scholarly journals The ATNF Pulsar Catalog

2004 ◽  
Vol 218 ◽  
pp. 139-140 ◽  
Author(s):  
G. Hobbs ◽  
R. Manchester ◽  
A. Teoh ◽  
M. Hobbs
Keyword(s):  
Command Line ◽  
Web Interface ◽  
The Past

The number of known pulsars has significantly increased over the past few years. We have searched the literature to find papers announcing the discovery of pulsars or giving improved parameters for them. Data from the papers have been entered into a new pulsar catalog that can be accessed via a web interface or from the command line (on Solaris or Linux machines). The user may request over 120 different parameters, select pulsars of interest, generate custom variables and choose between different ways of displaying or tabulating the datA. Full bibliographic references are available for all observed parameters.

scholarly journals The UCSC Genome Browser database: 2018 update

2017 ◽  
Vol 46 (D1) ◽  
pp. D762-D769 ◽  
Author(s):  
Jonathan Casper ◽  
Ann S Zweig ◽  
Chris Villarreal ◽  
Cath Tyner ◽  
Matthew L Speir ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Gene Interactions ◽  
Command Line ◽  
Web Interface ◽  
Variant Annotation ◽  
The Past ◽  
Ucsc Genome Browser Database ◽  
Genome Assemblies ◽  
Command Line Version

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

scholarly journals Web-Based Robotics Laboratory

2018 ◽  
Vol 164 ◽  
pp. 01034
Author(s):  
Petrus Santoso ◽  
Handry Khoswanto ◽  
Iwan Njoto Sandjaja
Keyword(s):  
Inverse Kinematics ◽  
Control Mechanism ◽  
Web Interface ◽  
Laser Pointer ◽  
Web Based ◽  
Turn On ◽  
The Past ◽  
Interface Usability ◽  
Web Based System ◽  
Projection Field

In the education world, the number of web-based system is growing substantially in the past few years. Many web-based teaching tools has been developed to help students expand his knowledge. This paper presents a web-based laboratory to augment learning experiences in the field of robotics. The designed laboratory consists of a robotic arm with laser pointer, projection platform and web-based interface. The laboratory is used to learn about inverse kinematics and forward kinematics problems. Students enter the input parameters through web interface, server calculate output parameters and sent it to the robot. The web interface displays the movement result and turn on the laser pointer to the projection field. Preliminary testing concerning interface usability, access control mechanism and command queueing shows that the system working as expected.

scholarly journals Coffea-casa: an analysis facility prototype

2021 ◽  
Vol 251 ◽  
pp. 02061
Author(s):  
Matous Adamec ◽  
Garhan Attebury ◽  
Kenneth Bloom ◽  
Brian Bockelman ◽  
Carl Lundstedt ◽  
...  
Keyword(s):  
Data Analysis ◽  
Data Access ◽  
End Users ◽  
Command Line ◽  
Web Interface ◽  
Command Line Interface ◽  
Interactive Interface ◽  
Batch Systems ◽  
Interactive Computing ◽  
Programming Paradigms

Data analysis in HEP has often relied on batch systems and event loops; users are given a non-interactive interface to computing resources and consider data event-by-event. The “Coffea-casa” prototype analysis facility is an effort to provide users with alternate mechanisms to access computing resources and enable new programming paradigms. Instead of the command-line interface and asynchronous batch access, a notebook-based web interface and interactive computing is provided. Instead of writing event loops, the columnbased Coffea library is used. In this paper, we describe the architectural components of the facility, the services offered to end users, and how it integrates into a larger ecosystem for data access and authentication.

scholarly journals Verification of Arabidopsis stock collections using SNPmatch - an algorithm for genotyping high-plexed samples

2017 ◽  
Author(s):  
Rahul Pisupati ◽  
Ilka Reichardt ◽  
Ümit Seren ◽  
Pamela Korte ◽  
Viktoria Nizhynska ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Phenotypic Variation ◽  
Large Scale ◽  
Command Line ◽  
Web Interface ◽  
Sequencing Data ◽  
Link Type ◽  
Gregor Mendel ◽  
Low Coverage

AbstractLarge-scale studies such as the ​Arabidopsis thaliana 1001 Genomes Project aim to understand genetic variation in populations and link it to phenotypic variation. Such studies require routine genotyping of stocks to avoid sample contamination and mix-ups. To genotype samples efficiently and economically, sequencing must be inexpensive a​nd data processing simple. Here we present SNPmatch, a tool which identifies the most likely strain (inbred line, or “accession”) from a SNP database. We tested the tool by performing low-coverage sequencing of over 2000 strains. SNPmatch could readily genotype samples correctly from 1-fold coverage sequencing data, and could also identify the parents of F1 or F2 individuals. SNPmatch can be run either on the command line or through AraGeno (https://arageno.gmi.oeaw.ac.at), a web interface that permits sample genotyping from a user-uploaded VCF or BED file.Availability and implementation: https://github.com/Gregor-Mendel-Institute/SNPmatch.git

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 Systematic and quantitative view of the antiviral arsenal of prokaryotes

2021 ◽  
Author(s):  
Florian Tesson ◽  
Alexandre Herve ◽  
Marie Touchon ◽  
Camille d'Humieres ◽  
Jean Cury ◽  
...  
Keyword(s):  
Open Source Software ◽  
Large Scale ◽  
Bacterial Species ◽  
Detailed Comparison ◽  
Command Line ◽  
Comprehensive Description ◽  
The Past ◽  
Prokaryotic Genomes ◽  
Command Line Tool ◽  
Abundance And Diversity

Facing the abundance and diversity of phages, bacteria have developed multiple anti-phage mechanisms. In the past three years, the number of known anti-phage mechanisms has been expanded by at least 5-fold rendering our view of prokaryotic immunity obsolete. Most anti-phage systems have been studied as standalone mechanisms, however many examples demonstrate strains encode not one but several anti-viral mechanisms. How these different systems integrate into an anti-viral arsenal at the strain level remains to be elucidated. Much could be learned from establishing fundamental description of features such as the number and diversity of anti-phage systems encoded in a given genome. To address this question, we developed DefenseFinder, a tool that automatically detects known anti-phage systems in prokaryotic genomes. We applied DefenseFinder to >20 000 fully sequenced genomes, generating a systematic and quantitative view of the anti-viral arsenal of prokaryotes. We show prokaryotic genomes encode on average five anti-phage systems from three different families of systems. This number varies drastically from one strain to another and is influenced by the genome size and the number of prophages encoded. Distributions of different systems are also very heterogenous with some systems being enriched in prophages and in specific clades. Finally, we provide a detailed comparison of the anti-viral arsenal of 15 common bacterial species, revealing drastic differences in anti-viral strategies. Overall, our work provides a free and open-source software, available as a command line tool or, on webserver. It allows the rapid detection of anti-phage systems, enables a comprehensive description of the anti-viral arsenal of prokaryotes and paves the way for large scale genomics study in the field of anti-phage defense.

scholarly journals tspex: a tissue-specificity calculator for gene expression data

2020 ◽  
Author(s):  
Antonio P. Camargo ◽  
Adrielle A. Vasconcelos ◽  
Mateus B. Fiamenghi ◽  
Gonçalo A. G. Pereira ◽  
Marcelo F. Carazzolle
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Web Application ◽  
Tissue Specificity ◽  
Source Code ◽  
Command Line ◽  
Expression Data ◽  
Web Interface ◽  
User Friendly ◽  
Different Tissues

Abstract When comparing gene expression data of different tissues it is often interesting to identify tissue-specific genes or transcripts. Even though there are several metrics to measure tissue-specificity, a user-friendly tool that facilitates this analysis is not available yet. We present tspex, a software that allows easy computation of a comprehensive set of different tissue-specificity metrics from gene expression data. tspex can be used through a web interface, command-line or the Python API. Its package version also provides visualization functions that facilitate inspection of results. The documentation and the source code of tspex are available at https://apcamargo.github.io/tspex/ and the web application can be accessed at https://tspex.lge.ibi.unicamp.br/

Keyboards, Screens, and Mice

2014 ◽  
pp. 19-33
Keyword(s):  
Gesture Recognition ◽  
User Interfaces ◽  
Wearable Devices ◽  
Graphical User Interfaces ◽  
Command Line ◽  
The Real ◽  
The Past ◽  
World Today ◽  
Digital World ◽  
Traditional Paradigm

This chapter deals generally with the developments in various interaction technologies. Interaction paradigms have shifted in the past from command line interfaces to graphical user interfaces exploiting heavily metaphors from the real to the digital world. Today, the traditional paradigm of interaction with a computer using a mouse, a keyboard, and a screen starts again to shift into new emerging paradigms employing a variety of technologies such as speech and gesture recognition. The functionality of a PC is now being transferred into devices such as mobile and wearable devices, exposing the need for new ways of interacting with devices. This chapter discusses how emerging interaction technologies can affect the eAccessibility domain by presenting opportunities, challenges, and dangers that lie ahead.

TPS (Task Preparation System): A Tool for Developing Tasks in Programming Contests

2019 ◽  
Vol 13 ◽  
pp. 209-215
Author(s):  
Kian MIRJALALI ◽  
Amir Keivan MOHTASHAMI ◽  
Mohammad ROGHANI ◽  
Hamid ZARRABI-ZADEH
Keyword(s):  
Command Line ◽  
Web Interface ◽  
Command Line Interface ◽  
System A ◽  
Task Preparation

The task preparation system (TPS) is a tool developed mainly for preparing IOI tasks. It was originally developed for, and successfully used in IOI 2017, and since then, it has been used in several other nationwide and international programming contests, including IOI 2019. The tool consists of a command-line interface for local (offline) work, and a web interface which integrates with git and provides more features. This article presents the main features of the task preparation system, and briefly describes how it works.

era5cli: The command line tool to download ERA5 data

2020 ◽  
Author(s):  
Jaro Camphuijsen ◽  
Ronald van Haren ◽  
Yifat Dzigan ◽  
Niels Drost ◽  
Fakhareh Alidoost ◽  
...  
Keyword(s):  
Source Code ◽  
Reanalysis Data ◽  
Command Line ◽  
Climate Data ◽  
Web Interface ◽  
Command Line Interface ◽  
Short Introduction ◽  
Data Store ◽  
Command Line Tool ◽  
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 era5cli. </p><p>The command line interface tool era5cli 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, era5cli adds several useful functionalities to the download pipeline.</p><p>One of the key options in era5cli 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 `info` command lists correct names of the available variables and pressure levels for 3D variables. For debugging purposes and testing the `--dryrun` 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. Source code is available on https://github.com/eWaterCycle/era5cli.</p><p>In this PICO presentation we will provide an overview of era5cli, as well as a short introduction on how to use era5cli.</p>

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