• Journal of Microbiology and Biotechnology
• /
• v.16 no.6
• /
• pp.832-848
• /
• 2006

Systems biology has recently become an important research paradigm that is anticipated to decipher the metabolic, regulatory, and signaling networks of complex living organisms on the whole organism level. Thus, various research outputs are being generated, along with the development of many tools and resources for systems biology research. Accordingly, this review provides a comprehensive summary of the current resources and tools for systems biology research that will hopefully be helpful to researchers involved in this field. The resources are categorized into the following five groups: genome information and analysis, transcriptome and proteome databases, metabolic profiling and metabolic control analysis, metabolic and regulatory information, and software for computational systems biology. A summary table and some future perspectives are also provided.

• Journal of Physiology & Pathology in Korean Medicine
• /
• v.30 no.6
• /
• pp.376-384
• /
• 2016

Systems biology is an emerging field aiming at a systems level understanding of living organisms and focusing on the characteristics of the whole network of them. The emergence of systems biology is partly because of the availability of huge amounts of data on organisms and the extensive support of computational technologies as the tools for understanding complex biological systems. The scientific understanding of Korean medicine has been obstructed because of the lack of proper methods examining the complex nature and the unique property of it. However, systems biology could give a chance understanding Korean medicine objectively and scientifically. Pattern classification is a unique tool of Korean medicine to diagnose and treat patients and systems biology would give a useful tool to interpret pattern classification. Various omics technologies has been used to explain the relations between pattern classification and biological factors and then many characteristics of pattern classification in various diseases have been discovered. Therefore, pattern classification could be a bridge to understand the features and differences of western medicine and Korean medicine and it could be a basis to develop pattern-based personalized medicine.

• East Asian mathematical journal
• /
• v.38 no.4
• /
• pp.463-496
• /
• 2022

The purpose of this study is to analyze the mathematical creativity and computational thinking of mathematically gifted elementary students through a convergence class using programming and to identify what it means to provide the convergence class using Python for the mathematical creativity and computational thinking of mathematically gifted elementary students. To this end, the content of the nine sessions of the Python-applied convergence programs were developed, exploratory and heuristic case study was conducted to observe and analyze the mathematical creativity and computational thinking of mathematically gifted elementary students. The subject of this study was a single group of sixteen students from the mathematics and science gifted class, and the content of the nine sessions of the Python convergence class was recorded on their tablets. Additional data was collected through audio recording, observation. In fact, in order to solve a given problem creatively, students not only naturally organized and formalized existing mathematical concepts, mathematical symbols, and programming instructions, but also showed divergent thinking to solve problems flexibly from various perspectives. In addition, students experienced abstraction, iterative thinking, and critical thinking through activities to remove unnecessary elements, extract key elements, analyze mathematical concepts, and decompose problems into small components, and math gifted students showed a sense of achievement and challenge.

• Bioinformatics and Biosystems
• /
• v.1 no.1
• /
• pp.1-7
• /
• 2006

현대 생물학은 온통 정보의 홍수에 넘쳐나고 있다. 이렇게 쏟아져 나오는 정보들을 체계적으로 정리하고 이해하고 파악하는 것은 매우 중요하다고 하겠다. 생물정보학은 이렇게 쏟아져 나오는 정보들을 수학, 전산학, 정보학 등의 방법론을 사용하여 체계화시키려는 새로운 학문이고 미래 지향적 융합 분야이다.

• Journal of applied mathematics & informatics
• /
• v.26 no.5_6
• /
• pp.1037-1048
• /
• 2008

The purpose of this paper is to present a differential equation with delay from biological excitable medium. Existence, uniqueness and data dependence (monotony, continuity, differentiability with respect to parameter) results for the solution of the Cauchy problem of biological excitable medium are obtained using weakly Picard operator theory.

• Proceedings of the Korean Biophysical Society Conference
• /
• 2002.06b
• /
• pp.14-14
• /
• 2002

Genome project is a research for discovering genomic information. Human genome sequence, under the title of HGP(human genome project), was drafted successfully at the end of June, 2000. And the academic world soon predicted that related research field would be activated and since then bioinformatics has been in the spotlight.(omitted)

• BMB Reports
• /
• v.41 no.3
• /
• pp.184-193
• /
• 2008

Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems biology investigates such systems by producing comprehensive global data that represent different levels of biological information, i.e., at the DNA, mRNA, protein, or metabolite levels, and by integrating this data into network models that generate coherent hypotheses for given biological situations. This review presents a systems biology framework, called the 'Integrative Proteomics Data Analysis Pipeline' (IPDAP), which generates mechanistic hypotheses from network models reconstructed by integrating diverse types of proteomic data generated by mass spectrometry-based proteomic analyses. The devised framework includes a serial set of computational and network analysis tools. Here, we demonstrate its functionalities by applying these tools to several conceptual examples.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.11 no.3
• /
• pp.971-977
• /
• 2010

A flood of biological data has caused many challenges in computing. Bioinformatics, the application of computational techniques to analyze the information associated with biomolecules on a large-scale, has now firmly established itself as an interdisciplinary subject in molecular biology, and encompasses a wide range of subject areas from structural biology, genomics, proteomics, systems biology, biostatistics to computer science. In this review, I provide an introduction and overview of the current state of bioinformatics. Looking at the types of biological information and databases that are commonly used, I also deals with some of bioinformatics application domains which are closely related to areas of computer science.

• BMB Reports
• /
• v.42 no.11
• /
• pp.697-704
• /
• 2009

Membrane proteins play important roles in the biology of the cell, including intercellular communication and molecular transport. Their well-established importance notwithstanding, the high-resolution structures of membrane proteins remain elusive due to difficulties in protein expression, purification and crystallization. Thus, accurate prediction of membrane protein topology can increase the understanding of membrane protein function. Here, we provide a brief review of the diverse computational methods for predicting membrane protein structure and function, including recent progress and essential bioinformatics tools. Our hope is that this review will be instructive to users studying membrane protein biology in their choice of appropriate bioinformatics methods.

• Genomics & Informatics
• /
• v.11 no.1
• /
• pp.55-57
• /
• 2013

Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.