How to think like scientists – A five step process.

Richard Buckland, a professor of computer science, has a very elegant explanation on how to think like a scientist. Even though these steps are aimed at his computer science students, for me this has more general meaning and purpose. Richard’s simple five step process of getting into a scientific mindset are:

  1. The moment you encounter an interesting problem, always try to solve it and never give up.
  2. While solving the problem, always ask more questions.
  3. To make the process of solving problems easier, break it into different parts.
  4. Profit from your path to solving the problem, and from the solutions you created.
  5. Look for more problems to solve.

I love this five step process because it summarizes concisely the thought process of a scientist. What we are doing at nanoveda with nanotechnology and cancer research is essentially a real world embodiment of this five step process. As a group, when we first met, we found a highly disturbing problem of accessible, precision cancer therapy. This problem has a very personal meaning to us at nanoveda.

Since each of us had our own unique expertise, we broke the problem down into components and came up with a solution. We didn’t stop there. We asked more questions like: how to improve the process, how to gather more data and information, how else can we solve this problem, who else can benefit from this work. Then we started looking for more problems to solve.

For providing benefits to a broader cross section of the society, we decided to form a company and scale-up our idea. Up until recently, we never formally addressed how our process worked. Then, I discovered this video of Richard and his five step process. It made me realize: this is exactly what we were doing subconsciously, all along the way.

I am a huge admirer of the course that Richard teaches. He teaches this course at University of New South Wales, Sydney, Australia. I am posting this video below, where he describes the five steps outlined above.

This video is part of a lecture series from his course on computing: Computing 1 – The Art of Programming. The course is also available online. I highly encourage everyone to check this video out and the entire course too. It will help everyone start thinking like a scientist.

For continuing nanoveda’s wonderful work, we are running a crowdfunding campaign using gofundme’s awesome platform. Donation or not, please share our crowdfunding campaign and support our cause.

Donate here: gofundme page for nanoveda.

(The illustration of the structure of deoxyribonucleic acid (DNA) is from Wikipedia.)

If I were a time traveler – Lessons learned.

If I were a time traveler, I would have traveled back exactly 121 years to witness one of the most important discoveries of modern medicine: x-ray. The photograph above on the left is the first ever recorded x-ray photograph of human anatomy and on the right is the photo of Wilhelm Röntgen, the man who took this picture. The hand in the picture is thought to depict Röntgen’s wife Bertha wearing her wedding ring.

X-ray was recognized back then as an unexplained physical phenomenon. Sir William Crooke noticed an odd phenomenon of blurry photographic papers that he used to wrap the vacuum tubes he was studying. No one could exactly explain this phenomenon well enough. This was despite Hermann von Helmholtz’s formulation of mathematical equations to predict the existence of x-ray without ever experimenting with them.

With ‘Hand mit Ringen’ photograph, Röntgen demonstrated unequivocally, the unique property of x-ray to travel through structures that were other wise thought to be impenetrable. This discovery started an important era in modern medicine: one that belongs to diagnostic medicine. X-ray is in many ways, one of the earliest diagnostic tools. The physics behind x-rays was difficult to understand, but a simple picture of the bones of the hand captivated the imagination of the scientists as well as the general public. Immediately after the publication of  ‘Hand mit Ringen’ photograph, there was a huge uptick in number of scientific publications dealing with these mysterious and powerful light sources. Even the general public weren’t immune to the charm of the mysterious x-rays. Among the general public, x-rays were often considered as magical phenomenon bordering on the paranormal.

An important lesson I would have learned from my time travelling adventure: the importance of capturing public’s imagination. As the old adage goes, a photograph is worth more than a thousand words. Surprisingly, modern medicine has a lot of work to do, when it comes to communicating some of its incredible feats to the public: clearly, eloquently and without distorting the facts.

In an age where hyperbole and mythical fantasies dominate the news cycle, a simple time travelling thought experiment would reveal the exact same events happening to us as human beings, at every juncture in our history. For individuals who understand the physical world better than most, we have a responsibility to convey our ideas, messages and findings; with great conviction and confidence.

Another lesson I would have learned from my journey to the pages of history is the importance of understanding the physical phenomenon to master the biological world. We often venture into experimentation and trial & error with very little grasp of some of the underlying phenomenon. In this day and age of powerful computing, development of simulation models to test the physical theories of interactions are easier and yet ever more important to create sophisticated biological experiments. Simulations and mathematical models often help us solve problems faster, despite the initial sweat and elbow grease associated with it.

To create the next generation cure for cancer, I am confident that the first step is to build simulation and mathematical models of how some of these sophisticated drugs work. As part of nanoveda’s ongoing attempts to advance cancer therapy, we are using advanced simulation tools to build models to predict how some of the drugs we have designed will work.

For continuing this work, we are running a crowdfunding campaign using gofundme‘s awesome platform. Donation or not, please share our crowdfunding campaign and support our cause.

Donate here: gofundme page for nanoveda.

What is next – The future of research.

Every year, from 2010 onward, Redmonk publishes a bi-annual comparison of the popularity of programming languages relative to one another using data from GitHub and Stack Overflow. One list is compiled for the summer and another one for the spring. Among top 15 programming languages in the spring 2016 list, only one exclusively scientific and statistical programming language is featured. It is: R.

Within a six month period: between January of 2016 and June of 2016, R climbed from its original 13th place to the current 12th place. The only other popular scientific and statistical programming language ranked higher than R is Python. But, mind you, Python is a general purpose programming language, with broader programming applications than the R’s primary focus of scientific and statistical computations.

I see this list as a bellwether or a canary in the coal mine or a harbinger. The message is clear. Since R and Python are opensource programming languages, any startup with a heavy focus on research and development should start investing in open platforms now. It will provide two benefits: 1) number of application developers, packages, platforms and programmers working with the language will be high; 2) the relative stability over time for the list of names featured in the top 15 programming languages indicate a very easy way to future proof the research and development side of the business.

Even if the underpinning technologies are opensource, there are mechanisms to protect and commercialize the intellectual property. If there is not much competition in the field of development, or if the resources and management strategy allows focusing more on: 1) cascading effect of lowered supply chain costs due to increased competition and  2) maintenance of developer momentum; then one can always choose to take the path of open sourcing every new research and development. A great example here is the electric car manufacturer Tesla.

In conclusion, open platforms are the next big bet for research and development focused startups like nanoveda. Our strategy for technology development is based on what the technology landscape will be for the medium term future of next 5 to 10 years. Cancer research is a very competitive field and monetization potential of startups in this field are measured using intellectual property. Once we reach a position of self sustaining business, nanoveda will opensource all our patents, similar to Elon Musk’s approach with Tesla.

Right now we need your support. We are running a crowdfunding campaign using gofundme‘s awesome platform. Donation or not, please share our crowdfunding campaign and support our cause.

Donate here: gofundme page for nanoveda.


Writing better code – Parallelize

Today, I am going to share a secret recipe for writing beautiful and efficient code that I learned, while creating simulation models for nanoveda.

Nanoveda is using advanced nanoscale simulations to design next generation cancer therapeutics.

The secret recipe is: parallelizing code.

Most modern PCs have a multicore processor inside it. We seldom code to exploit all the cores. The greatest advantage of coding for parallel processing is: getting things done faster. This is possible by utilizing all the available resources in your computer. The coding principles for parallel computing described here are applicable to cloud computing also. While using cloud computing infrastructure, we often buy virtual machines with multiple processing cores and seldom use all the processing power we paid for, to run the codes. Coding for parallel processing allows efficient use of available computing resources.

Here, I am using an example in R to demonstrate how to write a program for parallel processing.

The code above uses 2 cores to run the function: ‘some.function’. This was achieved using doParallel and foreach packages.

To utilize all the available cores for parallel processing, modify the doParallel parameters to:

Parallel processing has another huge advantage. Very lengthy and complex codes can be executed with limited resources without overwhelming the system. Parallel processing is one of the key steps in code optimization. Parallelized code facilitate efficient running of massive simulation models and machine learning codes. To take advantage of hardware solutions such as Xeon Phi require this skill to code for multiple processing cores.

Nanoveda has a crowdfunding campaign to support the awesome work to create next generation cancer therapy. Donation, or not, share our crowdfunding campaign and help spread the word.

Innovation at its core – Making nanoscience accessible.

In this blog post, I will detail two key philosophies that are behind nanoveda.

LEAP philosophy:

Most important guiding philosophy of nanoveda is very simple: bringing nano-science to masses. The first product we are developing is to address one of the toughest challenges known to human-kind: controlling and curing cancer.

Achieving this goal is a step-wise process. My four steps to achieve this goal are:

  1. Learn.
  2. Experiment.
  3. Analyse and adapt.
  4. Predict.

These four steps or the LEAP philosophy is pivotal to bringing success to any processes and summarizes my pathway to accelerate innovation at nanoveda.

Radical openness:

Another key philosophy at nanoveda is: radical openness. To control processes at the level  of nano-scale, nanoveda needs cutting edge tools. As a startup, the cost of researching and developing these tools are beyond our current capabilities. Also, the new learning and knowledge that we gain during nanoveda’s step-wise progress, needs to be implemented quickly in our tools. To achieve all this, we are embracing the philosophy of radical openness. An example of radical openness at work, is our love of open-source software. Open systems power our toolkit for predictive analytics of nano-scale systems. Another revolutionary toolkit is helping nanoveda build simulation models of nano-scale drugs.

Radical openness is an important driving force of nanoveda’s quest to succeed in building a next generation nano-sciences company.

Nanoveda has a crowdfunding campaign to support the awesome work to create next generation cancer therapy. Donation, or not, share our crowdfunding campaign and help spread the word.



Advancing cancer cure – Nanøveda.

About Nanøveda
I am a co-founder of cancer therapeutics startup: nanøveda. The name nanøveda is a neologism by combining three seed words: nano, eir (the goddess and valkyrie of healing in Norse mythology) and veda (sanskrit for knowledge). We are an early stage start-up developing advanced cancer treatments.

The technology we are developing combines our expertise in nanotechnology, personalized medicine and cancer pathways.

One of the disease models we are targeting using nanøveda’s technology, is to treat an incurable form of brain cancer called glioblastoma multiforme (GBM).

How You Can Help
The next step in making nanøveda’s technology a reality is to fund our efforts to secure necessary intellectual property. This development process is very time consuming and expensive.

Nanøveda has launched its first gofundme campaign. This crowdfunding campaign will cover the legal expenses related to filing patents for technology that nanøveda has developed.

Nanøveda’s Mission | Why It’s So Important
Nanøveda’s mission of advancing next generation cancer therapeutics has a great personal meaning to me.

I want you to be part of nanøveda’s journey to advance precision cancer therapy. Donation or not, please share our crowdfunding campaign and support our cause.

Donate here: gofundme page for nanøveda

Welcome to my blog – Life notes.

For 2017, my new year resolution is to organize and share my thoughts on my website. I have added this blog, to share my ideas and my life being a doctor, neuroscientist, researcher in applied artificial intelligence and my hobbies in PC gaming & green living.

Join me in this journey.