Browsing by Author "Lin, FM"

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Design and implementation of a fault tolerant ATM switch
(1999-07-01)
Wang, KC
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Lin, FM
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資訊工程學系
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Department of Computer Science
In this paper, we propose a new method to build a fault tolerant ATM switch. Using this method, we can build an ATM switch which has two disjoint paths between each input/ output pair. The key component in the proposed switch is a 2 x 2 FTSE (Fault Tolerant Switching Element), which can be used as the basic building block for high speed ATM switches. The design of the FTSE-based fault tolerant ATM switch is based on a multi-path, self-routing principle. In terms of modularity, the proposed FTSE is suitable for building any multistage interconnection network (MINs). Thus, we can construct an MIN which has two levels of fault tolerance ability, and in which the redundant paths are in proportion to the network size. From the results of mathematical analysis, we conclude that our ATM switch uses fewer switching elements and has more redundant paths than other comparable ATM switches. The ATM switch is described using VHDL. By means of VHDL simulation, we verify the functionality of the switch. We have also synthesized the ATM switch to evaluate its delay and area. The experimental results demonstrate that the reliability/cost ratio of the fault tolerant FTSE-based ATM switch is better than those of other comparable switches.
i-Genome: A database to summarize oligonucleotide data in genomes
(2004-10-09)
Lin, FM
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Huang, HD
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Chang, YC
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Horng, JT
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生物資訊及系統生物研究所
Background: Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. Results: The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. Conclusions: This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.
Identifying the combination of genetic factors that determine susceptibility to cervical cancer
(2004-03-01)
Horng, JT
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Hu, KC
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Wu, LC
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Huang, HD
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Lin, FM
Although infection with high-risk types of human papillomavirus (HPV) has been identified as the primary cause of cervical cancer, only some of those infected go on to develop cervical cancer. Obviously, the progression from HPV infection to cancer involves other environmental and host factors. Recent population-based twin and family studies have demonstrated the importance of the hereditary component of cervical cancer, associated with genetic susceptibility. Consequently, single-nucleotide polymorphism (SNP) markers and microsatellites should be considered genetic factors for determining what combinations of genetic factors are involved in precancerous changes to cervical cancer. This study employs a Bayesian network and four different decision tree algorithms, and compares the performance of these learning algorithms. The results of this study raise the possibility of investigations that could identify combinations of genetic factors, such as SNPs and microsatellites, that influence the risk associated with common complex multifactorial diseases, such as cervical cancer.
MultiProtident: Identifying proteins using database search and protein-protein interactions
(2005-05-01)
Huang, HD
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Lee, TY
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Wu, LC
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Lin, FM
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Juan, HF
Protein identification is important in proteomics. Proteomic analyses based on mass spectra (MS) constitute innovative ways to identify the components of protein complexes. Instruments can obtain the mass spectrum to an accuracy of 0.01 Da or better, but identification errors are inevitable. This study shows a novel tool, MultiProtldent, which can identify proteins using additional information about protein-protein interactions and protein functional associations. Both single and multiple Peptide Mass Fingerprints (PMFs) are input to MultiProtldent, which matches the PMFs to a theoretical peptide mass database. The relationships or interactions among proteins are considered to reduce false positives in PMF matching. Experiments to identify protein complexes reveal that MultiProtldent is highly promising. The website associated with this study is http://dbms104.csie.ncu.edu.tw/.
SpliceInfo: an information repository for mRNA alternative splicing in human genome
(2005-01-01)
Huang, HD
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Horng, JT
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Lin, FM
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Chang, YC
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Huang, CC
We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://Spliceinfo.mbc.NCTU.edu.tw/.