scholarly journals AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective

2019 ◽  
Vol 36 (8) ◽  
pp. 2599-2601 ◽  
Author(s):  
Tomasz Magdziarz ◽  
Karolina Mitusińska ◽  
Maria Bzówka ◽  
Agata Raczyńska ◽  
Agnieszka Stańczak ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Drug Design ◽  
Protein Engineering ◽  
Molecular Probes ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Comprehensive Method ◽  
And Performance ◽  
Insight Into ◽  
Small Ligands

Abstract Motivation Tunnels, pores, channels, pockets and cavities contribute to proteins architecture and performance. However, analysis and characteristics of transportation pathways and internal binding cavities are performed separately. We aimed to provide universal tool for analysis of proteins integral interior with access to detailed information on the ligands transportation phenomena and binding preferences. Results AQUA-DUCT version 1.0 is a comprehensive method for macromolecules analysis from the intramolecular voids perspective using small ligands as molecular probes. This version gives insight into several properties of macromolecules and facilitates protein engineering and drug design by the combination of the tracking and local mapping approach to small ligands. Availability and implementation http://www.aquaduct.pl. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals NACHO: an R package for quality control of NanoString nCounter data

2019 ◽  
Author(s):  
Mickaël Canouil ◽  
Gerard A Bouland ◽  
Amélie Bonnefond ◽  
Philippe Froguel ◽  
Leen M ’t Hart ◽  
...  
Keyword(s):  
Quality Control ◽  
R Package ◽  
Third Parties ◽  
Supplementary Information ◽  
Expression Data ◽  
Supplementary Data ◽  
Scaling Factors ◽  
Comprehensive Method ◽  
Normalization Methods

Abstract Summary The NanoStringTM nCounter® is a platform for the targeted quantification of expression data in biofluids and tissues. While software by the manufacturer is available in addition to third parties packages, they do not provide a complete quality control (QC) pipeline. Here, we present NACHO (‘NAnostring quality Control dasHbOard’), a comprehensive QC R-package. The package consists of three subsequent steps: summarize, visualize and normalize. The summarize function collects all the relevant data and stores it in a tidy format, the visualize function initiates a dashboard with plots of the relevant QC outcomes. It contains QC metrics that are measured by default by the manufacturer, but also calculates other insightful measures, including the scaling factors that are needed in the normalization step. In this normalization step, different normalization methods can be chosen to optimally preprocess data. Together, NACHO is a comprehensive method that optimizes insight and preprocessing of nCounter® data. Availability and implementation NACHO is available as an R-package on CRAN and the development version on GitHub https://github.com/mcanouil/NACHO. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

KEC: unique sequence search by K-mer exclusion

2021 ◽  
Author(s):  
Pavel Beran ◽  
Dagmar Stehlíková ◽  
Stephen P Cohen ◽  
Vladislav Čurn
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Source Code ◽  
Unique Sequence ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Laptop Computers ◽  
Sequence Search ◽  
Target Sequences ◽  
Cross Reference

Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. Availability and implementation KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Federico Zambelli ◽  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
David S Horner ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Ad Hoc ◽  
State Of The Art ◽  
Supplementary Information ◽  
Genomic Sequences ◽  
Supplementary Data ◽  
Evolutionary Patterns ◽  
Genomic Variants ◽  
Art Methods ◽  
Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy   http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals UniBioDicts: Unified access to Biological Dictionaries

2020 ◽  
Author(s):  
John Zobolas ◽  
Vasundra Touré ◽  
Martin Kuiper ◽  
Steven Vercruysse
Keyword(s):  
User Interface ◽  
Life Science ◽  
Biological Data ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Query Interface ◽  
Controlled Vocabularies ◽  
Search String ◽  
Software Packages ◽  
The Right

Abstract Summary We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms. Availability and implementation The UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Surrogate minimal depth as an importance measure for variables in random forests

2019 ◽  
Vol 35 (19) ◽  
pp. 3663-3671 ◽  
Author(s):  
Stephan Seifert ◽  
Sven Gundlach ◽  
Silke Szymczak
Keyword(s):  
Variable Selection ◽  
Supplementary Information ◽  
Predictor Variables ◽  
Importance Measure ◽  
Surrogate Variables ◽  
Machine Learning Approach ◽  
Complex Relationships ◽  
Minimal Depth ◽  
Insight Into ◽  
Causal Variables

Abstract Motivation It has been shown that the machine learning approach random forest can be successfully applied to omics data, such as gene expression data, for classification or regression and to select variables that are important for prediction. However, the complex relationships between predictor variables, in particular between causal predictor variables, make the interpretation of currently applied variable selection techniques difficult. Results Here we propose a new variable selection approach called surrogate minimal depth (SMD) that incorporates surrogate variables into the concept of minimal depth (MD) variable importance. Applying SMD, we show that simulated correlation patterns can be reconstructed and that the increased consideration of variable relationships improves variable selection. When compared with existing state-of-the-art methods and MD, SMD has higher empirical power to identify causal variables while the resulting variable lists are equally stable. In conclusion, SMD is a promising approach to get more insight into the complex interplay of predictor variables and outcome in a high-dimensional data setting. Availability and implementation https://github.com/StephanSeifert/SurrogateMinimalDepth. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CONCUR: quick and robust calculation of codon usage from ribosome profiling data

2020 ◽  
Author(s):  
Michaela Frye ◽  
Susanne Bornelöv
Keyword(s):  
Codon Usage ◽  
Ribosome Profiling ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Usage Analysis

Abstract Summary CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. Availability and implementation CONCUR is written in Perl and is freely available at https://github.com/susbo/concur. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CoKnowEMe: An Edge Evaluation Scheme for QoS of IoMT Microservices in 6G Scenario

2021 ◽  
Vol 13 (7) ◽  
pp. 177
Author(s):  
Grazia Veronica Aiosa ◽  
Barbara Attanasio ◽  
Aurelio La Corte ◽  
Marialisa Scatá
Keyword(s):  
Communication Networks ◽  
Systems Approach ◽  
Evaluation Model ◽  
Service Evaluation ◽  
Important Change ◽  
Supplementary Information ◽  
Analytical Scheme ◽  
Evaluation Scheme ◽  
Reducing Costs ◽  
And Performance

The forthcoming 6G will attempt to rewrite the communication networks’ perspective focusing on a shift in paradigm in the way technologies and services are conceived, integrated and used. In this viewpoint, the Internet of Medical Things (IoMT) represents a merger of medical devices and health applications that are connected through networks, introducing an important change in managing the disease, treatments and diagnosis, reducing costs and faults. In 6G, the edge intelligence moves the innovative abilities from the central cloud to the edge and jointly with the complex systems approach will enable the development of a new category of lightweight applications as microservices. It requires edge intelligence also for the service evaluation in order to introduce the same degree of adaptability. We propose a new evaluation model, called CoKnowEMe (context knowledge evaluation model), by introducing an architectural and analytical scheme, modeled following a complex and dynamical approach, consisting of three inter-operable level and different networked attributes, to quantify the quality of IoMT microservices depending on a changeable context of use. We conduct simulations to display and quantify the structural complex properties and performance statistical estimators. We select and classify suitable attributes through a further detailed procedure in a supplementary information document.

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