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