ARAGÓN ARTACHO, Francisco J., et al.[1] presents new ways to visualize large mathematical datasets. In particular, the paper goes into determining if a real number is "Normal" through visualizations.

”A real constant α is b-normal if, given the positive integer b ≥ 2, every m-long string of base-b digits appears in the base-b expansion of α with precisely the expected limiting frequency 1/b^m."

The paper shows a visualization of many base 4 numbers. The authors also go on to suggest applying this visualization technique to genome comparisons.

[1] ARAGÓN ARTACHO, Francisco J., et al. "Walking on real numbers". The Mathematical Intelligencer. Vol. 35, Issue 1 (March 2013). ISSN 0343-6993, pp. 42-60

Visualization

A walk for a base 4 number consists of steps where at each step the path moves one unit east, north, west or south, depending on the whether the
number at that position is 0, 1, 2 or 3.

I've applied this visualization technique to DNA. DNA consists of 4 nucleotides denoted by A, T, G and C. For each of these nucleotides, I assigned a direction to the step - North, East, South, and West respectively.

Instead of the HSV color scheme used in the paper, that generates a spectrum of colors from VIBGYOR, I've used fixed colors for each nucleotide to get an idea of the nucleotide content in the sequence which is of value in sequence analysis.

Color Scheme

• A - #D9042B
• T - #03588C
• G - #F29F05
• C - #F24B0F

I picked up the color scheme from Adobe Color.

Data Sources

• GenBank - Sequences posted by Nathan Grubaugh.
• Human Genome build hg19(GRCh37) from Ensembl

Thanks to

All the folks at the Andersen Lab.

For More Data ...

At the Andersen Lab we are sequencing Zika virus in samples from humans and mosquitoes in Florida, USA. We're regularly releasing data available here.

Code at Github

Nucleotide Walk Potraits

Fig 1 shows strains of Zika virus from humans and mosquitoes in Florida, USA sequenced at the Andersen Lab. Fig 2 shows a few flaviruses - Chaoyang Virus, Culiseta Virus, Powassan Virus and West Nile Virus. Notice how both the figures capture the difference in mutations.

Fig 1: Strains of Zika virus from GenBank.

Clockwise:

• Zika virus isolate from Aedes_aegypti. USA. 2016
• Zika virus isolate from Aedes_aegypti. USA. 2016
• Zika virus isolate from Human. USA. 2016
• Zika virus isolate from Human. USA. 2016

Fig 2: A few Flaviviruses from GenBank

Clockwise:

• Chaoyang virus strain ROK144
• Culiseta flavivirus strain
• Powassan virus strain P0375
• West Nile virus isolate FtC-3699

Human chromosome walks

Images of human chromosomes show very similar A,T,G and C content(except for Chr22 and Chr19). I'm looking into producing gigapixel images to allow zooming to make the walks clearer.

Disclaimer: I'm quite busy with my work at the lab so it will be a while before I can get around to doing it.

Fig3a: Chromosome 22

Fig3b: Chromosome 21

Fig3c: Chromosome 20

Fig3d: Chromosome 19

Fig3e: Chromosome 18

Fig3f: Chromosome 17

Fig3g: Chromosome 16

Fig3h: Chromosome 15

Fig3i: Chromosome 14

Fig3j: Chromosome 13

Fig3k: Chromosome 12

Fig3l: Chromosome 11

Fig3m: Chromosome 10

Fig3n: Chromosome 9

Fig3o: Chromosome 8

Fig3p: Chromosome 7

Fig3q: Chromosome 6

Fig3r: Chromosome 5

Fig3s: Chromosome 4

Fig3t: Chromosome 3

Fig3u: Chromosome 2

Fig3v: Chromosome 1

Fig3w: Chromosome X

Fig3x: Chromosome Y

Worked as part of team perfect posture at Inmobi Hack Day, Summer 2015. Idea was to develop an a chrome extension that with the help of sensors detect if the user was sitting in an awkward posture in the least intrusive way possible. Due to my ignorance of sensors, circuits and breadboards, I worked on the server side application.

App developed took input from sensors and pushed notifications to a chrome extension using google cloud messaging. To ensure that the server didn't have to parse junk data received from the sensors, an intermediate node server was also put into place.

App Repostiory and Node server

Developed a clone of the UI/UX of the Facebook chat heads on Android as part of the interview process at InMobi. The app basically shows a chat head which can be moved around and closed in a fashion similar to that of the Facebook Messenger App. In addition, the chat head is also visible on top of the lock screen.

Bonus: The chat head displays popular Instagram photos based on the location of the device.

App Repository

PS: I cleared the interview round ;)

I worked on BioBranch during my undergraduate thesis project at SuLab. Branch can be used by biologists to build decision trees to visualize data and test hypotheses on large biological datasets. The project contains many aspects of data visualization to make the construction of trees as intuitive as possible. The trees built are dynamically evaluated and the resulting evaluations are shown on a real time basis.

Branch currently uses a preloaded set of datasets.

Live and Code Repository

A simple simulation of a board game was used to determine if there would be any significant effect of a biased dice in a board game such as monopoly where the player ends up going around a board multiple times during one game.

The resulting spots on the board were arranged in a distribution that yielded no concrete result.

TODO: Look into whether the simulation was correct / Learn more Math.

Code Repo and
Distributions on Google+ Album

I used a Raspberry Pi along with a NoIR camera module to take photos of a plant with intervals of 10 minutes to assess the rate of photosynthesis. The images taken were falsely colored using Infragram's tool to see the rate of photosynthesis.

Key: The greater the red, the greater the photosynthesis.

You can see over time the rate increases and decreases almost uniformly.

Falsely Colored Photos

I worked with CrowdSourcing Biology during Google Summer of Code 2013. I worked on extending The Cure to include an expert level for users with more biological knowledge to have greater control in building decision trees.

Code Repository

Trees represent the simplest of fractals. I used d3 to generate lines that would grow into a forest of trees eventually. I set the upper limit on the number of trees to 20 in the demo.

Demo and Code

Notes on Fractals

I co-founded Tune Patrol during my sophomore year at BITS Pilani. Tune Patrol is a marketing platform for indie artists to monetize their music. I was the CTO and developed the technical platform along with two other students from my year. We were acquired in Sept, 2013.

Press

Top 50 Inspiring and Most Read Startup Stories of 2013
: #26 Tune Patrol

9 college startups that went on to become big companies(Tune Patrol on #6)

Tune Patrol: Launch

Tune Patrol: The Birth of an Idea

Tune Patrol: Exit

Screenshots

I worked with CrowdSourcing Biology during Google Summer of Code 2012. I developed an interactive network visualization built on GeneWikiPlus to better understand the relationships between diseases, genes and SNPs. The interface uses Cytoscape web which is a flash based tool with a javascript backend. Genewiki Plus is a semantic media wiki and the network is visualized using data obtained from querying the wiki.

Code Repository