2009 Analysis Platform Review Report

2009 ◽  
Author(s):  
John Ferrell
Keyword(s):  
Analysis Platform

scholarly journals BiSulfite Bolt: A bisulfite sequencing analysis platform

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

Abstract Background Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing to the computational demands of mapping a low-complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis-ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt), a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries. Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy. Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a Python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.

An automated image analysis platform for the study of weakly -adhered cells

Biofouling ◽  
2021 ◽  
pp. 1-10
Author(s):  
Zhijing Wan ◽  
Ben T. MacVicar ◽  
Shea Wyatt ◽  
Diana E. Varela ◽  
Rajkumar Padmawar ◽  
...  
Keyword(s):  
Image Analysis ◽  
Automated Image Analysis ◽  
Analysis Platform

scholarly journals Singing Transcription from Polyphonic Music Using Melody Contour Filtering

2021 ◽  
Vol 11 (13) ◽  
pp. 5913
Author(s):  
Zhuang He ◽  
Yin Feng
Keyword(s):  
Audio Signals ◽  
Continuity Properties ◽  
Information Retrieval Evaluation ◽  
Unique Method ◽  
Image Edge ◽  
Salience Function ◽  
Music Information ◽  
Melody Contour ◽  
Analysis Platform ◽  
Polyphonic Music

Automatic singing transcription and analysis from polyphonic music records are essential in a number of indexing techniques for computational auditory scenes. To obtain a note-level sequence in this work, we divide the singing transcription task into two subtasks: melody extraction and note transcription. We construct a salience function in terms of harmonic and rhythmic similarity and a measurement of spectral balance. Central to our proposed method is the measurement of melody contours, which are calculated using edge searching based on their continuity properties. We calculate the mean contour salience by separating melody analysis from the adjacent breakpoint connective strength matrix, and we select the final melody contour to determine MIDI notes. This unique method, combining audio signals with image edge analysis, provides a more interpretable analysis platform for continuous singing signals. Experimental analysis using Music Information Retrieval Evaluation Exchange (MIREX) datasets shows that our technique achieves promising results both for audio melody extraction and polyphonic singing transcription.

scholarly journals SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays

Cell Systems ◽  
2021 ◽  
Author(s):  
Samuel Katz ◽  
Jian Song ◽  
Kyle P. Webb ◽  
Nicolas W. Lounsbury ◽  
Clare E. Bryant ◽  
...  
Keyword(s):  
Web Based ◽  
Iterative Analysis ◽  
Network Approaches ◽  
Genome Scale ◽  
Analysis Platform

scholarly journals The administration of antisense oligonucleotide golodirsen reduces pathological regeneration in patients with Duchenne muscular dystrophy

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dominic Scaglioni ◽  
Francesco Catapano ◽  
Matthew Ellis ◽  
Silvia Torelli ◽  
Darren Chambers ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Antisense Oligonucleotide ◽  
De Novo ◽  
Exon Skipping ◽  
Significant Negative Correlation ◽  
Entire Cohort ◽  
Associated Proteins ◽  
Analysis Platform ◽  
Dystrophin Protein

AbstractDuring the last decade, multiple clinical trials for Duchenne muscular dystrophy (DMD) have focused on the induction of dystrophin expression using different strategies. Many of these trials have reported a clear increase in dystrophin protein following treatment. However, the low levels of the induced dystrophin protein have raised questions on its functionality. In our present study, using an unbiased, high-throughput digital image analysis platform, we assessed markers of regeneration and levels of dystrophin associated protein via immunofluorescent analysis of whole muscle sections in 25 DMD boys who received 48-weeks treatment with exon 53 skipping morpholino antisense oligonucleotide (PMO) golodirsen. We demonstrate that the de novo dystrophin induced by exon skipping with PMO golodirsen is capable of conferring a histological benefit in treated patients with an increase in dystrophin associated proteins at the dystrophin positive regions of the sarcolemma in post-treatment biopsies. Although 48 weeks treatment with golodirsen did not result in a significant change in the levels of fetal/developmental myosins for the entire cohort, there was a significant negative correlation between the amount of dystrophin and levels of regeneration observed in different biopsy samples. Our results provide, for the first time, evidence of functionality of induced dystrophin following successful therapeutic intervention in the human.

scholarly journals OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes

2020 ◽  
Vol 49 (D1) ◽  
pp. D380-D388 ◽  
Author(s):  
Marie A Brunet ◽  
Jean-François Lucier ◽  
Maxime Levesque ◽  
Sébastien Leblanc ◽  
Jean-Francois Jacques ◽  
...  
Keyword(s):  
Confidence Score ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Supporting Evidence ◽  
Initial Release ◽  
Ncbi Refseq ◽  
Computational Resources ◽  
Analysis Platform ◽  
Eukaryotic Genomes ◽  
Reading Frames

Abstract OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one’s bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.

scholarly journals GRACETOOLS—GRACE Gravity Field Recovery Tools

Geosciences ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 350 ◽  
Author(s):  
Neda Darbeheshti ◽  
Florian Wöske ◽  
Matthias Weigelt ◽  
Christopher Mccullough ◽  
Hu Wu
Keyword(s):  
Open Source ◽  
Gravity Field ◽  
Transition Matrix ◽  
State Transition ◽  
Satellite Observations ◽  
Gravity Field Recovery ◽  
Grace Data ◽  
Range Rate ◽  
Analysis Platform ◽  
Recovery Tools

This paper introduces GRACETOOLS, the first open source gravity field recovery tool using GRACE type satellite observations. Our aim is to initiate an open source GRACE data analysis platform, where the existing algorithms and codes for working with GRACE data are shared and improved. We describe the first release of GRACETOOLS that includes solving variational equations for gravity field recovery using GRACE range rate observations. All mathematical models are presented in a matrix format, with emphasis on state transition matrix, followed by details of the batch least squares algorithm. At the end, we demonstrate how GRACETOOLS works with simulated GRACE type observations. The first release of GRACETOOLS consist of all MATLAB M-files and is publicly available at Supplementary Materials.

OSNAP! Introducing the open semantic network analysis platform

2015 ◽  
Author(s):  
Peter J. Radics ◽  
Nicholas F. Polys ◽  
Shawn P. Neuman ◽  
William H. Lund
Keyword(s):  
Network Analysis ◽  
Semantic Network ◽  
Semantic Network Analysis ◽  
Analysis Platform
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