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    Towards reproducible computational drug discovery
    (2020-01-28)
    Schaduangrat, Nalini
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    Lampa, Samuel
    ;
    Simeon, Saw
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    Gleeson, Matthew Paul
    ;
    Spjuth, Ola
    The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference. This article provides an in-depth coverage on the reproducibility of computational drug discovery. This review explores the following topics: (1) the current state-of-the-art on reproducible research, (2) research documentation (e.g. electronic laboratory notebook, Jupyter notebook, etc.), (3) science of reproducible research (i.e. comparison and contrast with related concepts as replicability, reusability and reliability), (4) model development in computational drug discovery, (5) computational issues on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol. In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations (i.e. to drive the project further by introducing new ideas, growing the data, augmenting the code, etc.). It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.
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    Selection of a minimal number of significant porcine snps by an information gain and genetic algorithm hybrid model
    (2019-01-01)
    Rathasamuth, Wanthanee
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    Pasupa, Kitsuchart
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    Tongsima, Sissades
    A panel of a large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pigs. With the advent of SNP-array technology, a genome-wide genetic profile of a specimen can be easily observed. Among the large number of such variations, there exists a much smaller subset of the SNP panel that could equally be used to correctly identify the corresponding breed. This work presents a SNP selection heuristic that can still be used effectively in the breed classification. The features were selected by combining a filter method and a wrapper method-information gain method and genetic algorithm-plus a feature frequency selection step, while classification used a support vector machine. We were able to reduce the number of significant SNPs to 0.86 % of the total number of SNPs in a swine dataset with 94.80 % classification accuracy.
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    Nerve communication model by bio-cells and optical dipole coupling effects
    (2013-12-01)
    Zainol, Farrah Dilla
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    Thammawongsa, Nopparat
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    Mitatha, Somsak
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    Ali, Jalil
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    Yupapin, Preecha
    A novel design of nerve communications and networks using the coupling effects between bio-cells and optical dipoles is proposed. The electrical signals are coupled to the dipoles and cells which propagate within the optical networks for long distance without any electromagnetic interference. Results have shown that the use of optical spins in the spin networks, referred as Spinnet, can be formed. This technique can be used to improve the nerve communication performance. It is fabricated as a nano-biotic circuit system, and has great potential for future disability applications and diagnosis of the links of nerves across the dead cells. © 2013 Informa Healthcare USA, Inc.
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    An application of second derivative of Gaussian filters in fingerprint image enhancement
    (2010-09-06)
    Choomchuay, Somsak
    ;
    Sihalath, Keokanlaya
    In this paper we demonstrate the use of second derivative of Gaussian filters (SDG) together with pyramid technique for fingerprint image enhancement. The quality of enhanced image is measured by the success in core point detection employing poincare method. DB1-A of FVC-2004 database is used as an input in our experiment. It is found that the SDG works well and can offer the similar filtering performance as another directional filter: Gabor filter. Once the SDG is employed in the pyramid technique, the enhanced image is superior to that of applying SDG only (without pyramid scheme). ©2010 IEEE.