VOLUME 2 | ISSUE 3

About us

STAFF COORDINATORS : Ms. R. Mohana Priya, Mr Kaarthik

DESIGNER : Prithvi Rajan R, Raghavan Than

EDITORS : Ms. R. Mohana Priya, Bahashree Bhat

Kavya Prasad , Philip Merry, Shrramana Ganesh

‘When we think about it, caring for patients is 99 percent

information and 1 percent intervention, so it’s clear that

With or without genomics , the paradigm is shifting.

Bioinformatics brings a cutting edge capacity to healthcare.’

— Christopher G. Chute

editorials_bindas@gmail.com

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UPCOMING EVENTS : APP DEVELOPMENT WORKSHOP |

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BINDAS BIOINFORMATICS DATA ASSESSMENT SERVICES

OCTOBER 2017

FACTS, FORENSICS, AND MORE.

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QUANTUM COMPUTING

IMPACT OF QUANTOM COMPUTING

IN BIOINFORMATICS

P. 3

DNA AND DATA STORAGE

ENCODING DIGITAL DATA

IN DNA

P. 12

CONTENTS COVER STORY

IMPACT OF QUANTUM COMPUTERS

RECENT EVENTS: Learnings

from workshops &

conferences

SCOPE IN BIOINFORMATICS

DNA AND DATA STORAGE

ANTI- HIV MUTANTS

Our achievements

Gallery

The Bioinformatics Department at Karunya University, with its motto

“Information for innovation” aims to provide expert teaching and research

with its highly qualified faculty members and research staff in an effort to

create products to benefit humankind. The state-of- the-art Bioinformatics

Research Center houses a High Performance Computing facility which in-

cludes cluster platforms of high end servers with round-the-clock internet

connectivity. The combination of computer sciences and biology facilitate

the students towards employability in different companies of IT, Pharmaceu-

tical and Biotech industries.

ABOUT THE DEPARTMENT

BINDAS, OCTOBER 2017 | 2

GALLERY

WHITE HAT A hacker originally meant someone

who likes to new things with comput-

ers. This particular article is about

Yuvan(student of Bioinformatics)

who can program something. He

attended a training program with IIT

Kharagpur professors regarding ethi-

cal hacking at Wingfotech pvt ltd.

This was a summer internship pro-

gramme for 7 days. He has learnt

wifi, facebook and email hacking. He

has equipped himself in publishing

linux coding. To better describe hack-

ing, one needs to understand hack-

ers. He is the one who is intelligent

and highly skilled in computer lan-

guage. In fact, breaking a security re-

quires more intelligence and exper-

tise than actually creating one. In

other words he is a white hat hacker

who hacks to take control over the .

system for personal gains legally. It is

done by finding loopholes and weak-

nesses in the system. He is a skilled

programmer proficient in machine

code and computer operating

system. This culture is an idea de-

rived from a community of enthusi-

ast computer programmers and sys-

tem designers in the 1960s around

the Massachusetts Institute of tech-

nology. This is not a crime because

computer hacking is an act of ma-

nipulating a computer to do what

you want it to do and it is a very

valuable skill in the techworld. It is

not a criminal activity. The only sit-

uation when it becomes a crime is

based on the intent or motive of

the person sitting behind the com-

puter. All the best Yuvan.

BINDAS, OCTOBER 2017 | 14

VISHAAL(II BTECH)

WORDS of ENCOURAGEMENT

Dr S JACOB ANNAMALAI

" Bioinformatics is a collection of modern application tools for

computation and analysis to interpret biological data.The study

of biological systems with modelling and computational tech-

niques has hence been pursuing speedier solutions to newer and

challenging problems in engineering life.The field of Computa-

tional biology has enabled many biological insights and better

understanding of its complexity.

I am glad to know that the Bioinformatics Program,School of Bio

sciences and Agriculture ,Karunya University is organisinig NE-

OSEQ 2K17, a seminar and releasing the magazine BINDAS 2K17.

I appreciate the effort of the faculty members of Bioinformatics

in bringing out the Departmental newsletter ‘BINDAS’. It brings

out recent advances in BIOINFORMATICS. I am quite sure of its

success in achieving the purpose of its release. It gives a tech-

nical platform to the students of Bioinformatics for exposing

their expertise in various aspects. It is a branch with blooming

opportunities of placement and research.I hope that this

‘Bioinformatics Data Assessment Service’ will be yet another Dr BERLIN GRACE

NeoSeq: A Bioinformatics Students Association has experi-

enced an outstanding growth over the past few years. This

is reflected academically, throughout the development of

student career, inter and intrapersonal skill, and in the eco-

nomical/business sector with the establishment of new

start-up companies with national and international con-

nections. I wish all the very best to all association mem-

bers and congratulate them to bring Department magazine

to the public domain. Dr AFROZ ALAM

BINDAS, OCTOBER 2017 | 3

Quantum computing, in a grossly oversimpli-

fied nutshell, allows binary bits (the 0s and 1s) to

exist in both states at the same time – a quantum

bit, or qubit. Thus it is possible to represent every

possible combination of 0s and 1s simultaneous-

ly. As all data processed by current computers is

just 0s and 1s, and all problems revolve around

manipulating the state of those bits until they

match some predetermined requirement, a

quantum computer can bypass a lot of this com-

putational heavy lifting by representing every

possible combination of bits simultaneously,

therefore knowing at the same time every single

possible solution/outcome given the inputs.

Why is this important? There is a class of

computer science problems called NP-hard which

cannot be solved by any other means than con-

structing every possible solution then measuring

them all to see which one comes out best. The

classic example of this is the travelling salesman

problem – given a map with distances and roads

between cities that the salesman has to visit,

which route will be shortest? It sounds simple,

but it really is NP-hard.

Genome assembly is probably NP-hard –

depending on which way you look at it. The only

way to get the genuinely best assembly is to try

out all possible combinations, score them, and

select the best. All current approaches attempt

to avoid having to do this by clustering or prepro-

cessing the components of the assembly in order

to bypass the necessity of trying out every com-

bination. Given a quantum computer with suffi-

cient qubits to represent the completed

assembly you can straight away discover all possi-

ble variants of the assembly and score each in

turn, all in an instant, turning a job that used to

take hours or even days into one that takes se-

conds.

Other areas that could be impacted are bi-

omarker discovery (which combination of SNPs

best predict a certain disease? check them all sim-

ultaneously and find out instantly), and compara-

tive genomics (which species are the closest to

the sample? align/compare them all simultane-

ously and find out instantly). The possibilities are

endless.

The only drawback is the previously men-

tioned requirement to code everything in a partic-

ular way in order for the machine to be able to

process the problem. That's not new – people

working with GPUs already have to do this – so

although it is a short-term roadblock it won't be

long before tools are made available to make this

job easier. The hardest part will be gaining ac-

ceptance. As with GPU and other alternative pro-

cessors and new algorithms it can take time for

the scientific community to convince itself of the

accuracy and reliability of a new approach. But

given the huge benefits that this technology has

to offer I'm sure it won't take long for people to

be convinced.

D-WAVE QUANTUM COMPUTER

BINDAS, OCTOBER 2017 | 4

IMPACT OF QUANTUM

COMPUTING

KAVYA PRASAD (II BTECH)

THE EARLY BEGINNINGS . . .

Sea people

The identity of the Sea Peoples. Around 1200 BC civilization was progressing rapidly

in the Eastern Mediterranean, with the Egyptians, Hittites, Greeks, and Minoans all

having advanced cultures. Then suddenly a bunch of Bronze Age vikings appear out

of no where and destroy everything, setting back civilization by 1000 years. To this

day, no one knows who they were or where they came from

2000-year-old computer

Antikythera Mechanism. It’s an analog computer dating back 2000 years ago that

was used to display astronomical cycles. Nothing as complex as it was seen for an-

other 1000 years. (PBS Link)

Benjamin Kyle

Benjamin Kyle. Man who woke up behind burger King with absolutely no memory of

who he is. Every test done to find his identity has failed, his fingerprints, DNA, etc. do

not match any person on file. Nobody has a clue who this guy is.

Polynesians populating the Pacific

Polynesians populating the Pacific ocean islands and even parts of South America as

early as 1800 B.C. DNA tests have been done and confirmed the extent of their

“Explorations”, but the things that gets me are why they decided to travel into the

great unknown in the first place? and a how advanced their technology had to be to

find these islands. They didn’t just randomly drift into them. Tests have been done

showing how unlikely this is. They would have to possess complex knowledge of cur-

rents and what not.

The Baghdad Batteries

There are a lot of theories, but no proof of what they were actually used for (as far

as I know). But really cool to think that an ancient civilization might have had some

form of electricity for everyday use. BINDAS, OCTOBER 2017 | 13

DNA CAN NOW BE USED TO STORE DATA

Humanity has a data storage problem: More

data were created in the past 2 years than in

all of preceding history. And that torrent of

information may soon outstrip the ability of

hard drives to capture it. Now, researchers

report that they’ve come up with a new way

to encode digital data in DNA to create the

highest-density large-scale data storage

scheme ever invented. Capable of storing

215 petabytes (215 million gigabytes) in a

single gram of DNA, the system could, in

principle, store every bit of datum ever rec-

orded by humans in a container about the

size and weight of a couple of pickup trucks.

But whether the technology takes off may

depend on its cost.

Erlich and Dina Zielinski, an associate scien-

tist at the New York Genome Center, looked

at the algorithms that were being used to

encode and decode data. They started with

six files, including a full computer operating

system, a computer virus, an 1895 French

film called Arrival of a Train at La Ciotat, and

a 1948 study by information theorist Claude

Shannon. They first converted

the files into binary strings

of 1s and 0s, compressed them

into one master file, and then

split the data into short

strings of binary code. They

devised an algorithm called a

DNA fountain,

which randomly packaged the strings into so-called droplets, to which they added extra tags to help reassemble them in the proper order later. In all, the researchers generated a digital list of 72,000 DNA strands, each 200 bases long. They sent these as text files to Twist Biosci-ence which then synthesized the DNA strands. Two weeks later, Erlich and Zielinski received in the mail a vial with a speck of DNA encoding their files. To decode them, the pair used modern DNA sequencing tech-nology. The sequences were fed into a com-puter, which translated the genetic code back into binary and used the tags to reas-semble the six original files. The approach worked so well that the new files contained no errors. They were also able to make a vir-tually unlimited number of error-free copies of their files through polymerase chain reac-tion, a standard DNA copying technique. What’s more,they were able to encode 1.6 bits of data per nucleotide, 60% better than any group had done before and 85% the theoretical limit. However, the new approach isn’t ready for large-scale use yet. It cost $7000 to synthe-size the 2 megabytes of data in the files, and another $2000 to read it. And compared with other forms of data storage, writing and reading to DNA is relatively slow. So the new approach would currently be better suited for archival applications

-KAVYA PRASAD (II BTECH)

BINDAS, OCTOBER 2017 | 12

ANTI-HIV mutants

The human immunodeficiency virus (HIV) is

a lentivirus (a genus of retroviruses that cause

chronic and deadly diseases characterized by

long incubation periods, in the human and

other mammalian species. They can be-

come endogenous (ERV), integrating their ge-

nome into the host germline genome, so that

the virus is henceforth inherited by the host's

descendants.) That causes HIV infection and

over time acquired immunodeficiency syn-

drome (AIDS)

CD4 (cluster of differentiation 4) is

a glycoprotein found on the surface of im-

mune cells such as T helper

cells, monocytes, macrophages, and dendritic

cells. In humans, the CD4 protein is encoded

by the CD4 gene. CD4+ T helper cells are white

blood cells that are an essential part of the

human immune system. They are often re-

ferred to as CD4 cells, T-helper cells or T4

cells. They are called helper cells because one

of their main roles is to send signals to other

types of immune cells, including CD8 killer

cells, which then destroy the infectious parti-

cle or harmful antigens.As due to this signal-

ling nature of CD4 cells they can be consid-

ered the switch which starts the immune sys-

tem. If this system is suppressed somehow as

in this case the entire immune

system goes

into a dormant stage HIV virus, after entering

the cell undergoes reverse transcriptase using

reverse transcriptase enzyme, however while

transcripting it does lot of errors. Eventually

giving rise to new forms of HIV strains, in

which many won’t be able to make it, howev-

er a part of it concludes to be better than

their parent. Out of this new strains not all

will be using CCR5 protein as the entry point,

proteins such as CCX4( also a type of corecep-

tor) also gets into the play as an entry point

for these new HIV viruses This arises new

complications This proves CCR5 not to be the

whole story of immunity to HIV infection.

Some resistant people have been found, who

have two perfectly normal copies of CCR5. So

other genes also contribute to slowing down

HIV infection or providing complete re-

sistance to the infection.

The mutation giving rise to resistance is still

under study, scientists are still trying to find

out the cause of the mutation, why it is only

present in the part of European population?,

what are the other factors than CCR5 respon-

sible for the resistance. However with the ad-

vancement in the bioinformatics tools, it has

become much easier to understand this mu-

tation, providing a confidence towards the

total eradication of HIV.

-BLESSY RAJAN(II BTECH)

BINDAS, OCTOBER 2017 | 5

WHAT IS BIOINFORMATICS??

SCOPE AND CAREER OPPORTUNITIES!!

Bioinformatics is the application of computer technology to the management of biological

information. Bioinformatics has been used for insilico analyses of biological queries us-

ing mathematical and statistical techniques. Bioinformatics is the latest buzzword in the

field of Science & Technology in which Biology, Computer Science and Information Tech-

nology merge into a single discipline. There is a great scope for Bioinformatics in India. The

career prospects in the field have been gradually increasing with more and more use of in-

formation technology in the field of molecular biology. One can get job opportunities in all

sectors of biotechnology, pharmaceutical and biomedical sciences, in research institutions,

hospital and industry. Some of the specific career areas that fall within the scope of bioinfor-

matics include Sequence assembly, Database design and maintenance, Sequence analysis.

JOB OPPORTUNITIES IN THE FIELD OF BIOINFORMATICS

Professor Science technician Research assistant

Bioinformatics scientist Bioinformatics analyst Junior researcher

Research associate Bioinformatics software de-veloper

Scientific Curator

Gene or protein analyst Phylogeneticist Database programmer

Bio-statistician Cheminformatician Pharmacogenetician

Pharmacogenomics Molecular modeller Network administrator

TOP COLLEGES / UNIVERSITIES IN ABROAD OFFERING

University of Copenhagen, Denmark

University of Queensland, Australia

University of New South Wales, Australia

Stanford university, USA

Harvard university, USA BINDAS, OCTOBER 2017 | 6

FOR

ENSI

CS

What’s forensic biotechnology ?

We recently attended a national conference on forensic biotechnology at Center for

Biosciences and Nanoscience Research (CBNR). Initially we had no idea about the sub-

ject- we only knew that the word ‘forensic’ had something to do with analysis of

crimes and murders (thanks to ‘The Mysteries That Cannot Be Solved’ series!) Never-

theless, the title of the conference piqued our interest, and we decided to attend (who

doesn’t want an OD?!).

We happened to arrive a little early and saw informative charts pasted all over- this

got us intrigued into what to expect further in the conference. Four speakers were in-

vited; among them was Dr.Mohamed Hatha, whose CV ran into well over thirty pages!

He gave an interesting introduction to the field of microbial forensics, and briefed us

about the analytical methods used for identifying organisms used in a biocrime.

Another very interesting talk was given by the director of the center, Dr.Ragunathan

on the topic ‘thanatomicrobiome’, which means the study of the microbes colonizing

the internal organs and orifices after death. He let us in on an unbelievable fact-90% of

the cells in a healthy adult body are microorganisms! He hence outlined the im-

portance of studying these microbes especially for forensic field. He also interspersed

his talk with various supporting case studies that appropriatley demonstrated how

these techinques had been successfully applied.

- PHILIP MERRY, KAVYA PRASAD (II BTECH)

RECENT EVENTS

BINDAS, OCTOBER 2017 | 11

RECENT EVENTS

NATIONAL CONFERENCE Recent advances in zebra fish immunology

The National Conference on Recent advances

in zebra fish immunology, which is an ideal

model for human health, was conducted on

September 20-21, 2017 at Sathyabama Uni-

versity, Chennai. This conference was an ideal

platform for finding more on my area of inter-

est because it was a national forum, con-

sisting of students, researchers, education sci-

entists, technologists who are experts in

health sciences, to present their research

workshave known a number of academics and

professionals from different universities who

have similar research interests such as immu-

nology and neuroscience. The conference was

very interesting and enriched my experience

with more information, knowledge and confi-

dence. In addition it was divided as three ses-

sions per day – discussion, lecture, presenta-

tion. In fact, I presented a poster titled “A

subway to Artificial Intelligence” that de-

scribed “Blue brain technology” and bagged

the third prize, along with my classmates Ms.

Nagomi, and Ms. Srinitha. I feel so happy for

it, because we were the only undergraduates

among a crew of research scholars and post

graduates who have published papers. Also

many thanks, to my mentors Mr. Kaarthik and

Ms. Mohana Priya along with the programme

coordinator Dr. Afroz Alam for their generous

support and guidance.

- MONICA (II BTECH)

POSTER PRESENTED DURING CONFERENCE

BINDAS, OCTOBER 2017 | 10

TOP COMPANIES FOR BIOINFORMATICS IN INDIA

1. Accelrys Software Solution Pvt Ltd., Bangalore

www.accelrys.com

2. Apticraft Systems (P) Ltd., Indore (M.P.), India

www.apticraft.com

3. Aptuit Informatics, Bangalore

www.aptuit.com

4. Bigtec, Bangalore

www.bigteclabs.com

TOP COMPANIES FOR BIOINFORMATICS ABROAD

Company Location Business Type

Transcriptic Menlo Park, CA Cell-based, biochemical, & biomarker assay services using our robotic cloud lab.

IFOWON Vancouver, BC in-silico Drug Discovery

Zymeworks Vancouver, BC In Silico Biologics Development

Verge Genomics Bay Area, CA Algorithm-based Drug Discovery

Collaborative Drug Discovery Burlingame, CA Biological & Chemical Database

iRhythm Technologies Cypress, CA Remote heart analysis

Protein Metrics San Carlos, CA Protein characterization software

Interpreta San Diego, CA Clinical & Genomic Data Analysis

Phalanx Biotech San Diego, CA Gene Expression and miRNA Expression, NGS, qPCR and Genomic Data Analysis

SciGenom San Francisco, CA Next-gen sequencing services, bioinformatics

SeaChange Pharmaceuticals San Jose, CA Computational drug discovery

Maverix Biomics San Mateo, CA Sequencing Data Analysis

BINDAS, OCTOBER 2017 | 7 MONICA (II BTECH)

IAESTE INTERN

My name is Lars Pelz. I am a 5th year student

of Pharmaceutical Bioprocess Engineering

from Technical University of Munich, Germa-

ny. I am here as an Intern for 3 months. My

specification is upstream processing and phar-

maceutical technology. I will carry out work on

pharmacophore and virtual screening of drug

analogues that inhibit tubulin polymerization.

Besides the internship I am able to visit India. I

really like the Indian food and landscapes. The

people here are really nice to me and I have

an amazing time here in India.

IAESTE- Karunya University gave me a won-

derful opportunity to work as an intern in

one of the well-known institutions, Max

Planck Institute of Molecular Plant Physiolo-

gy, Potsdam, Germany. I applied and attend-

ed the interview with hesitation. After all se-

lection process, here I am at Max Planck. I

am appointed in the Bioinformatics service

infrastructure lab headed by Dr. Dirk Wal-

ther. I am the first Indian student in this lab. I

am working on the topic “Identification of

Alternative Splicing Events in Arabidopsis

thaliana using RNA-Seq approach”. The

cutting edge research facility and freedom

given by Max Planck is really helping me to

gain experience.

Mr.Lars Pelz

Ms. Monica Steffi

BINDAS, OCTOBER 2017 | 8

SHINING ALL THE WAY

S. No

Name Fellowship Year Organization

1 Mr. Lars Pelz Technical University of Mu-nich, Germany

September 2017 Department of Bioinformat-ics, Karunya University

2 Ms. Monica Steffi Department of Bioinformatics, Karunya University

August 2017 Max Plank Institute, Germany

3 Ms. Jagriti Mukherjee Department of Bioinformatics, Karunya University ,Karunya University

August 2017 Universidad Autónoma de Occidente, Cali, Colombia

IAESTE INTERNS

FACULTY FOR POST DOCTORAL FELLOWSHIP

S.No Name Designation Research Area Host Institute

1 Dr. Jobin Varkey Assistant Profes-

sor Protein structure function relationship

Keck School of Medicine , USC, USA

2 Dr. Sowmya Lokappa Assistant Profes-

sor Protein structure function relationship

Keck School of Medicine , USC, USA

3 Dr. D. Premnath Assistant Profes-

sor Molecular Modeling and Drug Design

University of Manitoba, Canada

4 Dr. Sachidanand Singh Assistant Profes-

sor System Biology The Ohio State University, Co-

lumbus, USA 5

Dr. Atul Kumar Assistant Profes-sor

Next Generation Sequencing The University of Chikago, USA

NOTABLE ACHIEVEMENTS

Ms. Smiriti 2015 passed out has qualified KBET (Karnataka Bioinformatics Entrance Test).

Dr. Sanu Sameer has got Post Doctoral fellowship position at Oxford University, United Kingdom (UK).

Ms. Nishanthi G has received full scholarship at The University of Nottingham, U.K for Master of Scienc-

es in Stem Cell Technology.

Ms. Angelina Thomas (2017 passed out) has selected to take admission in Postgraduate research pro-

gram at Ulster University, Northern Ireland-UK wherein the awarding title would be a PhD.

Ms. Kavya Prasad of II B.Tech Bioinformatics successfully completed the third course in the Bioinfor-

matics Specialisation - Comparing Genes, Proteins and Genomes on Coursera.

Ms. Devagudi Pujitha of I M.Tech Bioinformatics has been selected for Internship at National Institute of

Oceanography, Goa.

BINDAS, OCTOBER 2017 | 9