally after 8 weeks (May 11 - July 10) of work within the lab, our internship concluded on 10th of July with a report submission, followed by a presentation on the 15th of July.

Working with pore forming toxin-1

A learning experience is one of those things that says, “You know that thing you just did? Don’t do that.” Douglas Adams, The Salmon of Doubt Douglas Adam was correct about Experience. It is a harsh teacher. The fact that words like “struggle”, “fail fast”, “don’t give up” are commonly used to describe some of its lessons, speaks about the inherent difficulty of the whole process — and none of it more visible anywhere than when learning something new.

research needs funding

Brian Farley writes .. I’ve said this before on Quora, and I’m probably going to say it many more times, but, all of the problems in academia can be traced back to scarce funding and the ridiculous competition it engenders. The reluctance to fund academia and research, in turn, comes from a completely skewed perception by the public of what academia is supposed to accomplish – which in no small part comes from the capitalist marketplace thinking that permeates almost everything our society does.

Papers per week

Research is to see what everybody else has seen, and to think what nobody else has thought. Albert Szent-Gyorgyi Reading research papers, literature survey as one may call it, is one of the primary tasks of any research enthusiast, student, academician, or researcher. As we advance through our academic career, the complexity and quantity of content keeps increasing until the text books give up. The inflow of information is too rapid and too vast to be contained and sufficiency conveyed to the target audience, thus necessitating the need of specialized sources.