The microarray manual curation tool (MMCT): A Web server for microarray probe evaluations

Quality control of probe sequences is a major concern in microarray technology. The presence of poor quality probes has a negative impact on the microarray data analysis process. The Microarray Manual Curation Tool (MMCT) is a web server application that provides computational and visual means to investigate the quality of individual probes for oligo microarrays. The MMCT quality metrics assess the free energy of hybridization and the secondary structure of duplexes formed by selected targets and probes, which are specific to various microarray platforms

MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures

<p>Abstract</p> <p>Background</p> <p>One-dimensional ¹H-NMR spectroscopy is widely used for high-throughput characterization of metabolites in complex biological mixtures. However, the accurate identification of individual compounds is still a challenging task, particularly in spectral regions with higher peak densities. The need for automatic tools to facilitate and further improve the accuracy of such tasks, while using increasingly larger reference spectral libraries becomes a priority of current metabolomics research.</p> <p>Results</p> <p>We introduce a web server application, called MetaboHunter, which can be used for automatic assignment of ¹H-NMR spectra of metabolites. MetaboHunter provides methods for automatic metabolite identification based on spectra or peak lists with three different search methods and with possibility for peak drift in a user defined spectral range. The assignment is performed using as reference libraries manually curated data from two major publicly available databases of NMR metabolite standard measurements (HMDB and MMCD). Tests using a variety of synthetic and experimental spectra of single and multi metabolite mixtures show that MetaboHunter is able to identify, in average, more than 80% of detectable metabolites from spectra of synthetic mixtures and more than 50% from spectra corresponding to experimental mixtures. This work also suggests that better scoring functions improve by more than 30% the performance of MetaboHunter's metabolite identification methods.</p> <p>Conclusions</p> <p>MetaboHunter is a freely accessible, easy to use and user friendly ¹H-NMR-based web server application that provides efficient data input and pre-processing, flexible parameter settings, fast and automatic metabolite fingerprinting and results visualization via intuitive plotting and compound peak hit maps. Compared to other published and freely accessible metabolomics tools, MetaboHunter implements three efficient methods to search for metabolites in manually curated data from two reference libraries.</p> <p>Availability</p> <p><url>http://www.nrcbioinformatics.ca/metabohunter/</url></p

Simple Learning Design 2.0

Contemporary learning design specifications are rarely implemented in learning platforms even though they would bring value to end-users. Unlike its predecessors, Simple Learning Design 2.0 (SLD 2.0) proposes a straight-forward and cost effective approach to learning design. SLD 2.0 was designed and implemented in a course management system by experienced learning systems developers, instructional designers and learning designers. SLD 2.0 proposes an XML binding usable as an unofficial add-on to the IMS-CC v1.0 specification.Peer reviewed: YesNRC publication: Ye

HyDEn: A Hybrid Steganocryptographic Approach for Data Encryption Using Randomized Error-Correcting DNA Codes

This paper presents a novel hybrid DNA encryption (HyDEn) approach that uses randomized assignments of unique error-correcting DNA Hamming code words for single characters in the extended ASCII set. HyDEn relies on custom-built quaternary codes and a private key used in the randomized assignment of code words and the cyclic permutations applied on the encoded message. Along with its ability to detect and correct errors, HyDEn equals or outperforms existing cryptographic methods and represents a promising in silico DNA steganographic approach

Use of chemometrics and laser-induced breakdown spectroscopy for quantitative analysis of major and minor elements in aluminium alloys

In the present work, quantitative analysis of major and minor elements in aluminum alloys is investigated using chemometrics and laser-induced plasma spectroscopy with a commercially available laser-induced breakdown (LIBS) spectrometer. Multivariate calibrations use the entire signal matrix for all elements in a single multivariate regression model. This enables accounting for the correlation between variables often referred to as matrix effects in conventional univariate modeling. Modeling the entire signal matrix improves robustness over traditional univariate calibration since it can compensate for matrix effects. Several nonlinear data pretreatment methods have been used to correct for nonlinear behaviors of the analytical signals prior to performing the multivariate calibration. The use of multivariate calibration in combination with cubic implicit nonlinear data pretreatment showed the most accurate results. The accuracy reported with the developed multivariate calibration is better than 5% for the major alloying elements. Based on the results obtained, the use of chemometrics and laser-induced plasma spectroscopy have been successfully applied to the quantitative analysis of major and minor alloying elements in aluminum.Peer reviewed: YesNRC publication: Ye