Scientific Computing: Bioinformatics and Computational Biology

Bioinformatics is an interdisciplinary field with biology, computer science, statistics and information technology at its core.

A colossal amount of data is generated by biological experiments. When biologists need tools to analyse, store and interpret this data, Bioinformatics comes for the rescue. The job of a bioinformatician entails writing algorithms, creating user interface, creating databases and help molecular biologists in interpreting the computed data.

Nussinov's Algorithm - Traceback Step

In my basic and advanced courses of bioinformatics, we were taught about dynamic programming algorithms, namely, Nussinov’s algorithm for RNA secondary structure prediction, Viterbi algorithm for Decoding of HMM and UPGMA for phylogenetic tree construction. Though these algorithms are accurate, they are very slow for large data sets. Heuristic algorithms were used instead of dynamic programming algorithms as they gave approximate but fast solutions.

Protein Structure

There are tons of algorithms to solve any problem in any other field. However, it is extremely difficult to solve a biology problem because, the living system is so complex and divergent. It becomes almost impossible to device a perfect algorithm. For example, finding the actual representation of the protein structure and all its function is one of the biggest challenges faced by bioinformaticians today.

A myriad of packages for predicting genes (Ex: GenScan), for aligning sequences (Ex: BLAST, CLUSTALW and CLUSTAL Omega), constructing phylogenetic trees are available, but none of these give an accurate solution for all types of problems. Though researchers are facing new problems every day, they are being helped immensely by computer scientists. It will certainly take a number of years to solve complicated problems, but we must remain dedicated to this field since it offers great hope in solving diseases like HIV, Cancer, Alzheimer’s etc that plague the society today.

References:

Dr. Sami Khuri – Bioinformatics CS123A and CS223

http://iase-web.org/documents/papers/icots7/5D2_ARHI.pdf

Computer Graphics: Computer-generated imagery (CGI)

CGI is an application of Computer Graphics to create or contribute to images in art, printed media, video games, films, commercials, etc. The visual scenes may be static or dynamic and may be 2D or 3D. Think of it this way, CGI attempts to do with numbers, what a camera does with light. Our world is bound by many physical constraints, but with CGI we can create many things that are impossible in reality. One may wonder what would be the advantage of such a tool; let’s go over some of them.

Medical Visualizations

In medicine, Computer generated anatomical models are used for both instructional and operational purposes. Using CGI, a three dimensional image can be created from a bunch of single slice X-rays which can help in a speedy and accurate diagnosis. In modern medical applications patient specific models are constructed in “computer assisted surgery”. For example, in a total knee replacement surgery, such a model can be used to carefully plan a surgery.

Conceptual rendering of a Planetary Resources spacecraft
preparing to capture asteroid

CGI is also used in courtrooms to help judges and jury to better visualize the sequence of events, evidence or hypothesis. CGI is used in product advertisements; CGI can produce images with no greasy fingerprints and are unmarred by dust, just perfect in every sense.  CGI is also used for scientific visualization to present meteorological data, medical imaging, architecture and technology.

Avatar pushed CGI to a whole new level

CGI is used in movies to create artificial reality which is very close and in many cases better than actual reality. This certainly helps in cutting down expenses. For example, in the movie Titanic, a miniature model of the ship was created and extrapolated to create a real world effect.

Thus, CGI has opened a new world full of possibilities and it is up to us to explore and reap the benefits.

References:

http://www.mindactive.com/cgi-computer-generated-imagery

http://www.sciencedaily.com/articles/c/computer-generated_imagery.htm

http://en.wikipedia.org/wiki/Computer-generated_imagery

http://blogs.voanews.com/science-world/2012/04/25/titanic-director-backs-venture-to-mine-platinum-from-asteroids/
http://computerstories.net/a-computer-generated-imagery-cgi-history/

Communication and Security: Transport Layer Security (TLS)

Transport Layer Security is a layer 4 protocol that is based on Secure Sockets Layer (SSLv3). It makes use of Public Key Infrastructure (PKI) which provides user authentication and hence provides confidentiality. This protocol mainly prevents packet sniffing, forgery and tampering.

Communication between client and server

Since, TLS uses PKI, it provides two types of authentication, namely, mutual authentication and server authentication. If a highly secure communication is required, then mutual authentication comes in handy even though it is very computationally expensive due to public key encryption. Server side authentication is the one we commonly see these days, like HTTPS. Though this type of authentication provides mid-level security, it is preferred for normal systems, since it reduces the computation cost involved with PKI.

What are some of the pros and cons of using TLS?

Pros:

• It is a recommended security mechanism specified by IETF.
• TLS supports network address translation (NAT) traversal at the protocol layer.
• It ensures privacy.
• It supports user authentication which is very much preferred in e-commerce solutions such as online banking.
• Easier porting to multiple hardware architectures since TLS is implemented at the application level and not at the kernel level.

Cons:

• Mutual and server side authentications require PKI operations. Using PKI makes a system very complex.
• PKI is computationally costly.
• Only one side is authenticated in server side authentication.
• TLS can’t guarantee security for Voice over IP RTP media streams.
• TLS runs on TCP only and not on UDP.

When should we use it?

The only bottleneck with TLS is the public key infrastructure features. TLS is the best choice when a system requires highly secure authentication mechanisms even at the cost of slower sessions and additional complexity. The system that has this type of requirements is fundamentally used in online banking and e-commerce solutions.

References:

http://www.k2esec.com/secure-communications/network-security-protocols-ipsec-vs-tlsssl-vs-ssh-part-ii

Artificial Intelligence: Multiple ways in which it will affect our lives.

Robotics is a field which has boomed since the start of 21st century. Robots in modern days can mimic lots of human actions, for example, walking over an uneven surface, running, climbing stairs, dancing etc. The next step researchers are planning to achieve is to make robots think like humans. Artificial Intelligence is the field that is trying to make machines think analytically. If AI provides such a capability to robots, it will have a very big impact on humans. Lets look at few examples:

Driverless cars: Most of the trains and airplanes in present days are almost entirely controlled by computers. If trains can be driverless, then why not cars? Driverless cars can make our journey safe and take a correct decision in case of an emergency, as reaction time of a computer is much faster than a human. It also helps older people and physically challenged people tremendously in their commute.

Financial implications: AI software can study patterns in a stock market and can help investors tremendously. It will also be able to spot spending changes or credit card use and detect frauds with ease.

Medicine: Only intelligent devices these days can differentiate between life-saving medications and stale medications. If robots are made to think like humans, they can act as assistants to doctors where they not only can pass correct tools but also keep track of doctors’ preferences. May be one day into the future, machines will be capable of performing life saving operations.

Transhumanism: It is one of the extreme applications of AI to human life. It is a cultural and intellectual movement that believes we can use advanced technologies to improve human life. Some of its most important goals of it include, eliminating disabilities, diseases, or even life extension. Though it sounds next to impossible, but a time may come when life expectancy of humans increases to 150 years.

References:

http://dsc.discovery.com/tv-shows/curiosity/topics/ways-artificial-intelligence-will-affect-our-lives.htm

http://www.extremetech.com/extreme/152240-what-is-transhumanism-or-what-does-it-mean-to-be-human

History of Computer Science: Von Neumann Architecture

Computers that were developed in the earlier era had fixed programs. These computers or devices are not completely obsolete. People use these machines because of their simplicity and for training students. You can take an example of a simple calculator; all it does is some basic mathematical operations. Can it do text processing? Absolutely not! How would you feel, if you had to reprogram your device every time your requirements changed or use different devices for different purposes? Tedious right! It led to the invention of stored-program computer.

Von Neumann Model, developed in 1945 is the base of a stored-program computer in which data and instructions are in the same electronic memory. This fact distinguishes it from the Harvard model which stores data and instructions in different memory. On a large scale this treatment of instructions as data is what makes compilers, assemblers and other automated programming model possible.  ENIAC discussed in earlier blog is a stored-program computer. Though Von Neumann Model was developed as early as in World War II, yet it is one of the most popular architecture even today. It has three main components: memory that stores instructions and data, a control unit and arithmetic and logic unit that moves the data and program in and out of memory along with executing these instructions, the last one being a bus through which data flows between the other components.

Von Neumann Model has its drawbacks and few mentioned are:

• It performs inefficiently under modern pipelining architecture.
• One program may break other’s programs, including the operating system and even crash the system.

Program modification by design or by accident can cause a serious bottleneck for this architecture. However, most of these problems can be alleviated by using branch prediction logic, using hybrid architecture by using a cache to separate data and instructions.  This architecture is one of the major milestones in computer science history and its simplicity has maintained its popularity all along.

References:                                                                                        

http://www.csupomona.edu/~hnriley/www/VonN.html http://en.wikipedia.org/wiki/Von_Neumann_architecture

History of Computer Science: Electronic Numerical Integrator and Computer

The first milestone in the History of Computer Science was the invention of the abacus about 2000 years ago. Moving the beads accomplished several simple mathematical operations. Blaise Pascal is usually credited with building the first digital calculator in 1642. It performed addition operations to help his father who was a tax collector. The world’s first commercially successful calculator that could add, subtract, divide and multiply was built by Charles Xavier Thomas, a century later. Around the same time, Charles Babbage proposed the first general mechanical computer called the Analytical engine. It contained Arithmetic Logical Unit (ALU), basic flow control and an integrated memory. Thus began the evolution of computer science. Computers those days looked very different from those that we have today. Let’s take a look at one of them.

In 1945, University Pennsylvania came up with the first electronic computer called Electronic Numerical Integrator and Computer (ENIAC). Can you imagine a computer more than 1000 square-feet? Yes, ENIAC was that big with several fans to prevent overheating of the device. Programmers made use of punch cards or tape to feed program instructions. Though ENIAC could compute 5000 operations in seconds, yet it failed frequently because it consumed 150KW of power, leading to a rumour that lights dimmed in Philadelphia whenever it was switched on. It performed 385 multiplications per second, or forty division operations per second or three square root operations per second.

ENIAC

Were engineers crazy to construct such huge computers? In fact, they were extremely smart; it was their thoughts and ideas that shaped computer science as we know today. Gradual progressions in hardware and software then were accelerated not just due to the demand but due to inane human curiosity. Being a computer scientist myself, and a part of this evolution I can’t wait to contribute and advance this science even further!

References:

http://blog.oup.com/2012/03/short-history-computer-science/

http://ezinearticles.com/?The-History-Of-Computer-Science&id=5239791

http://www.jeremymeyers.com/comp

http://en.wikipedia.org/wiki/ENIAC

File Sharing: Cloud based file sharing

We regularly backup our photos, music and data. Once backed up, it is incredibly easy and convenient to access these files remotely from our laptops, tablets, and smart phones. The well-known products that offer such services include Google Drive, Microsoft Sky Drive, Dropbox, Box, SugarSync and many others. Almost all of them offer the file storage service free of cost up to a certain storage limit. When individuals rely so much on these services it is natural for corporate IT departments to bring in such services into the workplace. Well it does have its pros and cons. 

Let us look at the pros first. Sharing files with multiple people is now a click of a button; it especially reduces the hassles with sharing image heavy presentations and videos. It reduces the costs required to set up a Virtual Private Network (VPN) and manage the file storage servers in an internal Data centre. It also helps with business continuity; a coffee spill on a laptop or any other natural catastrophes does not cause any loss of data. Since it’s a shared file, updating is really easy and everyone is guaranteed to get the latest version of the file. More importantly, companies need not educate their employees on how to use these services as they use the same in their personal lives.

However, there is increased complexity to manage the files outside of the internal data centre. Security is a greatest concern; a malicious hacker can gain access to the entire database at once. A disgruntled employee can copy the entire data into his personal cloud, or corrupt the central database. If companies are relying on a third party cloud then is their data really secure? The third party has complete access the all the data. Downtime of the cloud due to a virus, surrounding weather or power outages are serious concerns.

Fortunately, it is possible to work around the negatives with well drafted and enforced policies. Firstly, rely on cloud providers with security certifications. Have access restrictions in place, so that not everyone has access to each and every file. Create a culture in the company that ensures a sense of responsibility among every employee about confidential corporate data.

Finally, cloud file sharing is a boon, whose advantages weigh far more and the disadvantages can be overcome with proper workarounds. The onus is on every one of us.

References:

http://searchcloudstorage.techtarget.com/feature/Everything-you-need-to-know-about-cloud-based-file-sharing

http://searchconsumerization.techtarget.com/tip/Top-five-personal-cloud-storage-and-file-sharing-services-and-what-they-mean-for-IT

http://hr.blr.com/HR-news/HR-Administration/HR-Strategy/zns-Working-in-cloud-Pros-cons-file-sharing-servic

http://hr.blr.com/HR-news/HR-Administration/HR-Strategy/Part-2-cloud-Pros-cons-file-sharing-services-http://intelasip.nebrina.com/redfort/Secure-File-Sharing/