The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the characteristics and patterns of duplicate and shared vertices, which is crucial for bioinformatics software developers. In this paper, we provide the results of parsing KEGG XML files from a graph-theoretical perspective, for future research in the area of automatic layout techniques in biological pathway domains.
Computational Biology ; Metabolic Networks and Pathways ; Systems Biology

Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.
2,5-Dimethoxy-4-Methylamphetamine ; Biology ; Computational Biology ; Indonesia ; Systems Biology

The explosion in biological data resulting from highthroughput experiments requires new software tools to manipulate and display pathways in a way that can integrate disparate sources of information. A visual Java-based CAD tool for drawing and annotating biological pathways with semiautomatic image-processing features is described in this paper. The result of the image-editing process is an XML file for the appropriate links. This tool integrates the pathway images and XML file sources. The system has facilities for linking graphical objects to external databases and is capable of reproducing existing visual representations of pathway maps.
Computational Biology ; Computer-Aided Design ; Explosions ; Software ; Systems Biology

Bioinformatics is the information technology to deal with biological data. Recently emerging systems biology has drawn great interest inspired by world-wide efforts for modeling and analyzing biological processes with a systems perspective. Bioinformatics, which has analyzed multi-omics data such as genomics, transcriptomics, and proteomics, and explored novel biological patterns embedded within the data, now has a transition to its application to systems biology, called systems bioinformatics. Systems bioinformatics includes various research areas: system modeling, system structure and dynamics analysis, causality analysis, and multi-omics data fusion. In this review, we introduce bioinformatics for genomics, transcriptomics, proteomics, and systems biology according to the different aspects of biological processes.
Biological Processes ; Computational Biology ; Genomics ; Proteomics ; Systems Biology

Since its establishment 30 years ago, the discipline of metabolic engineering has developed rapidly based on its deep integration with molecular biology, systems biology and synthetic biology successively, which has greatly contributed to advancing and upgrading biotechnology industry. This review firstly analyzes the current status of academic research and China's competence in the area of metabolic engineering according to the data of papers published in SCI-indexed journals in the past 30 years. Subsequently, the article summarizes the development of systems biology methods and enabling technologies of synthetic biology and their applications in metabolic engineering in the past 10 years. Finally, the major challenges and future perspectives for the development of metabolic engineering are briefly discussed.
Biotechnology ; Industry ; Metabolic Engineering ; Synthetic Biology ; Systems Biology

Phenotypic characteristics of complex diseases such as rheumatoid arthritis are a consequence of interactions of genetic and environmental factors. Biomolecules closely interact with other molecular components and form functional modules, resulting in significant biologic action capability. While traditional biochemical research focuses on a single disease using narrowly constrained data, systems biology aims to interpret large volumes of highly complex and multilevel data obtained from high-through-put technologies to understand how biological systems function as a whole. Such a systems approach to complex diseases, so-called network medicine, can shape our comprehensive understanding of disease mechanisms by identifying modules temporally and spatially perturbed in the context of health and diseases. Given the unmet needs for diagnosis, monitoring, and treatment in rheumatoid arthritis, systems biology is obviously an emerging powerful tool to gain insight into disease mechanisms, study comorbidities, analyze therapeutic drugs and their targets, and discover novel network-based biomarkers.
Arthritis, Rheumatoid* ; Biomarkers ; Comorbidity ; Diagnosis ; Systems Biology

Traditional Chinese medicine (TCM) is the scientific therapeutics derived from the traditional Chinese physician's considerable clinical practice during the long history, with the characteristic of significant clinical therapeutic effects. The therapeutic philosophy of TCM is integrative medicine and pattern differentiation. The ideas of systems biology on the study of TCM were formed after the micro-and macro-outcome of systems biology being used into the practice of study on TCM. It is very important for the inheritance and development of TCM to disclose the basic mechanism of the clinical therapeutic effects of TCM and find new drugs, from the herbal preparation, pharmacology and pharmacokinetic to drug development using modern science technologies based on the theory of TCM.
Medicine, Chinese Traditional ; methods ; Systems Biology ; methods

Medicine, Chinese Traditional ; methods ; Systems Biology

The integration of Chinese medicine (CM) and Western medicine (WM) is the only way for the development of medicine, and it is the best form for unifying systems theory and reductionism. In this paper, systems biology and its application in medical research were discussed. The authors put forward that systems biology may possibly interpret the scientific connotation of the complex theoretic systems of CM, which will make WM to well know the human body and disease. We hold that systems biology is a bridge of integrated CM and WM.
Integrative Medicine ; Medicine, Chinese Traditional ; Systems Biology

With the range of application of computational biology and systems biology gradually expanding, the complexity of the bioprocess models is also increased. To address this difficult problem, it is required to introduce positive alternative analysis method to cope with it. Taking the dynamic model of the epidemic control process as research object, we established an evaluation model in our laboratory. Firstly, the model was solved with nonlinear programming method. The results were shown to be good. Based on biochemical systems theory, the ODE dynamic model was transformed into S-system. The eigen values of the model showed that the system was stable and contained oscillation phenomenon. Next the sensitivities of rate constant and logarithmic gains of the three key parameters were analyzed, as well as the robust of the system. The result indicated that the biochemical systems theory could be applied in different fields more widely.
Computational Biology ; Epidemics ; Humans ; Models, Biological ; Nonlinear Dynamics ; Systems Biology ; Systems Theory