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 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.

CAFE 5 models variation in evolutionary rates among gene families

2020 ◽  
Author(s):  
Fábio K Mendes ◽  
Dan Vanderpool ◽  
Ben Fulton ◽  
Matthew W Hahn
Keyword(s):  
Software Package ◽  
Computational Analysis ◽  
Source Code ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Supplementary Information ◽  
Rate Variation ◽  
Gene Gain ◽  
Command Line ◽  
Gains And Losses

Abstract Motivation Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, Computational Analysis of gene Family Evolution (CAFE), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. Results Here, we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modeling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. Availability and implementation CAFE 5 source code, documentation, test data and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals READemption - A tool for the computational analysis of deep-sequencing-based transcriptome data

2014 ◽  
Author(s):  
Konrad Ulrich Förstner ◽  
Jörg Vogel ◽  
Cynthia Mira Sharma
Keyword(s):  
Data Processing ◽  
Deep Sequencing ◽  
Computational Analysis ◽  
Command Line ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Command Line Interface ◽  
Parallel Data ◽  
Full Power ◽  
Computationally Intensive

Summary: RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. In order to draw biological conclusions based on RNA-Seq data, several steps some of which are computationally intensive, have to betaken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes, RNA immunoprecipitated with proteins, not only from bacteria, but also from eukaryotes and archaea. Availability and Implementation: READemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http://pythonhosted.org/READemption (DOI:10.6084/m9.figshare.977849).

scholarly journals A PLUGIN TO INTERFACE OPENMODELLER FROM QGIS FOR SPECIES' POTENTIAL DISTRIBUTION MODELLING

2016 ◽  
Vol III-7 ◽  
pp. 251-256 ◽  
Author(s):  
Daniel Becker ◽  
Christian Willmes ◽  
Georg Bareth ◽  
Gerd-Christian Weniger
Keyword(s):  
Information System ◽  
Software Package ◽  
Potential Distribution ◽  
Data Conversion ◽  
Command Line ◽  
Command Line Interface ◽  
Species Occurrence ◽  
Distribution Models ◽  
Distribution Modelling ◽  
Project Folder

This contribution describes the development of a plugin for the geographic information system QGIS to interface the openModeller software package. The aim is to use openModeller to generate species’ potential distribution models for various archaeological applications (site catchment analysis, for example). Since the usage of openModeller’s command-line interface and configuration files can be a bit inconvenient, an extension of the QGIS user interface to handle these tasks, in combination with the management of the geographic data, was required. The implementation was realized in Python using PyQGIS and PyQT. The plugin, in combination with QGIS, handles the tasks of managing geographical data, data conversion, generation of configuration files required by openModeller and compilation of a project folder. The plugin proved to be very helpful with the task of compiling project datasets and configuration files for multiple instances of species occurrence datasets and the overall handling of openModeller. In addition, the plugin is easily extensible to take potential new requirements into account in the future.

scholarly journals Phylommand - a command line software package for phylogenetics

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2903
Author(s):  
Martin Ryberg
Keyword(s):  
Software Package ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Command Line ◽  
File Formats

Phylogenetics is an intrinsic part of many analyses in evolutionary biology and ecology, and as the amount of data available for these analyses is increasing rapidly the need for automated pipelines to deal with the data also increases. Phylommand is a package of four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments. It is built to be easily implemented in software workflows, both directly on the command prompt, and executed using scripts. Inputs can be taken from standard input or a file, and the behavior of the programs can be changed through switches. By using standard file formats for phylogenetic analyses, such as newick, nexus, phylip, and fasta, phylommand is widely compatible with other software.

scholarly journals A PLUGIN TO INTERFACE OPENMODELLER FROM QGIS FOR SPECIES' POTENTIAL DISTRIBUTION MODELLING

2016 ◽  
Vol III-7 ◽  
pp. 251-256 ◽  
Author(s):  
Daniel Becker ◽  
Christian Willmes ◽  
Georg Bareth ◽  
Gerd-Christian Weniger
Keyword(s):  
Information System ◽  
Software Package ◽  
Potential Distribution ◽  
Data Conversion ◽  
Command Line ◽  
Command Line Interface ◽  
Species Occurrence ◽  
Distribution Models ◽  
Distribution Modelling ◽  
Project Folder

This contribution describes the development of a plugin for the geographic information system QGIS to interface the openModeller software package. The aim is to use openModeller to generate species’ potential distribution models for various archaeological applications (site catchment analysis, for example). Since the usage of openModeller’s command-line interface and configuration files can be a bit inconvenient, an extension of the QGIS user interface to handle these tasks, in combination with the management of the geographic data, was required. The implementation was realized in Python using PyQGIS and PyQT. The plugin, in combination with QGIS, handles the tasks of managing geographical data, data conversion, generation of configuration files required by openModeller and compilation of a project folder. The plugin proved to be very helpful with the task of compiling project datasets and configuration files for multiple instances of species occurrence datasets and the overall handling of openModeller. In addition, the plugin is easily extensible to take potential new requirements into account in the future.

ANISOtime: Traveltime Computation Software for Laterally Homogeneous, Transversely Isotropic, Spherical Media

2021 ◽  
Author(s):  
Kensuke Konishi ◽  
Anselme F. E. Borgeaud ◽  
Kenji Kawai ◽  
Robert J. Geller
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Software Package ◽  
Transversely Isotropic ◽  
Earth Model ◽  
Spherically Symmetric ◽  
Command Line ◽  
Command Line Interface ◽  
Software Packages ◽  
Cross Platform

Abstract Software packages for computing seismic traveltimes and raypaths in an isotropic, spherically symmetric, Earth model are well known and widely used. However, even though the theory for transversely isotropic (TI), spherically symmetric, models has been known since the late 1960s, readily available programs for traveltime calculations are restricted to isotropic models. We have developed a new software package, ANISOtime, for computing seismic traveltimes and raypaths in laterally homogeneous, TI, spherical media. This package calculates traveltime tables for both immediate and subsequent use. ANISOtime has both graphical user interface and command-line interface modes. The package is available for free public download. As it offers cross-platform compatibility through Java 8, it runs on Windows, macOS, Unix, and Linux.

Organizing and Managing Data Analytics Teams for Procurement

2020 ◽  
Author(s):  
Benjamin Shao ◽  
Robert D. St. Louis
Keyword(s):  
Best Practices ◽  
Business Strategy ◽  
Data Analytics ◽  
Team Members ◽  
Procurement Process ◽  
Using Data ◽  
And Training ◽  
Different Levels ◽  
The Way

Many companies are forming data analytics teams to put data to work. To enhance procurement practices, chief procurement officers (CPOs) must work effectively with data analytics teams, from hiring and training to managing and utilizing team members. This chapter presents the findings of a study on how CPOs use data analytics teams to support the procurement process. Surveys and interviews indicate companies are exhibiting different levels of maturity in using data analytics, but both the goal of CPOs (i.e., improving performance to support the business strategy) and the way to interact with data analytics teams for achieving that goal are common across companies. However, as data become more reliably available and technologies become more intelligently embedded, the best practices of organizing and managing data analytics teams for procurement will need to be constantly updated.

ESIS ON THE WORLD WIDE WEB

1994 ◽  
Vol 05 (05) ◽  
pp. 805-809 ◽  
Author(s):  
SALIM G. ANSARI ◽  
PAOLO GIOMMI ◽  
ALBERTO MICOL
Keyword(s):  
World Wide Web ◽  
Web Application ◽  
World Wide ◽  
Markup Language ◽  
Command Line ◽  
Command Line Interface ◽  
The World ◽  
Hypertext Transfer Protocol ◽  
Hypertext Markup Language ◽  
Near Future

On 3rd November, 1993, ESIS announced its Homepage on the World Wide Web (WWW) to the user community. Ever since then, ESIS has steadily increased its Web support to the astronomical community to include a bibliographic service, the ESIS catalogue documentation and the ESIS Data Browser. More functionality will be added in the near future. All these services share a common ESIS structure that is used by other ESIS user paradigms such as the ESIS Graphical User Interface (Giommi and Ansari, 1993), and the ESIS Command Line Interface. A forms-based paradigm, each ESIS-Web application interfaces to the hypertext transfer protocol (http) translating queries from/to the hypertext markup language (html) format understood by the NCSA Mosaic interface. In this paper, we discuss the ESIS system and show how each ESIS service works on the World Wide Web client.

A Framework for Engineering Dissection Exercise Creation and Implementation

2009 ◽  
Author(s):  
Kathleen M. Hart ◽  
Steven B. Shooter ◽  
Charles J. Kim
Keyword(s):  
Active Learning ◽  
Best Practices ◽  
Reverse Engineering ◽  
Engineering Education ◽  
Learning Outcomes ◽  
Positive Impact ◽  
Rigorous Approach ◽  
Engineering Activity ◽  
Hands On ◽  
Different Levels

Hands-on product dissection and reverse engineering exercises have been shown to have a positive impact on engineering education, and many universities have incorporated such exercises in their curriculum. The CIBER-U project seeks to examine the potential to utilize cyberinfrastructure to enhance these active-learning exercises. We have formulated a framework for product dissection and reverse engineering activity creation to support a more rigorous approach to assessing other exercises for satisfaction of the CIBER-U project goals and adapting the best practices. This framework is driven by the fulfillment of learning outcomes and considers the maturity of students at different levels. Prototype exercises developed with the framework are presented. The approach is sufficiently general that it can be applied to the consideration and adaption of other types of exercises while ensuring satisfaction of the established goals.

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