An evaluation of galaxy and ruffus-scripting workflows system for DNA-seq analysis

>Magister Scientiae - MScFunctional genomics determines the biological functions of genes on a global scale by using large volumes of data obtained through techniques including next-generation sequencing (NGS). The application of NGS in biomedical research is gaining in momentum, and with its adoption becoming more widespread, there is an increasing need for access to customizable computational workflows that can simplify, and offer access to, computer intensive analyses of genomic data. In this study, the Galaxy and Ruffus frameworks were designed and implemented with a view to address the challenges faced in biomedical research. Galaxy, a graphical web-based framework, allows researchers to build a graphical NGS data analysis pipeline for accessible, reproducible, and collaborative data-sharing. Ruffus, a UNIX command-line framework used by bioinformaticians as Python library to write scripts in object-oriented style, allows for building a workflow in terms of task dependencies and execution logic. In this study, a dual data analysis technique was explored which focuses on a comparative evaluation of Galaxy and Ruffus frameworks that are used in composing analysis pipelines. To this end, we developed an analysis pipeline in Galaxy, and Ruffus, for the analysis of Mycobacterium tuberculosis sequence data. Furthermore, this study aimed to compare the Galaxy framework to Ruffus with preliminary analysis revealing that the analysis pipeline in Galaxy displayed a higher percentage of load and store instructions. In comparison, pipelines in Ruffus tended to be CPU bound and memory intensive. The CPU usage, memory utilization, and runtime execution are graphically represented in this study. Our evaluation suggests that workflow frameworks have distinctly different features from ease of use, flexibility, and portability, to architectural designs

Influence of Weed Control Methods on Viability and Vigour of Maize (Zea mays L.) Seeds

Weed control method of choice should achieve the objective of controlling weeds without sacrificing seed quality. The influence of Combination of mechanical method (slashing at 2, and 4 week intervals), and herbicide (pre-emergence and post emergence) for weed control in maize on seed quality (viability and vigour) of maize seeds were evaluated.. Field and laboratory experiments were conducted to investigate the influence of pre-emergence (Diuron 50% SC {N (3, 4-dichlorophenyl) N, N-dimethyl urea} and post-emergence (Atrazine 50FW-{6 chloro-N-methyl-N-(1-methylethyl) 1, 3, 5-triazine, 2, 4 diamine}) herbicides either alone, or in combination with slashing at two and four-week, on seed quality. Combination of pre-emergence herbicide and slashing 2-weeks after planting  slashing gave the highest viability (91.37%) and lowest conductivity value (2.79 µS/cm/g), whereas combination of post emergence herbicide and 4 week slashing gave the lowest viability (77.67%) and the highest conductivity value (15.71 µS/cm/g). In accelerated ageing test, combination of pre-emergence herbicide with either 2 week slashing, or 4 week slashing  WAP gave the highest viability (84%), whereas combination of post emergence herbicide with 2 week slashing gave the lowest viability (51.33%) and lowest germination rate index (10.37). Combination of pre-emergence herbicide and 2-week slashing is the best complementary option for weed control in maize seed crop. Keywords; pre-emergence, post-emergence herbicides,  seed physiology,  maize seed viabilit

An Investigation of the Statistical Distribution of Total Station Measured Data

It has been investigated and discovered that the Global Positioning System (GPS) measured quantities are normally distributed [1]. Can we say the same of other digital equipment used for measurement in surveying? In this paper, an attempt is made to investigate whether or not the Total Station, which is digital equipment, measured quantities are normally distributed. The data used are the repeated Total Station measured distances of a line at the Federal Polytechnic, Ado-Ekiti. The investigation is carried out using both the graphical approach and numerical testing. The chi-square for goodness-of-fit test was used in the numerical testing. The plotted histogram and normal curve shows that the observed quantities of a total station instrument are normally distributed. The computed statistic (T) (5.4655) is neither more than the table statistic (T) (17.53) at the upper limit) nor less than the table statistic (T) (at lower limit). Therefore, the Null hypothesis which states that total station measured quantities are normally distributed is not rejected at five percent level of significance. It is concluded that total station measured quantities are normally distributed

SysBiolPGWAS: Simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets

Post-genome-wide association studies (pGWAS) analysis is designed to decipher the functional consequences of significant single-nucleotide polymorphisms (SNPs) in the era of GWAS. This can be translated into research insights and clinical benefits such as the effectiveness of strategies for disease screening, treatment and prevention. However, the setup of pGWAS (pGWAS) tools can be quite complicated, and it mostly requires big data. The challenge however is, scientists are required to have sufficient experience with several of these technically complex and complicated tools in order to complete the pGWAS analysis. We present SysBiolPGWAS, a pGWAS web application that provides a comprehensive functionality for biologists and non-bioinformaticians to conduct several pGWAS analyses to overcome the above challenges. It provides unique functionalities for analysis involving multi-omics datasets and visualization using various bioinformatics tools. SysBiolPGWAS provides access to individual pGWAS tools and a novel custom pGWAS pipeline that integrates several individual pGWAS tools and data. The SysBiolPGWAS app was developed to be a one-stop shop for pGWAS analysis. It targets researchers in the area of the human genome and performs its analysis mainly in the autosomal chromosomes

Development of a Single-Axis Sun Seeker using Three Sensors

The output power generated by the solar photovoltaic panel is directly proportional to the amount of solar energy it receives. Therefore, for maximum efficiency, a solar photovoltaic panel must be perpendicular to the sun. As a result of this, a tracking device is required to ensure that solar panels are always directly perpendicular to the direct component of the sun. Such a tracking device is referred to as a sun seeker. This research work describes the development of a single-axis sun seeker using three sensors. Light-dependent resistors are used as sensors. The light intensity received by two of the sensors is compared by two comparators and an appropriate signal is sent to the driving mechanism which moves the solar panel tray until the right and left sensors receive an equal amount of light intensity. The middle sensor was designed to activate the speed control unit of the system when it senses the required light intensity. The whole system runs on a 12V rechargeable battery. A battery charger circuit with automatic cut-off was incorporated to the design to keep the battery topped-up and to prevent overcharging

Gas Chromatography-Mass Spectrometric (GC-MS) Analysis of Ethanolic Extract of the Peel of Dioscorea bulbifera Linn (Air Potatoe)

The bioactive chemical compounds in the ethanolic extracts of the peel of Dioscorea bulbifera Linn, native to Nigeria was investigated and characterized using gas chromatography-mass spectrometric (GC-MS) analysis. The relatively high concentration of the phytochemicals in the peel of this tuber; saponin (32.28mg/g), terpenoid (22.90mg/g), cardiac glycoside (15.90mg/g), flavonoid (9.17mg/g), tannin (4.79mg/g) and phlobatannin (1.87mg/g), was the most attractive factors that triggered the present study. The GC-MS analysis of the ethanolic extract of the peel of D. bulbifera shows 4 prominent peaks as R-(-)-1,2-Propanediol (C3H8O2) with retention time of 6.103min and the highest peak area of 86.05%; 1-Methylhexylhydroperoxide (C7H16O2) with retention time of 42.567min and peak area of 5.57%; Cis-3-hexenyllactate (C9H16O3) with retention time of 45.395min and peak area of 5.01%; and Pyrrole (C4H5N) showed peak of 3.37% with retention time of 45.508min. Other less prominent peaks at other retention times included; 2-Nitro-Dimethylnitromethane (C3H7NO2) with retention time of 37.355min, Ethylenimine (C2H5N) with retention time of 42.665min, N-Formyl-N-Methyl-formamide (C3H5NO2) with retention time of 44.225min, and Guanidine (CH5N3) with retention 44.225min. This work which is the first-time report on the bioactive compounds in the organic crude extracts of Dioscorea bulbifera native to Nigeria, using the GC-MS, has however established the presence of quite number of chemical compounds in the peel of the tuber, to which their pharmacological activities could be attributed. The presence of these secondary metabolites in the peel of Dioscorea bulbifera, is hence, the major contributing factors behind its antimicrobial potential. Keywords: GC-MS, Dioscorea bulbifera, antimicrobial properties, bioactive compounds, ethanolic extrac

Analysis of Physical and Chemical Composition of Sweet Orange (Citrus sinensis) Peels

Sweet orange is one of the most common fruits in the World. The waste generated from the fruits needs to be put into a beneficial use. In this study some physical and chemical properties of the primary waste of sweet orange was investigated. The result showed sweet orange rinds (peels) as the major waste and contains 45-50% of the total mass of sweet orange fruits. The chemical analysis showed sweet orange rinds to be rich in protein of 7.15% and crude fibre of 12.79% which can be used as ingredients in processed food. These uses will promote sustainable disposal of orange rinds

Antibiotic Residues in Food Samples Sold In Abeokuta Metropolis: A Cause for Concern

The use of antibiotic plays a major role in the emerging public health crisis of antibiotic resistance. Although, the majority of antibiotics usage occurs in animal husbandry and relatively little attention has been paid to how these antibiotics in farm animals contribute to the overall problems of antibiotics resistance in human. This research focuses on antibiotics residues in seven different most commonly consumed food samples in Abeokuta, Ogun State, Nigeria as a case study.  These food samples are: Chicken, Eggs, Cow-meat, Cheese, Goat-meat, Pork-meat and Turkey-meat. The antibiotics tested were: tetracycline, penicillin and streptomycin. The result, however, gave an inhibition zone of 8mm, 5mm, 6mm in frozen Turkey;  Nill, 5mm, 4mm in Cow-meat; Nill, Nill, 5mm in boiled Cheese; Nill, 4mm, 5mm in frozen Pork; 6mm, 7mm , 4mm in Eggs; 5mm, 4mm, 6mm in frozen Chicken and 4mm, Nill , 5mm in Goat-meat for Tetracycline, Penicillin and Streptomycin respectively. Most of the results obtained showed relatively high amount of antibiotics residues above the permissible limit of 2mm

Numerical optimisation of conjugate Hexagonal cooling channels with internal heat generation using Al2O3-water nanofluid

Papers presented to the 11th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, South Africa, 20-23 July 2015.This paper presents a three-dimensional geometric optimisation of conjugate cooling channels in forced convection with internal heat generation within the solid. Hexagonal cooling channels configuration are considered and Al2O3-water nanofluid is used as cooloing fluid because of its promising superior thermal properties over traditional cooling fluids The main objective is to optimise the configuration in such a way that the peak temperature is minimised subject to the constraint of fixed global volume of solid material. The cooling fluid is driven through the channels by the pressure difference across the channel.The elemental volume of the structure and hydraulic diameter of the cooling channel were considered as design variables. Also, different values of volume fraction of Al2O3 nanoparticles added into water that enhanced the cooling effect are considered. The shape of the channel is allowed to morph to determine the best configuration that gives the lowest peak temperature. A gradient-based mathematic optimisation algorithm (Dynamic-Q) is applied in order to search for the best optimal geometric configuration that improves thermal performance by minimising peak temperature for a wide range of pressure difference. Results obtained show that there are unique optimal geometry for a given pressure difference. Also, the results show that the effects of pressure difference, volume fraction of Al2O3 nanoparticles on minimum peak temperature and hydraulic diameter of the channel are consistent with those obtained in the open literature.The funding obtained from NRF, TESP, Stellenbosch University / University of Pretoria, SANERI/SANEDI, CSIR, EEDSM Hub and NAC is acknowledged and duly appreciated. Also, Olabode Olakoyejo appreciates the support received from the National Centre for Energy Efficiency and conservation, University of Lagos, Nigeria.am201

Numerical optimisation of forced convection in a vascularised solid with triagular channels

Paper presented to the 10th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, Florida, 14-16 July 2014.In this paper we employ the constructal design and theory to seek the optimal cooling channels in forced convection of vascularised material with the localised self-cooling property subject to heat flux. The isosceles right triangular channel configuration was studied for family of porosities. The isosceles right triangle is special case of triangle which can easily and uniformly be packed and arranged to form a larger constructs. The objective was to optimise the configurations in such a way that the peak temperature was minimised at every point in the solid body. The optimisation was subject to the constraint of fixed global volume of solid material, but the elemental volume was allowed to morph. The solid material was subject to heat flux on one side and the cooling fluid was forced through the channels in opposite direction of the heated side of the solid body by the specified pressure differencecf201