scholarly journals Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees

2020 ◽  
Vol 16 ◽  
pp. 117693431989938
Author(s):  
Van D Nguyen ◽  
Thanh H Nguyen ◽  
Abu Saleh Md Tayeen ◽  
H Dail Laughinghouse ◽  
Luna L Sánchez-Reyes ◽  
...  
Keyword(s):  
Tree Of Life ◽  
Online Resources ◽  
Research Education ◽  
Geologic Time ◽  
Current State ◽  
Mapping Software ◽  
As Species ◽  
Custom Made ◽  
Special Knowledge ◽  
Thumbnail Images

A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy. Yet, accessing the tree of life typically requires special knowledge, complex software, or long periods of training. The Phylotastic project aims make it as easy to get a phylogeny of species as it is to get driving directions from mapping software. In prior work, we presented a design for an open system to validate and manage taxon names, find phylogeny resources, extract subtrees matching a user’s taxon list, scale trees to time, and integrate related resources such as species images. Here, we report the implementation of a set of tools that together represent a robust, accessible system for on-the-fly delivery of phylogenetic knowledge. This set of tools includes a web portal to execute several customizable workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); more than 30 underlying web services (accessible via a common registry); and code toolkits in R and Python (allowing others to develop custom applications using Phylotastic services). The Phylotastic system, accessible via http://www.phylotastic.org , provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.

scholarly journals Phylotastic: improving access to tree-of-life knowledge with flexible, on-the-fly delivery of trees

2018 ◽  
Author(s):  
Van D. Nguyen ◽  
Thanh H. Nguyen ◽  
Abu Saleh Md. Tayeen ◽  
H. Dail Laughinghouse ◽  
Luna L. Sánchez-Reyes ◽  
...  
Keyword(s):  
Web Services ◽  
Tree Of Life ◽  
Online Resources ◽  
Species List ◽  
Geologic Time ◽  
Current State ◽  
Custom Made ◽  
Special Knowledge ◽  
Research And Education ◽  
Thumbnail Images

Abstract(1) A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts in research and education. This potential is limited if accessing the tree of life requires special knowledge, complex software, or long periods of training.(2) The Phylotastic project aims to use web-services technologies to lower the barrier for accessing phylogenetic knowledge, making it as easy to get a phylogeny of species as it is to get online driving directions. In prior work, we designed an open system of web services to validate and manage species names, find phylogeny resources, extract subtrees matching a user’s species list, calibrate them, and mash them up with images and information from online resources.(3) Here we report a publicly accessible system for on-the-fly delivery of phylogenetic knowledge, developed with user feedback on what types of functionality are considered useful by researchers and educators. The system currently consists of a web portal that implements 3 types of workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); 19 underlying web services accessible via a common registry; and toolbox code in R and Python so that others can create applications that leverage these services. These resources cover most of the use-cases identified in our analysis of user needs.(4) The Phylotastic system, accessible viahttp://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.

scholarly journals Web tools to fight pandemics: the COVID-19 experience

2020 ◽  
Author(s):  
Daniele Mercatelli ◽  
Andrew N Holding ◽  
Federico M Giorgi
Keyword(s):  
Clinical Data ◽  
State Of The Art ◽  
Online Resources ◽  
Current State ◽  
Web Tools ◽  
Current Outbreak ◽  
Online Methods

Abstract The current outbreak of COVID-19 has generated an unprecedented scientific response worldwide, with the generation of vast amounts of publicly available epidemiological, biological and clinical data. Bioinformatics scientists have quickly produced online methods to provide non-computational users with the opportunity of analyzing such data. In this review, we report the results of this effort, by cataloguing the currently most popular web tools for COVID-19 research and analysis. Our focus was driven on tools drawing data from the fields of epidemiology, genomics, interactomics and pharmacology, in order to provide a meaningful depiction of the current state of the art of COVID-19 online resources.

The Oxford Handbook of Interdisciplinarity

2017 ◽  
Keyword(s):  
Interdisciplinary Research ◽  
Academic Community ◽  
Education Administration ◽  
Public And Private ◽  
Policy Makers ◽  
Research Education ◽  
Multiple Networks ◽  
Current State ◽  
Societal Needs ◽  
International Advisory

The second edition of The Oxford Handbook of Interdisciplinarity constitutes an update and revision of a topic of growing academic and societal importance. Interdisciplinarity continues to be prominent both within and outside academia. Academics, policy makers, and members of public and private sectors seek approaches to help organize and integrate the vast amounts of knowledge being produced today, both within research and at all levels of education. This compendium is distinguished by its breadth of coverage, with chapters written by experts from multiple networks and organizations, on topics ranging across science and technology; social sciences, humanities, and arts; and professions. The volume is edited by respected interdisciplinary scholars and supported by an international advisory board to ensure the highest quality and breadth of coverage. The Oxford Handbook of Interdisciplinarity provides a synoptic overview of the current state of interdisciplinary research, education, administration and management, and problem solving—knowledge that spans the disciplines and interdisciplinary fields while also crossing the boundary between the academic community and society at large. Offering the most broad-based account of inter- and transdisciplinarity to date, its essays bring together many of the globe’s leading thinkers on interdisciplinary research, education, and institutional parameters as well as reflections on how knowledge can be better integrated with societal needs.

scholarly journals DateLife: Leveraging databases and analytical tools to reveal the dated Tree of Life

2019 ◽  
Author(s):  
Luna L. Sánchez-Reyes ◽  
Brian C. O’Meara
Keyword(s):  
Science Communication ◽  
Divergence Time ◽  
Analytical Techniques ◽  
Branch Length ◽  
Molecular Data ◽  
Academic Community ◽  
Tree Of Life ◽  
Published Data ◽  
Research Education ◽  
Patristic Distance

abstractThe combination of new analytical techniques, availability of more fossil and molecular data, and better practices in data sharing has resulted in a steady accumulation of chronograms in public and open databases such as TreeBASE, Dryad, and Open Tree of Life for a large quantity and diversity of organisms in the last few decades. However, getting a tree with branch lengths proportional to time remains difficult for many biologists and the non-academic community, despite its importance in many areas of research, education, and science communication. datelife is a service implemented via an R package and a web site (http://www.datelife.org/) for efficient reuse, summary and reanalysis of published data on lineage divergence times. The main workflow starts with at least two taxon names as input, either as tip labels on a tree, or as a simple comma separated character string. A name search is then performed across the chronogram database and positively identified source trees are pruned to maintain queried taxa only and stored as a named list of patristic distance matrices. Source chronogram data can be summarised using branch length summary statistics or variance minimizing approaches to generate a single summary chronogram. Source chronogram data can also be used as calibration points to date a tree containing some or all names from the initial query. If there is no information available for any queried taxa, data can be simulated. All source and summary chronograms can be saved in formats that permit easy reuse and reanalysis. Summary and newly generated trees are potentially useful to evaluate evolutionary hypothesis in different areas of research in biology. How well this trees work for this purpose still needs to be tested. datelife will be useful to increase awereness on the existing variation in expert time of divergence data, and might foster exploration of the effect of alternative divergence time hypothesis on the results of analyses, nurturing a culture of more cautious interpretation of evolutionary results.

Profiler as an expert – selected issues

2017 ◽  
Vol 298 ◽  
pp. 69-75
Author(s):  
Karolina Olszak-Häußler ◽  
Keyword(s):  
Literature Review ◽  
Present Article ◽  
Expert Opinion ◽  
Criminal Procedure ◽  
Criminal Profiling ◽  
Media Attention ◽  
Expert Opinions ◽  
Current State ◽  
Special Knowledge ◽  
Criminal Profile

Despite the fact that criminal profiling attracts massive media attention, our knowledge about the process of elaborating expert opinions containing criminal profiles is very limited. Based on the literature review, the author attempts to answer the questions: what is the objective of appointing an expert in the field of criminal profiling? and, which criteria should be applied to the evaluation of expert opinion?. Based on the content of the present article, it can be concluded that the current state of knowledge does not allow to determine unequivocally whether the profiler needs special knowledge, nor what should be the scope of such knowledge. Moreover, it cannot be clearly determined, whether the profile provides information of relevance to the resolution of the case. However, there is no doubt that wherever criminal profile takes the form of an expert opinion, it should be subject to very careful control, in accordance with the provisions of the Code of Criminal Procedure and doctrine recommendations regarding this matter.

scholarly journals Middle Ages for Educators 1st Edition (June 2020) Archiving Dossier Narrative

2020 ◽  
Author(s):  
Merle Eisenberg ◽  
Sara McDougall ◽  
Laura Morreale
Keyword(s):  
Middle Ages ◽  
Late Antiquity ◽  
Lesson Plans ◽  
Primary Sources ◽  
Online Resources ◽  
Bulletin Board ◽  
Digital Resources ◽  
Online Resource ◽  
Custom Made ◽  
The Middle Ages

Middle Ages for Educators is an online resource created in April 2020 to aggregate digital resources for the study of Late Antiquity and the Middle Ages. The site includes links to online resources, custom-made videos on medieval topics by experts in the field with discussion questions and further readings, primary sources translated into English, lesson plans, and a bulletin board for research exchange.

Capability for continuous improvement

2016 ◽  
Vol 28 (2) ◽  
pp. 250-274 ◽  
Author(s):  
Rodrigo Valio Dominguez Gonzalez ◽  
Manoel Fernando Martins
Keyword(s):  
Employee Engagement ◽  
Continuous Improvement ◽  
Qualitative Approach ◽  
Automotive Sector ◽  
Capital Goods ◽  
Content Type ◽  
Current State ◽  
Custom Made ◽  
Improvement Programs ◽  
Two Sectors

Purpose – The current state of the art on continuous improvement takes into consideration that capabilities and organizational behaviors are more important elements for conduction and sustainability than the technical aspects. This set of capabilities and behaviors, initially addressed by Bessant and Caffyn in the 1990s, essentially considers that organizations should build an environment focussed on continuous learning. Thus, the purpose of this paper is to analyze the development of capabilities that support continuous improvement programs in two distinct productive environments: the automotive sector and the custom made capital goods sector. Design/methodology/approach – From a theoretical reference on the subject, a set of capabilities that are related to the practice of continuous improvement is raised and, through a qualitative approach, four companies of the two sectors considered are analyzed using a case study strategy. Findings – The research results suggest that the companies researched in the automotive sector have a higher level of employee engagement in relation to continuous improvement programs compared to the companies in the capital goods sector, which is justified by the strategy adopted by the organizations. Research limitations/implications – As any qualitative approach, this research presents restrictions regarding the generalization of the results for the studied sectors. Originality/value – The contribution of this paper can be divided into two parts. The first one refers to the identification of a current framework of capabilities that support continuous improvement, and the second one is the evaluation of the development of these capabilities in two sectors with different productive contexts (automotive and custom made capital goods).

scholarly journals ON THE FORENSIC EXPERT RESEARCH OF THE DECISION CONTENT MADE BY THE COMMANDER

2017 ◽  
Vol 17 ◽  
pp. 381-391
Author(s):  
I. V. Bogdanyuk
Keyword(s):  
Decision Making ◽  
Research Work ◽  
International Standards ◽  
Decision Making Process ◽  
Management Activity ◽  
Armed Struggle ◽  
Current State ◽  
Organization Process ◽  
Special Knowledge ◽  
Forensic Expert

The paper presents the factors which stipulated inadequate efficiency of application of antiterrorist operation forces. Their military character and the relation to a component of such sphere of military art as military management are defined. It’s specified that decision-making constituents a basis of management activity in various spheres of human activity. There is noted a problem of deficiency of the scientific-methodical support oriented at the decision offorensic expert problems within the limits of military researches. The attention is focused that the current state of the struggle against criminality demands an increase of an expert work efficiency, namely, to work out expert techniques according to the international standards. It’s noticed that in this relation the Kharkiv research institute of forensic examination initiated performing research work on the theme «The technique of forensic-expert research of the work of commanders (staffs) and militaryformations in preparing and performing of combat (service-combat) tasks». It’s noticed that development and improvement of the means of armed struggle leads to the change of characteristics of the battle and essentially influences on the content and the technique of the commander and staff work as to its organization. The content of the organization process of the battle (combat operations) is presented. The methods of the commander (staff) work on the organization of combat operations are considered. The purpose of each element of decision-making process and the content of conclusions from them, made the commander, are specified. There’s defined that forensic experts on a specialty «Military researches», using special knowledge in the analysis of the commander decision by means of researching conformity of the process content and the technique on elaborating conclusions on evaluating situation elements, have a possibility to determine its expediency.

scholarly journals Changes in vegetation of the Mszar Bogdaniec nature reserve

2016 ◽  
Vol 77 (2) ◽  
pp. 104-116
Author(s):  
Marcin K. Dyderski ◽  
Andrzej M. Jagodziński
Keyword(s):  
Plant Communities ◽  
Nature Reserve ◽  
Detrended Correspondence Analysis ◽  
Woody Species ◽  
Monitoring And Evaluation ◽  
Ecological Traits ◽  
Current State ◽  
As Species ◽  
Phytosociological Relevés

Abstract Changes of vegetation in forests and wetlands require continuous monitoring and evaluation. Due to the lack of in-depth knowledge, it is still very challenging to predict and record vegetation changes. This study attempts to evaluate changes in forest and transitional bog vegetation over 14 years in the Mszar Bogdaniec nature reserve (West Poland; 21.98 ha). We described the current vegetation using 50 phytosociological relevés conducted in 2012 and 2013. Moreover, we calculated and compared ecological indices describing ecological traits of the vegetation in two different times. We also used Detrended Correspondence Analysis (DCA) to assess changes in floral composition. Most of the studied vegetation traits did not change significantly during the last 14 years. Statistically significant changes occured in the proportion of mosses and cover of the herb layer, both of which increased, as well as species richness in forest plant communities, and the cover of species from Scheuchzerio-Caricetea class in peat bog plant communities, both of which decreased. The current state of the vegetation is a result of former human activity such as drainage and planting monoculture tree stands. The observed changes during the last 14 years were fluctuations rather than direct changes. Encroachment of the woody species into transitional bog is a fluctuation, which may be secondary succession in the long-term.

scholarly journals Current state of 3D-printed custom-made spinal implants

2019 ◽  
Vol 1 (4) ◽  
pp. e149-e150 ◽  
Author(s):  
Wen Jie Choy ◽  
Ralph J Mobbs
Keyword(s):  
Spinal Implants ◽  
Current State ◽  
Custom Made ◽  
3D Printed
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