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 paents is 99 percent informaon and 1 percent intervenon, so it’s clear that With or without genomics , the paradigm is shiſting. Bioinformacs brings a cung edge capacity to healthcare.’ — Christopher G. Chute [email protected]SCAN TO VISIT OUR FACEBOOK PAGE UPCOMING EVENTS : APP DEVELOPMENT WORKSHOP | ‘We, The BINDAS Team’ BINDAS BIOINFORMATICS DATA ASSESSMENT SERVICES OCTOBER 2017 FACTS, FORENSICS, AND MORE. SCAN TO VISIT OUR FACEBOOK PAGE QUANTUM COMPUTING IMPACT OF QUANTOM COMPUTING IN BIOINFORMATICS P. 3 DNA AND DATA STORAGE ENCODING DIGITAL DATA IN DNA P. 12
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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.’
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.