YeonJung Mun

 

 In bioinformatics, biological data are considered as information rather than the organism itself. With the help of bioprogramming the data can be analyzed and studied in forms of statistical or computational use. 

 

Bioinformatics

Bioinformatics is the combination of two words: biology and information. In this field of study, biological subjects are considered differently than living organisms. Rather, all biological data are regarded as information. Simply put, the major difference between biology and bioinformatics is the difference in views of biological data. Therefore in bioinformatics, the data can be analyzed and studied using statistical or computational programs using computers.

 

Bioprogramming

Bioprogramming is all programming activities for analyzing biological data.

 

Programming

Programming is a process that makes new algorithm from programming languages called codes through a compiler. It can convert a set of programming languages into executable programs. Programs can perform various activities like computation, analysis, algorithmic flow, and more.

The computer is the electrical machine or device that carries out the programs. Computers exist in many different forms such as desktop, laptop, tablet, and etc.

 

Compiler

Compiler is a program that transforms programming languages into computer languages. With this process, computer can recognize the commands. The compilers have own specific programming language. C⁺⁺, for example, has c language. They are classified according to the languages and the operating systems.

 

Programming language

Programming languages are generally high-level languages that are used in coding by programmers.If you compare the programming to a country, then the language is the communication medium. The 3 major types of bioprogramming languages are S, R, and Matlab. All of them are for statistical and computational use. Grammar is the rule of the languages.

 

Perl programming

Perl is a programming language that supports scripts called a script lanuguage. It is developed by Larry wall in 1987. It is a powerful tool for varied applications such as network programming, finance, and bioinformatics. An operating system of perl is basically Linux but almost systems support the program. 

(www.perl.org)

 

BioPerl programming

BioPerl is a collection of Perl modules for biological data processing. It is an open source software for biological applications in bioinformatics. In the Human Genome Project, the program has played a central role.

(www.bioperl.org)

 

BioOS

BioOS denotes an operationg system for bioinformatics

(www.bioos.org) 

 

Classroom Discussion

What is a lecture?

 Lecture is a form of presentation that conveys information and opens a discussion time. Not only does lecture require the informative material to teach people, communication between the participants takes a big role. Two-way communication between the lecturer and audience is one type and multi-way communication between the audiences is another. Also, by orally presenting the information, the audience can increase the efficiency of comprehending, and by asking questions and getting answers, full knowledge is transmitted.

What is real?

 A real object must have atoms to be composed of. Every material in the “real world” consists of atoms and molecules. Sometimes they are unable to touch, feel, see, or smell by naked human sense, but as long as they are made of atoms, they are real. In that sense, cyber space is not real. They are just imaginary space which is expressed in special method such as electrical monitors. Codes are similar to our thoughts or opinion; in other words, they are just an expression of real object (especially human in this case). What is real is the medium that transmits that expressions.

 

Genomics

Genomics is the study of the whole genetic system involving the sequencing of DNA, analyzing structure and function of genes, and more.

 

The Human Cancer Genome Project

     A group of scientists works on a megaproject which aims to catalog all somatic mutations from primary tumors. By detecting major oncogenes and regulatory regions, clinical treatment can be applied in order to fight cancer. By this way, there would be less or none gene products of mutated regions, thus suppressing cancer. 
     However, questions arise: are primary tumors the appropriate focus for the cure and therapeutic use for cancer? Experiments of treatment intervening in cancer networks at a single oncoprotein or tumor suppressor protein have bought mixed results. The approach was affective in some types of cancers, but the most deadly ones like breast, prostate, and lung cancer, the effect was rather insignificant. Therefore, the author of this paper doubts this megaproject because of two main reasons. First, even though curing primary tumor-related gene is effective, it is unlikely to eradicate cells that have already left the tumor and that are evolving along different genomic trajectories. Second, evidences on the effects of methylation changes on tumors and relevance between aneuploidy and caner are increasing. These study areas might be alternative breakthroughs.
     In conclusion, as the author says that “the human cancer genome project is fundamentally flawed”, questions remain for the role of genomics in cancer treatment. Would they still take the big part in cancer treatments? Or was the cancer genome project just a waste of effort? The answers can be disputable depending on situations, but I still believe that the project was significant. Thanks to the work, the information of cancer-causing gene and its regulatory sites have been discovered. While the appliance to clinical use is uncertain, the study was worth a shot.

 Miklos, George L Gabor. "The Human Cancer Genome Project—One More Misstep in the War on Cancer." Nature biotechnology 23.5 (2005): 535-37. Print.<o:p></o:p>

Transcriptomics

Proteomics

Proteomics in the Diagnosis of Autism

Autism is a neurodevelopmental disease that is associated with multi-factors including environmental, genetic, and neurological perspectives. The scientists have long been researched about the cure of this disorder, but the full recovery seems to be far further in the future. However, recently biological researchers have discovered a way to diagnose this disease using proteomics. Proteomics is the combination of proteins and genomes: the whole study of quantitative and qualitative protein functions in various types of tissues. It has already been proven with the usefulness in discovering biomarkers for cancer or other neurodevelopmental disorders and the effect of several drugs. Thus, the article shows an example of proteomic approach to autism and explains about its capabilities.
             A scientist named Junaid researched about the abnormal protein expression in 8 brains of autism patients. Out of eight brains, four showed an increase in polarity of glyoxalase I, and the sequencing result revealed a single nucleotide polymorphism causing an AlaGlu exchange. He discovered that this set of gene has some effects for the aetiology of autism. Other than this study, with the help of many useful biological techniques like 2-D gel electrophoresis and mass spectrometry, study of proteins has been helpful in studying biomarkers for autism.
             The author argues for the important role of proteomics in autism biomarker research. However, drawbacks exist in this type of approach. Only small part of protein role was detected to be effective, and the high abundance protein blocks the detection of the activities of low abundance protein. Is proteomics still useful despite these hindrances? The author says it is worth a go, but in my opinion, the study of genomes is the first step to be taken. A priori approach is the most fundamental and first to study proteins. To know the sequence of amino acids we should know the codons that translate the amino acids, which lead to the study of genes. Without knowing deeply about genes (Genomic approach of autism is still under research), proteomics may be useful in diagnostic aspect but not enough in cure. I believe the ultimate goal of disease study is the treatment. Thus proteomic approach may be insufficient.
             In conclusion, the study of proteins in autism is proven to be effective in diagnosing the disorder. Specific details are introduced briefly above, and using these as a supporting fact, the author argues for the importance of proteomics in autism study. This may be true but not sufficient in the full cure of the disease. Therefore, since autism is a very complicated disorder, several studies should be propelled in various aspects including genomics and proteomics.

 

Laila, AL-Ayadhi, and Dost Muhammad Halepoto. "Role of Proteomics in the Discovery of Autism Biomarkers." Journal of the College of Physicians and Surgeons Pakistan 23.2 (2013): 137-43. Print.

 

Epigenomics and Phenomics

Canceromics and Geromics

Reference