scholarly journals OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life

2020 ◽  
Author(s):  
Emily Jane McTavish ◽  
Luna L Sanchez Reyes ◽  
Mark T. Holder
Keyword(s):  
Phylogenetic Trees ◽  
Tree Of Life ◽  
University Of California ◽  
Life Project ◽  
Application Programming ◽  
Service Application ◽  
The University ◽  
User Friendly ◽  
Programming Interfaces ◽  
Python Package

The Open Tree of Life project constructs a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the python package 'opentree', which provides a user friendly python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.

scholarly journals TreeSwift: a massively scalable Python tree package

2018 ◽  
Author(s):  
N. Moshiri
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Phylogenetic Information ◽  
Large Trees ◽  
Wide Range ◽  
User Friendly ◽  
Python Package

AbstractPhylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt to extract phylogenetic information applicable to a wide range of disciplines, such as epidemiology and metagenomics. Currently, the three main Python packages for trees are Bio.Phylo, DendroPy, and the ETE Toolkit, but as dataset sizes grow, parsing and manipulating ultra-large trees becomes impractical for these tools. To address this issue, we present TreeSwift, a user-friendly and massively scalable Python package for traversing and manipulating trees that is ideal for algorithms performed on ultra-large trees.

Case Studies: Stahl's Essential Psychopharmacology

2021 ◽  
Keyword(s):  
Case Studies ◽  
Real Life ◽  
Clinical Encounter ◽  
University Of California ◽  
Clinical Scenarios ◽  
The Everyday ◽  
Representative Selection ◽  
The University ◽  
User Friendly ◽  
Selection Of

Following the success of the first two volumes in Stahl's Case Studies series, a brand new collection of clinical stories have been collated in Volume 3, derived from cases seen by medical students, residents and faculty from the University of California at Riverside (UCR) Department of Psychiatry and Neuroscience. The highly popular and unique user-friendly presentation of previous volumes has been maintained, with extensive use of icons, questions/answers, and tips. The cases address multifaceted issues in an understandable way and with direct relevance to the everyday experience of clinicians. Covering a wide-ranging and representative selection of clinical scenarios, each case is followed through the complete clinical encounter, from start to resolution, acknowledging all the complications, issues, decisions, twists and turns along the way. The book is about living through the treatments that work, the treatments that fail, and the mistakes made along the journey. This is psychiatry in real life.

scholarly journals Meeting Users Where They Are

2020 ◽  
Vol 39 (1) ◽  
Author(s):  
Graham Sherriff ◽  
Dan DeSanto ◽  
Daisy Benson ◽  
Gary S. Atwood
Keyword(s):  
User Profile ◽  
High Impact ◽  
Self Management ◽  
Online Spaces ◽  
One Stop ◽  
Application Programming ◽  
The University ◽  
University Of Vermont ◽  
Programming Interfaces

Campus portals are one of the most visible and frequently used online spaces for students, offering one-stop access to key services for learning and academic self-management. This case study reports how instruction librarians at the University of Vermont collaborated with portal developers in the registrar’s office to develop high-impact, point-of-need content for a dedicated “Library” page. This content was then created in LibGuides and published using the Application Programming Interfaces (APIs) for LibGuides boxes. Initial usage data and analytics show that traffic to the libraries’ portal page has been substantially and consistently higher than expected. The next phase for the project will be the creation of customized library content that is responsive to the student’s user profile.

scholarly journals Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luna L. Sánchez-Reyes ◽  
Martha Kandziora ◽  
Emily Jane McTavish
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Open Science ◽  
Tree Of Life ◽  
Matrix Assembly ◽  
Life Project ◽  
Character Matrix ◽  
Molecular Dataset ◽  
Phylogenetic Hypotheses

Abstract Background Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. Results Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. The program can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). Conclusion The Physcraper workflow showcases the benefits of doing open science for phylogenetics, encouraging researchers to strive for better scientific sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and usage are available at https://physcraper.readthedocs.io.

scholarly journals AITSO: A Tool for Spatial Optimization Based on Artificial Immune Systems

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Xiang Zhao ◽  
Yaolin Liu ◽  
Dianfeng Liu ◽  
Xiaoya Ma
Keyword(s):  
Spatial Analysis ◽  
Optimization Problems ◽  
Artificial Immune Systems ◽  
Spatial Optimization ◽  
Artificial Immune ◽  
Immune Systems ◽  
Standard Application ◽  
Application Programming ◽  
User Friendly ◽  
Programming Interfaces

A great challenge facing geocomputation and spatial analysis is spatial optimization, given that it involves various high-dimensional, nonlinear, and complicated relationships. Many efforts have been made with regard to this specific issue, and the strong ability of artificial immune system algorithms has been proven in previous studies. However, user-friendly professional software is still unavailable, which is a great impediment to the popularity of artificial immune systems. This paper describes a free, universal tool, named AITSO, which is capable of solving various optimization problems. It provides a series of standard application programming interfaces (APIs) which can (1) assist researchers in the development of their own problem-specific application plugins to solve practical problems and (2) allow the implementation of some advanced immune operators into the platform to improve the performance of an algorithm. As an integrated, flexible, and convenient tool, AITSO contributes to knowledge sharing and practical problem solving. It is therefore believed that it will advance the development and popularity of spatial optimization in geocomputation and spatial analysis.

Dialogues

2020 ◽  
Vol 2 (3) ◽  
pp. 53-59
Keyword(s):  
Los Angeles ◽  
New Spain ◽  
American Art ◽  
Historical Trauma ◽  
State Building ◽  
University Of California ◽  
Religious Experiences ◽  
Political Space ◽  
California Missions ◽  
The University

The California missions, whose original church spaces and visual programs were produced by Iberian, Mexican, and Native artisans between 1769 and 1823, occupy an ambiguous chronological, geographical, and political space. They occupy lands that have pertained to conflicting territorialities: from Native nations, to New Spain, to Mexico, to the modern multicultural California. The physical and visual landscapes of the missions have been sites of complex and often incongruous religious experiences; historical trauma and romantic vision; Indigenous genocide, exploitation, resistance, and survivance; state building and global enterprise. This Dialogues section brings together critical voices, including especially the voices of California Indian scholars, to interrogate received models for thinking about the art historical legacies of the California missions. Together, the contributing authors move beyond and across borders and promote new decolonial strategies that strive to be responsive to the experience of California Indian communities and nations. This conversation emerges from cross-disciplinary relationships established at a two-day conference, “‘American’ Art and the Legacy of Conquest: Art at California’s Missions in the Global 18th–20th Centuries,” sponsored by the Terra Foundation for American Art and held at the University of California, Los Angeles, in November 2019.

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