Kasikrit Damkliang

Taverna Workflow and Supporting Service for Single Nucleotide Polymorphisms Analysis

This paper describes a Taverna workflow environment with supporting web services for Single Nucleotide Polymorphisms (SNP) analysis of genes in shrimp. The workflow is used to investigate SNPs advantages for gene development. Our first workflow environment did not give satisfying results for the phylogenetic tree processes because the data flows between the web services would frequently time-out. Our solution employs local web service interfaces in a cluster, which Taverna accesses with the aid of Soaplab analysis tools. The cluster enables the modified workflow to rapidly process the large amount of sequenced data required by phylogenetic trees, and is highly reliable.

Ranaad-Xek: A Prototype Design of Traditional Thai Musical Instrument Application for Android Tablet PC

This paper proposes a prototype of an architectural, algorithms, and graphical user interface (GUI) design of “Ranaad-Xek,” a traditional Thai musical instrument application for Android tablet PCs. The application provides percussion methods for a player as real as a physical instrument with both of traditional Thai and universal organology. The application supports both of soft and hard sound tone, which generated by percussion mallet types. The player can freely multitouches on wooden bar to produce instrument sounds and record the user own songs.

An efficient process for enhancing genotype imputation in Genome-wide association studies using high performance computing

Genotype imputation based analysis usually consumes computational and data intensive. This paper presents a practical and efficient process for enhancing the genotype imputation based analysis on Single Nucleotide Polymorphism (SNP) using High Performance Computing (HPC). Our process is split into data quality control, haplotype estimation, and imputation. We validate and measure the process on a standard workstation and a server for pilot dataset of chromosome 22 from Genetic Analysis Workshop 16 (GAW16) provided by the North American Rheumatoid Arthritis Consortium (NARAC). The NARAC dataset consists of 2,062 individuals and 545,080 SNP variants. We use 1000 Genomes database as reference panels. Our process correctly and rapidly produces results more than ordinary steps of the genotype imputation based analysis.

Thai Handwriting Practice on Android Tablets

This paper describes the design, implementation, testing, and evaluation of a Thai handwriting practice application for pre-primary school students, aged 4 to 6 years old, aimed at Android tablets. The application provides mechanisms for alphabet validation, score calculation, and handwriting tutorial animations.

Guessing English vocabularies: A game application for children on multiple mobile platforms

This paper proposes a game application prototype of an architectural, algorithms, graphical user interface (GUI) design, implementation, and evaluation for guessing English vocabularies for mobile devices, both smartphones and tablets on multiple platforms supported. The application aims to conduct participation amongst the people who use smartphones and tablets to practice English, especially for children. The guessing words application requires at least two players for each gameplay role acting as hinter and guesser. A competition mode of multiple team gameplay is archived by the Bluetooth connection. The application provides mechanisms for both logical and physical game rules using a devices accelerometer. The players can select playing modes which consisting of four modes such as words and pictures in English vocabularies. The players can also create their own customized games including given vocabulary lists from a teacher. Furthermore, the application prototype has been implemented, built, and technical tested. Full implementation of the game is freely distributed on an on-line place already.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services

Summary At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow’s execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th

A Preliminary Design of Recommended Nutrition and Energy Expenditure Application for Smartphone

This paper proposes the design and a prototype for nutrition recommendation and energy expenditure application. The application runs on iOS smartphones. The application advises the users about their food energy intake in calories and their energy expenditure on exercises in daily life. The application consists of five functions which are food nutrition and exercise list, calories intake and burn history, calories and BMI calculator, food and health articles, and application configuration.

A Prototype of Calligraphy Application Design for Students on Tablet Computer

This paper proposes an architectural design of a prototype for handwriting practice application for pre-primary school students, 4 to 6 years old, on Android tablet computer. The application provides mechanisms for alphabets validation and score calculation. The application also provides handwriting tutorial animation for motivating the students.

Taverna Workflow for Validating BioMart Services

This paper present a novel Taverna workflow for validating BioMart Services. It saves a significant amount of time by avoiding incorrect workflows caused by out-of-date services. It also reduces debugging time by finding out-of-date processor query fields (filters) and output fields (attributes). In addition, it provides associated information required for future validation.