Scientific Computing: Bioinformatics and the Role of Computers in Modern Biology

Currently, computers are using largely in most of the fields in science. There should not be any arguments about how sufficient benefits of applying computational technology bring to our lives. Bioinformatics and computational biology are where scientific computing lands its touch into the biology field in which computers are used to gather, analyze the biological information. Computational biology is the study about biology by using computer tools and techniques, and  its goal of learning is about new biology, species, or living system. Bioinformatics, however, uses computer as a powerful tool to solve its complex biological data such as Human Genome project. Both are very important under aspects of science and engineering.

In this post, I would like focus more on Bioinformatics’ applications and how computer plays an important role in modern biology.

DNA Sequence in analyzing computer tool

1. Collect and process data: biological data is one of the most complicated data that human can be able to analyze with the help from computer. For example, DNA sequencer and spectrophotometer are common lab equipment that can get connected to a computer to convert its analog to digital data.

2. Track and manage experiments: without computer running restlessly in most of the labs nowadays, it is impossible to get the data tracked and managed. Most automated lab management works are using computational software to maintain all the result records.

3. Store and unify data: database references are very important in biology research. It is a need of having a public database that can easily access and get updated throughout for all scientists within the field. A public biological database can be built and managed as same as any computational database.

Molecular Dynamics Simulation

4. Analyze and predict from collected data: this is all about bioinformatics can do. A computational tool can help to recognize and extract a pattern from experimental data.

5. Annotation and simulation: when finding a new uncharacteristic data, an annotation tool can use automated sequence to compare with a pattern to identify any new potential molecules such as proteins, acid amides, DNA, RNA in a genome system. In addition, a simulation tool can help to draw a biochemical model of interactive molecules in a testing system.

References:

1. Bioinformatics & Computational Biology

http://rbaltman.wordpress.com/2009/02/18/bioinformatics-computational-biology-same-no/

2. Computers + Biology = Bioinformatics

http://oreilly.com/news/bioinformatics_0401.html

Computer Graphics

Computer graphics are changing the world in all aspects of our lives. It is used today in many different areas of science, business, education, entertainment, medicine, etc. Behind the algorithms for generating visual images synthetically; computer graphics are used as a tool that can be able to bring all people visual information sampled from the real world. In this post, I would like to discuss how computer graphics benefits to us in 4 of the following areas.

1. User interface
From the very first personal computer in 1970s, user interface was a big invention of computer history. Without a user interface, we might now have to type a very complex command to run some normal tasks. All computers’ operation systems and applications implement the user interface to manage and operate multiple task activities. For example, point-and-click facility via a user interface can help users to select a menu, an icon on the computer screen. It clearly changes the way how people interact with a device.

First User Interface of Computer History - Apple Lisa I

2. Computer aided drafting and design (CADD)
Currently, computer graphics really help in designing electronic components, architectural design, mechanical devices, etc. The designer can generate an engineering drawing using 2-dimensional and 3-dimensional via computer graphics software. As a result, it can increase the productivity and improves the quality of the work.

Computer Graphics is wildly used in CADD

3. Simulation and modeling
Computer graphics can help to simulate any condition, which is encountered in the real world. Through simulation, people can learn how to react via the programmed environment that they might have to face in the real one. For example, a training program can really help the pilot react with a rough environment condition in a simulated flight, or astronauts can practice in a non-gravity simulator to get used to with the feeling of weightlessness. A video graphics simulator can also help to improve and optimize of a system or product via the reaction of the trainee.

A flight simulator for pilot training

4. Entertainment
Computer Generated Imagery (CGI) rendering technology is currently being used in most movies. From the 2D to 3D cartoon such as Lion King and Toy Stories series, or scientific movies like Jurassic Park and Avatar, CGI rendering effect was an important key to their success. Meanwhile, all games in Xbox, Play Station and PC are built from graphic software programming. Without computer graphics, our entertainment world would have been so different right now. It changes everything.

CGI is present in most of modern film nowadays

References:
Computer Graphics
http://computegraphics.blogspot.com/2012/10/v-behaviorurldefaultvmlo.html

Communications and Security

Communications and Security are a challenge for most computer scientists, who are trying to build a secure and reliable system against attack from outsiders. There are too many technologies that applying for such different services in a communication system like VoIP, video conferences, chat, and email. The problem is how a security system can handle all of them and protect users at a time. As the way people connect together through computers has become more complex and more accessible, the security threat clearly has increased.

In this post, I would like to discuss the solution that can make our communication system more secure and reliable in connecting people-to-people.


1. Setting up properly a network firewall

One of the best solutions to against attack is to block all unrecognized traffic come in and out the network. The system should only allow traffic from trusted sources. Most of the firewall software has a blacklist of websites, and IP addresses that are being used to attack common users. Firewall will block all traffic from those ones in the list. It is important that users need to get the list updated because the malicious sites always increase by the time.





2. Deploy a Virtualized Private Network (VPN) for remote users 
Currently, most of the routers and firewalls support VPN. As the devices that support VPN are now very common and affordable, the system needs to get the VPN deployed properly for all remote users. This is one way to make the connected devices from any public Internet services can go through an encrypted tunnel to the system securely. As a result, VPN will keep all the traffic in-out the system safe.

3. Turn off all unused features and services in the system
One of the easy ways to protect the network is to turn off all unused features and services. It likes a house that has a lot of doors, and the owner cannot handle all guests come in and out if all the doors are open at once. If a feature or service is not being used, we should turn it off to reduce the potential attacks and improve network security. Another benefit from this is to improve the system performance, as the system will use fewer resources to operate all activities. Using each feature and service in intended purpose will keep the network securely.


4. Monitor all the call logs
For a communication system, monitoring all the call logs is very important to track down the attack and take action early. In network security, reading the system logs is only way to know what is going on in the system. Setting a baseline for a normal activity is also important. When pulling a call log report, the system can notice users if all recorded activities exceed the baseline. It will help to avoid the system getting compromised from outsiders.

References:
1. Tips for an Effective Unified Communications Security Strategy
http://www.smbnation.com/content/news/entry/guest-blog-7-tips-for-an-effective-unified-communications-security

2. Communication Security (COMSEC)
http://www.securestate.com/Federal/ESS/Pages/Communication-Security-COMSEC.aspx