scholarly journals Recent developments in theCCP-EMsoftware suite

2017 ◽  
Vol 73 (6) ◽  
pp. 469-477 ◽  
Author(s):  
Tom Burnley ◽  
Colin M. Palmer ◽  
Martyn Winn
Keyword(s):  
Easy Access ◽  
Software Framework ◽  
Command Line ◽  
Command Line Interface ◽  
Software Suite ◽  
Computational Support ◽  
Recent Developments ◽  
User Friendly ◽  
Different Levels ◽  
Friendly Graphical User Interface

As part of its remit to provide computational support to the cryo-EM community, the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced a software framework which enables easy access to a range of programs and utilities. The resulting software suite incorporates contributions from different collaborators by encapsulating them in Python task wrappers, which are then made accessibleviaa user-friendly graphical user interface as well as a command-line interface suitable for scripting. The framework includes tools for project and data management. An overview of the design of the framework is given, together with a survey of the functionality at different levels. The currentCCP-EMsuite has particular strength in the building and refinement of atomic models into cryo-EM reconstructions, which is described in detail.

scholarly journals UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

2021 ◽  
Vol 9 ◽  
Author(s):  
Caio Ribeiro ◽  
Lucas Oliveira ◽  
Romina Batista ◽  
Marcos De Sousa
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Phylogenetic Trees ◽  
Computational Analysis ◽  
Data Matrix ◽  
Command Line ◽  
Command Line Interface ◽  
Ultraconserved Elements ◽  
Research Software ◽  
Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

scholarly journals DamageProfiler: Fast damage pattern calculation for ancient DNA

2021 ◽  
Author(s):  
Judith Neukamm ◽  
Alexander Peltzer ◽  
Kay Nieselt
Keyword(s):  
Ancient Dna ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Central Importance ◽  
Command Line Interface ◽  
Analysis Pipeline ◽  
File Formats ◽  
Programming Knowledge ◽  
User Friendly

Abstract Motivation In ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline. Results DamageProfiler is a Java based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline. Availability All of the source code is freely available on GitHub (https://github.com/Integrative-Transcriptomics/DamageProfiler). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters

2020 ◽  
Author(s):  
Cameron L.M. Gilchrist ◽  
Thomas J. Booth ◽  
Yit-Heng Chooi
Keyword(s):  
Source Code ◽  
Gene Clusters ◽  
Rapid Identification ◽  
Large Datasets ◽  
Homologous Gene ◽  
Command Line ◽  
Local Sequence ◽  
Search Tool ◽  
User Friendly ◽  
Friendly Graphical User Interface

AbstractGenes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalised as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Here, we present cblaster, a Python based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface (GUI). It generates outputs that enable intuitive visualisations of large datasets, and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox. cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster).

era5cli: the command line interface to ERA5 data

2021 ◽  
Author(s):  
Stef Smeets ◽  
Jaro Camphuijsen ◽  
Niels Drost ◽  
Fakhereh Alidoost ◽  
Bouwe Andela ◽  
...  
Keyword(s):  
High Resolution ◽  
Source Code ◽  
Reanalysis Data ◽  
Command Line ◽  
Climate Data ◽  
Web Interface ◽  
Command Line Interface ◽  
Data Store ◽  
Recent Developments ◽  
Advanced Knowledge

<p>With the release of the ERA5 dataset, worldwide high-resolution reanalysis data became available with open access for public use. The Copernicus CDS (Climate Data Store) offers two options for accessing the data: a web interface and a Python API. Consequently, automated downloading of the data requires advanced knowledge of Python and a lot of work. To make this process easier, we developed <em>era5cli</em>. </p><p>The command line interface tool <em>era5cli </em>enables automated downloading of ERA5 using a single command. All variables and options available in the CDS web form are now available for download in an efficient way. Both the monthly and hourly dataset are supported. Besides automation, <em>era5cli </em>adds several useful functionalities to the download pipeline.</p><p>One of the key options in <em>era5cli </em>is to spread one download command over multiple CDS requests, resulting in higher download speeds. Files can be saved in both GRIB and NETCDF format with automatic, yet customizable file names. The <em>info </em>command lists correct names of the available variables and pressure levels for 3D variables. For debugging purposes and testing the <em>dryrun </em>option can be selected to return only the CDS request. An overview of all available options, including instructions on how to configure your CDS account, is available in our documentation. Recent developments include support for ERA5 back extension and ERA5-Land. The source code for era5cli is available on https://github.com/eWaterCycle/era5cli.</p>

scholarly journals DamageProfiler: Fast damage pattern calculation for ancient DNA

2020 ◽  
Author(s):  
Judith Neukamm ◽  
Alexander Peltzer ◽  
Kay Nieselt
Keyword(s):  
Ancient Dna ◽  
Command Line ◽  
Central Importance ◽  
Command Line Interface ◽  
Analysis Pipeline ◽  
Crucial Step ◽  
Damage Pattern ◽  
File Formats ◽  
Programming Knowledge ◽  
User Friendly

AbstractIn ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline. Here, we present DamageProfiler, a Java based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline.

scholarly journals Systematising troubleshooting of disputes in network

2021 ◽  
Vol 10 (1) ◽  
pp. 32
Author(s):  
Sowmya K. B. ◽  
Thejaswini A.
Keyword(s):  
Technical Assistance ◽  
Software Defined Networking ◽  
Relevant Information ◽  
Network Size ◽  
Log Analysis ◽  
Command Line ◽  
Command Line Interface ◽  
User Friendly ◽  
Growing Network

With the growing network size, virtualization everywhere, it is getting more difficult to configure and manage the network devices. Software Defined Networking (SDN) is a way to address these problems. Application Centric Infrastructure (ACI) is the Cisco’s solution to SDN, with centralized automation and policy-driven application profiles. If there is any bug in the network or problem with the expected functionality of the network, ACI cases are opened in the Technical Assistance Centre (TAC) for troubleshooting the issue. Engineers currently troubleshoot ACI cases manually by using Command Line Interface (CLI) and trace for different events triggered by the policy pushes by logs generated at different stages of the ACI and from different servers responsible for this, which indeed is a very tedious, time consuming task and is prone to manual errors. This paper describes a way to automate the entire ACI troubleshooting process with the user-friendly GUI which can show the entire information needed for troubleshooting by extracting relevant information at every layer. By making use of FSM models the proposed solution can be extended to other areas which involve log analysis using CLI to extract relevant information and is not just limited to ACI.

scholarly journals Going standalone and platform-independent, an example from recent work on the ATLAS Detector Description and interactive data visualization

2019 ◽  
Vol 214 ◽  
pp. 02035
Author(s):  
Sebastian Andreas Merkt ◽  
Riccardo Maria Bianchi ◽  
Joseph Boudreau ◽  
Paul Gessinger-Befurt ◽  
Edward Moyse ◽  
...  
Keyword(s):  
Data Visualization ◽  
Lessons Learned ◽  
Easy Access ◽  
Software Framework ◽  
Great Effort ◽  
Atlas Experiment ◽  
Platform Independence ◽  
Visualization Tools ◽  
Interactive Data ◽  
User Friendly

Until recently, the direct visualization of the complete ATLAS experiment geometry and physics objects was confined within the software framework of the experiment. To provide a detailed interactive data visualization capability to users, as well as easy access to geometry data, and to ensure platform independence and portability, great effort has been recently put into the modernization of both the core kernel of the detector description and the visualization tools. In this proceedings we will present the new tools, as well as the lessons learned while modernizing the experiment’s code for an efficient use of the detector description and for user-friendly data visualization.

scholarly journals MoloVol: an easy-to-use program to calculate various volumes and surface areas of chemical structures and identify cavities

2021 ◽  
Author(s):  
Jasmin B. Maglic ◽  
Roy Lavendomme
Keyword(s):  
Open Source Software ◽  
Command Line ◽  
Command Line Interface ◽  
Guest Molecules ◽  
Transport And Transformation ◽  
Graphic Interface ◽  
Chemical Structures ◽  
Surface Areas ◽  
User Friendly ◽  
Structure Calculations

Cavities are a ubiquitous feature of chemical structures encountered in various fields ranging from supramolecular chemistry to molecular biology. They are involved in the encapsulation, transport, and transformation of guest molecules, thus necessitating a precise and accessible tool for estimating and visualizing their size and shape. MoloVol, a free, user-parametrizable, open-source software, developed for calculating a range of geometric features for both unit cell and isolated structures is presented here. MoloVol utilizes up to two spherical probes to define cavities, surfaces, and volumes. The program was optimized by combining an octree data structure with voxel-partitioned space allowing for even high-resolution protein structure calculations at reasonable timescales. MoloVol comes with a user-friendly graphic interface along with a command line interface for high throughput calculations. It was written in C++ and is available on Windows, macOS, and Linux distributions.

scholarly journals SOFTWARE FRAMEWORK FOR HYPERSPECTRAL DATA EXPLORATION AND PROCESSING IN MATLAB

2017 ◽  
Vol XLII-3/W3 ◽  
pp. 47-50 ◽  
Author(s):  
M. A. Eskelinen
Keyword(s):  
Hyperspectral Data ◽  
Data Exploration ◽  
Easy Access ◽  
Software Framework ◽  
Command Line ◽  
Data Manipulation ◽  
Data Cubes ◽  
Efficient Data ◽  
Development Methods ◽  
Efficient Data Analysis

This paper presents a user introduction and a general overview of the MATLAB software package <tt>hsicube</tt> developed by the author for simplifying the data manipulation and visualization tasks often encountered in hyperspectral analysis work, and the design principles and software development methods used by the author. The framework implements methods for slicing, masking, visualization and application of existing functions to hyperspectral data cubes without the need to use explicit indexing or reshaping, as well as enabling expressive syntax for combining these operations on the command line for highly efficient data analysis workflows. It also includes utilities for interfacing with existing file reader scripts for easy access to files using the framework. The <tt>hsicube</tt> framework is released as open source to promote the free use and peer review of the code and enable collaborative development.

scholarly journals Sampo-UI: A full stack JavaScript framework for developing semantic portal user interfaces

Semantic Web ◽  
2021 ◽  
pp. 1-16
Author(s):  
Esko Ikkala ◽  
Eero Hyvönen ◽  
Heikki Rantala ◽  
Mikko Koho
Keyword(s):  
User Interfaces ◽  
Linked Data ◽  
State Of The Art ◽  
Software Framework ◽  
End User ◽  
Faceted Search ◽  
Software Developer ◽  
Current State ◽  
Knowledge Graphs ◽  
User Friendly

This paper presents a new software framework, Sampo-UI, for developing user interfaces for semantic portals. The goal is to provide the end-user with multiple application perspectives to Linked Data knowledge graphs, and a two-step usage cycle based on faceted search combined with ready-to-use tooling for data analysis. For the software developer, the Sampo-UI framework makes it possible to create highly customizable, user-friendly, and responsive user interfaces using current state-of-the-art JavaScript libraries and data from SPARQL endpoints, while saving substantial coding effort. Sampo-UI is published on GitHub under the open MIT License and has been utilized in several internal and external projects. The framework has been used thus far in creating six published and five forth-coming portals, mostly related to the Cultural Heritage domain, that have had tens of thousands of end-users on the Web.

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