Magnetic field simulation of golay coil

In the field of magnetic resonance imaging (MRI), besides the main magnetic field and the radio frequency (RF) system, the gradient coils system also plays an important role in signal acquisition. Generally, there are 2 transverse gradient coils and 1 longitudinal gradient coil. In this research, the magnetic field (or gradient) generated by the conventional transverse coil, namely the Golay coil was mapped. The calculation algorithm of the magnetic field generated was written in C-programming language, compiled by the GNU-compiler collection (GCC) and was based on a forward analytical approach by using the Biot-Savart Law. The data was then visualized by Gnuplot. The magnetic field was successfully calculated and plotted using open-source softwares running under Ubuntu operating system and will provide valuable data especially for gradient coil designe

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics

Summary: birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware

Magnetic field simulation of golay and maxwell coils

Magnetic field gradient coils are essential in obtaining accurate magnetic resonance imaging (MRI) or nuclear magnetic resonance (NMR) signals by generating magnetic field gradient in each x, y and z direction. Two of the parameters to determine the performance of such gradient coils are the magnetic field linearity and magnetic field gradient uniformity. This research emphasizes on the analysis of the geometrical effect of the conventional Golay-Maxwell pair gradient coils to these two parameters through computer simulation. The results show that the geometrical parameters of ? and d affect Golay coil’s magnetic field gradient. Usable volume is improved 50% while gradient strength is increased 11% when ? is 1600 compared to the original 1200. The increase of d results in increase of usable volume, which is a maximum of 3374 cm3 at 0:8r but a loss of gradient strength of 36% compared to -0.34 mT/m at 0:2r. The other geometrical parameters of Golay coil are found not to affect much on the magnetic field gradient generated because of two reasons; the longitudinal sections of Golay coil do not contribute to Bz generation and the outer arcs are just acting as current return paths. For Maxwell coil, the usable volume can be improved until 19196.128 cm3 when d is 2:0r although the gradient value obtained is lower compared to a maximum of -0.066 mT/m at 1:2r. Application wise, the higher the gradient value and the bigger the usable volume, the better since the resolution can be improved, not to mention, a bigger specimen accomodation. A computer simulation is written fully in Open-source environment and feature variation of output as well as faster vectorized algorithm. The simulation results will definitely provide useful information for gradient coil designers without the need for physical development of prototype

Genome sequence of ralstonia sp. strain PBA, a bacterium involved in the biodegradation of 4-Aminobenzenesulfonate

Ralstonia sp. strain PBA was isolated from textile wastewater in a coculture with Hydrogenophaga sp. strain PBC. Here we present the assembly and annotation of its genome, which may provide further insights into the mechanism of its interaction with strain PBC during 4-aminobenzenesulfonate degradation

Development of a mobile application for amphibian species recognition

The smartphones mobility and its pervasiveness are beginning to transform practices in biodiversity conservation. The integrated functionalities of a smartphone have created for the public and biodiversity specialists means to identify, gather and record biodiversity data while simultaneously creating knowledge portability in the digital forms of mobile guides. Smartphones enable beginners to recreate the delight of species identification usually reserved for specialist with years of experience. Currently, the advent of Android platform has enabled stakeholders in biodiversity to harness the ubiquity of this platform and create various types of mobile application or "apps" for use in biodiversity research and conservation. However, there is an apparent lack of application devoted to the identification in herpetofauna or amphibian science. Amphibians are a large class of animals with many different species still unidentified under this category. Here we describe the development of an app called Amphibian Recognition Android Application (ARAA) to identify frog amphibian species as well as an accompanying field guide. The app has the amphibian taxonomic key which assists the users in easy and rapid species identification, thus facilitating the process of identification and recording of species occurrences in conservation work. We will also present an overview of the application work flow and how it is designed to meet the needs a conservationist. As this application is still in its beta phase, further research is required to improve the application to include tools such automatic geolocation and geotagging, participative sensing via crowdsourcing and automated identification via image capture. We believe that the introduction of this app will create an impetus to the awareness of nature via species identificatio

A protein short motif search tool using amino acid sequence and their secondary structure assignment

We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short motifs searches against PDB structural data from the RCSB Protein Databank, with the users defining the type of secondary structures of the amino acids in the sequence motif. The output utilises 3D visualisation ability that highlights the position of the motif in the structure and on the corresponding sequence. Researchers can easily observe the locations and conformation of multiple motifs among the results. Protein short motif search also has an application programming interface (API) for interfacing with other bioinformatics tools

BIRGHPC: creating instant computing clusters for bioinformatics and molecular dymics

birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware