Most biological systems are by nature hybrids consist of interacting discrete and continuous components,which may even operate on different time scales. Therefore,' it is desirable to establish modeling frameworks...
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Most biological systems are by nature hybrids consist of interacting discrete and continuous components,which may even operate on different time scales. Therefore,' it is desirable to establish modeling frameworks that are capable of combining deterministic and stochastic, discrete and continuous, as well as multi-timescale features. In the context of molecular systems biology, an example for the need of such a combination is the investigation of integrated biological pathways that contain gene regulatory, metabolic and signaling components, which may operate on different time scales and involve on-off switches as well as stochastic effects. The implementation of integrated hybrid systems is not trivial because most software is limited to one or the other of the dichotomies above. In this study, we first review the motivation for hybrid modeling. Secondly, by using the example of a toggle switch model, we illustrate a recently developed modeling framework that is based on the combination of biochemical systems theory (BST) and hybrid functional Petri nets (HFPN). Finally, we discuss remaining challenges and future opportunities.
Many biological systems are genuinely hybrids consisting of interacting discrete and continuous components and processes that often operate at different time scales. It is therefore desirable to create modeling framew...
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This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany throu...
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This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://***/.
The use of microfluidic systems in the life sciences is still limited due to the high-level fabrication expertise required for construction. A novel assembly approach for microdevice construction is presented. This ap...
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In this study, we attempts to develop a sensing method to detect mismatched DNA in order to diagnose cancer. The sensing method will be developed to use for early diagnosis of cancer. Thus, protein immobilization was ...
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In this study, we attempts to develop a sensing method to detect mismatched DNA in order to diagnose cancer. The sensing method will be developed to use for early diagnosis of cancer. Thus, protein immobilization was applied on the surface of the sensor in order to facilitate the detection of mismatched DNA. This method was designed to achieve the Ni-His-Tag to selectively bond with MutS, which has a covalent bond with the His-Tag, by using Ni-NTA. This method is troublesome because it involves a number of repeated composition processes. This method need gold surface to immobilize NTA (nitrotriamino acid). But this process is very complicated and expensive cost. Therefore, we try to immobilize NTA using PMMA (poly methyl methacrylate) polymer in this research to improve this method. In this study revealed that we could directly immobilize the NTA to the PMMA substrate not used Gold substrate. Also, we could directly immobilize the MutS to the NTA using the EDC solution. In addition, we can expect that the mismatched DNA can be detected from the results.
The study of gene function is critical in various genomic and proteomic fields. Due to the availability of tremendous amounts of different types of protein data, integrating these datasets to predict function has beco...
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The study of gene function is critical in various genomic and proteomic fields. Due to the availability of tremendous amounts of different types of protein data, integrating these datasets to predict function has become a significant opportunity in computational biology. In this paper, to predict protein function we (i) develop a novel Bayesian framework combining relational,hierarchical and structural information with improvement in data usage efficiency over similar methods, and (ii) propose to use it in conjunction with an integrative protein-protein association network, STRING (Search Tool for the Retrieval of INteracting Genes/proteins), which combines information from seven different sources. At the heart of our work is accomplishing protein data integration in a concerted fashion with respect to algorithm and data source. Method performance is assessed by a 5-fold cross-validation in yeast on selected terms from the Molecular Function ontology in the Gene Ontology database. Results show that our combined use of the proposed computational framework and the protein network from STRING offers substantial improvements in prediction. The benefits of using an aggressively integrative network, such as STRING, may derive from the fact that although it is likely that the ultimate gene interaction matrix (including but not limited to protein-protein, genetic, or regulatory interactions) will be sparse, presently it is still known only incompletely in most organisms, and thus the use of multiple distinct data sources is rewarded.
We propose a method for microdevice construction where non-expert users can assemble the blocks on glass slides to build their custom devices in minutes without any complicated fabrication steps. This approach involve...
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ISBN:
(纸本)9780816910502
We propose a method for microdevice construction where non-expert users can assemble the blocks on glass slides to build their custom devices in minutes without any complicated fabrication steps. This approach involves prefabrication of individual microfluidic assembly blocks (MABs) in PDMS are pre-fabricated and readily assembled to form microfluidic systems. We describe the construction process, the assembly of the devices, and various bonding techniques to accomplish hermetic assembly. Finally, we demonstrate common microfluidic applications including laminar flow development, valve control, and cell culture.
The effectiveness of the visual feedback to improve ability with the sense and muscular strength of human in our bicycle system was quantitatively verified in our study. Experiments were performed to find the factors ...
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The effectiveness of the visual feedback to improve ability with the sense and muscular strength of human in our bicycle system was quantitatively verified in our study. Experiments were performed to find the factors related to the training of equilibrium sense. The subjects consisted of young and the aged and the group of young people was compared against the group of the aged. We investigated three different training modes, non-visual feedback (NVF), visual feedback of the weight (VFW), and visual feedback of the center of pressure (VFC) and measured the riding time and speed, the weight shift, and the center of pressure (COP) for twenties and seventies. The results showed that the running capability of the young and the aged became much better after repeated training. In addition, it was found out that the ability to control postural balance and the capability of equilibrium sense were improved with the presentation of the visual feedback information. These results will be effective in the diagnosis of equilibrium sense and vestibular function with the aged.
Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Bec...
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The Gene Ontology (GO) offers a comprehensive and standardized way to describe a protein's biological role. Proteins are annotated with GO terms based on direct or indirect experimental evidence. Term assignments ...
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ISBN:
(纸本)9812560467
The Gene Ontology (GO) offers a comprehensive and standardized way to describe a protein's biological role. Proteins are annotated with GO terms based on direct or indirect experimental evidence. Term assignments are also inferred from homology and literature mining. Regardless of the type of evidence used, GO assignments are manually curated or electronic. Unfortunately, manual curation cannot keep pace with the data, available from publications and various large experimental datasets. Automated literature-based annotation methods have been developed in order to speed up the annotation. However, they only apply to proteins that have been experimentally investigated or have close homologs with sufficient and consistent annotation. One of the homology-based electronic methods for GO annotation is provided by the InterPro database. The InterPro2GO/PFAM2GO associates individual protein domains with GO terms and thus can be used to annotate the less studied proteins. However, protein classification via a single functional domain demands stringency to avoid large number of false positives. This work broadens the basic approach. We model proteins via their entire functional domain content and train individual decision tree classifiers for each GO term using known protein assignments. We demonstrate that our approach is sensitive, specific and precise, as well as fairly robust to sparse data. We have found that our method is more sensitive when compared to the InterPro2GO performance and suffers only some precision decrease. In comparison to the InterPro2GO we have improved the sensitivity by 22%, 27% and 50% for Molecular Function, Biological Process and Cellular GO terms respectively.
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