scholarly journals Simplifying the development of portable, scalable, and reproducible workflows

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Stephen R Piccolo ◽  
Zachary E Ence ◽  
Elizabeth C Anderson ◽  
Jeffrey T Chang ◽  
Andrea H Bild

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents conform to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create ‘input-object’ files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine. ToolJig and our examples are available at https://github.com/srp33/ToolJig.

2021 ◽  
Author(s):  
Stephen R Piccolo ◽  
Zachary E Ence ◽  
Elizabeth C Anderson ◽  
Jeffrey T Chang ◽  
Andrea H Bild

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool's inputs, outputs, and other execution details in a manner that fosters use of shared computational methods and reproducibility of complex analyses. CWL documents can include instructions for executing tools inside software containers-isolated, operating-system environments. Accordingly, CWL tools are portable-they can be executed on diverse computers-including personal workstations, high-performance clusters, or the cloud. This portability enables easier adoption of bioinformatics pipelines. CWL supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents confirm to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create "input-object" files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine.


2017 ◽  
Vol 2017 ◽  
pp. 1-4
Author(s):  
Vojtech Vigner ◽  
Jaroslav Roztocil

Comparison of high-performance time scales generated by atomic clocks in laboratories of time and frequency metrology is usually performed by means of the Common View method. Laboratories are equipped with specialized GNSS receivers which measure the difference between a local time scale and a time scale of the selected satellite. Every receiver generates log files in CGGTTS data format to record measured differences. In order to calculate time differences recorded by two receivers, it is necessary to obtain these logs from both receivers and process them. This paper deals with automation and speeding up of these processes.


1994 ◽  
Vol 05 (05) ◽  
pp. 805-809 ◽  
Author(s):  
SALIM G. ANSARI ◽  
PAOLO GIOMMI ◽  
ALBERTO MICOL

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.


2021 ◽  
Vol 83 (10) ◽  
Author(s):  
Alfonso Ruiz-Herrera ◽  
Pedro J. Torres

AbstractIn this paper, we analyze the influence of the usual movement variables on the spread of an epidemic. Specifically, given two spatial topologies, we can deduce which topology produces less infected individuals. In particular, we determine the topology that minimizes the overall number of infected individuals. It is worth noting that we do not assume any of the common simplifying assumptions in network theory such as all the links have the same diffusion rate or the movement of the individuals is symmetric. Our main conclusion is that the degree of mobility of the population plays a critical role in the spread of a disease. Finally, we derive theoretical insights to management of epidemics.


2021 ◽  
Author(s):  
Clare Guss-West

The Western approach to dance is largely focused on control and mastery of technique, both of which are certainly necessary skills for improving performance. But mindful attention, despite its critical role in high performance, has gotten short shrift—until now. Attention and Focus in Dance, a how-to book rooted in the 20 years of attentional focus findings of researcher Gabriele Wulf, will help dancers unlock their power and stamina reserves, enabling efficient movement, heightening their sensory perception and releasing their dance potential. Author Clare Guss-West—a professional dancer, choreographer, teacher and holistic practitioner—presents a systematic, science-based approach to the mental work of dance. Her approach helps dancers hone the skills of attention, focus and self-cueing to replenish energy and enhance their physical and artistic performance. A Unique, Research-Based Approach Here is what Attention and Focus in Dance offers readers: • A unique approach, connecting the foundations of Eastern movement with Western movement forms • Research-based teaching practices in diverse contexts, including professional dance companies, private studios, and programmes for dancers with special needs or movement challenges • Testimonies and tips from international professional dancers and dance educators who use the book's approach in their training and teaching • A dance-centric focus that can be easily integrated into existing training and teaching practice, in rehearsal, or in rehabilitation contexts to provide immediate and long-term benefits Guss-West explores attentional focus techniques for dancers, teachers and dance health care practitioners, making practical connections between research, movement theory and day-to-day dance practice. “Many dancers are using excessive energy deployment and significant counterproductive effort, and that can lead to a global movement dysfunction, lack of stamina and an increased risk of injury,” says Guss-West. “Attentional focus training is the most relevant study that sport science and Eastern-movement practice can bring to dance.” Book Organisation The text is organised into two parts. Part I guides dancers in looking at the attentional challenges and information overload that many professional dancers suffer from. It outlines the need for a systematic attention and focus strategy, and it explains how scientific research on attentional focus relates to dance practice. This part also examines the ways in which Eastern-movement principles intersect with and complement scientific findings, and it examines how the Eastern and scientific concepts can breathe new life into basic dance elements such as posture, turnout and port de bras. Attention and focus techniques are included for replenishing energy and protecting against energy depletion and exhaustion. Part II presents attention and focus strategies for teaching, self-coaching and cueing. It addresses attentional focus cues for beginners and for more advanced dancers and professionals, and it places attentional focus in the broader context of holistic teaching strategies. Maximising Dance Potential “Whether cueing others or yourself, cueing for high performance is an art,” Guss-West says. “Readers will discover how to format cues and feedback to facilitate effective neuromuscular response and enhance dancer recall of information and accessibility while dancing.” Attention and Focus in Dance offers an abundance of research-backed concepts and inspirational ideas that can help dancers in their learning and performance. This book aids readers in filtering information and directing their focus for optimal physical effect. Ultimately, it guides dancers and teachers in being the best version of themselves and maximising their potential in dance.


2018 ◽  
Vol 2018 ◽  
pp. 1-13
Author(s):  
Manuel Romana ◽  
Marilo Martin-Gasulla ◽  
Ana T. Moreno

Most of the rural transportation system is composed of two-lane highways, and many of them serve as the primary means for rural access to urban areas and freeways. In some highways, traffic volumes can be not high enough to justify a four-lane highway but higher than can be served by isolated passing lanes, or can present high number of head-on collisions. In those conditions, 2 + 1 highways are potentially applicable. This type of highway is used to provide high-performance highways as intermediate solution between the common two-lane highway and the freeway. Successful experiences reported in Germany, Sweden, Finland, Poland, or Texas (US) may suggest that they are potentially applicable in other countries. The objective of this white paper is to provide an overview of the past practice in 2 + 1 highways and discuss the research directions and challenges in this field, specially focusing on, but not limited to, operational research in association with the activities of the Subcommittee on Two-Lane Highways (AHB40 2.2) of the Transportation Research Board. The significance of this paper is twofold: (1) it provides wider coverage of past 2 + 1 highways design and evaluation, and (2) it discusses future directions of this field.


2017 ◽  
Vol 12 (5) ◽  
pp. 704-706 ◽  
Author(s):  
Alan McCall ◽  
Maurizio Fanchini ◽  
Aaron J. Coutts

In high-performance sport, science and medicine practitioners employ a variety of physical and psychological tests, training and match monitoring, and injury-screening tools for a variety of reasons, mainly to predict performance, identify talented individuals, and flag when an injury will occur. The ability to “predict” outcomes such as performance, talent, or injury is arguably sport science and medicine’s modern-day equivalent of the “Quest for the Holy Grail.” The purpose of this invited commentary is to highlight the common misinterpretation of studies investigating association to those actually analyzing prediction and to provide practitioners with simple recommendations to quickly distinguish between methods pertaining to association and those of prediction.


2010 ◽  
Vol 135 (2) ◽  
pp. 115-134 ◽  
Author(s):  
Susan Meier ◽  
Neslihan N. Tavraz ◽  
Katharina L. Dürr ◽  
Thomas Friedrich

The Na+/K+-ATPase mediates electrogenic transport by exporting three Na+ ions in exchange for two K+ ions across the cell membrane per adenosine triphosphate molecule. The location of two Rb+ ions in the crystal structures of the Na+/K+-ATPase has defined two “common” cation binding sites, I and II, which accommodate Na+ or K+ ions during transport. The configuration of site III is still unknown, but the crystal structure has suggested a critical role of the carboxy-terminal KETYY motif for the formation of this “unique” Na+ binding site. Our two-electrode voltage clamp experiments on Xenopus oocytes show that deletion of two tyrosines at the carboxy terminus of the human Na+/K+-ATPase α2 subunit decreases the affinity for extracellular and intracellular Na+, in agreement with previous biochemical studies. Apparently, the ΔYY deletion changes Na+ affinity at site III but leaves the common sites unaffected, whereas the more extensive ΔKETYY deletion affects the unique site and the common sites as well. In the absence of extracellular K+, the ΔYY construct mediated ouabain-sensitive, hyperpolarization-activated inward currents, which were Na+ dependent and increased with acidification. Furthermore, the voltage dependence of rate constants from transient currents under Na+/Na+ exchange conditions was reversed, and the amounts of charge transported upon voltage pulses from a certain holding potential to hyperpolarizing potentials and back were unequal. These findings are incompatible with a reversible and exclusively extracellular Na+ release/binding mechanism. In analogy to the mechanism proposed for the H+ leak currents of the wild-type Na+/K+-ATPase, we suggest that the ΔYY deletion lowers the energy barrier for the intracellular Na+ occlusion reaction, thus destabilizing the Na+-occluded state and enabling inward leak currents. The leakage currents are prevented by aromatic amino acids at the carboxy terminus. Thus, the carboxy terminus of the Na+/K+-ATPase α subunit represents a structural and functional relay between Na+ binding site III and the intracellular cation occlusion gate.


2011 ◽  
Vol 36 (4) ◽  
pp. 214-218 ◽  
Author(s):  
Sylvia Holthoff ◽  
Lotte Junker Harbo

“Now I can actually play soccer with the young people without fearing that my colleagues think I am escaping the paper work.”These were the words from a participant in a social pedagogy training course in England a few years ago. This understanding emerged through in-depth discussions and activities around key social pedagogical concepts, such as the ‘common third’, the ‘3Ps’, the ‘zone of proximal development’ and the ‘learning zone model’. In this article we will explore how a joint activity, for example, playing soccer, can be seen as a pedagogical activity and with what intentions it is undertaken to make it pedagogically purposeful.


Author(s):  
Oyuna Tsydendambaeva ◽  
Olga Dorzheeva

This article is dedicated to the examination of euphemisms in the various-system languages – English and Buryat that contain view of the world by a human, and the ways of their conceptualization. Euphemisms remain insufficiently studied. Whereupon, examination of linguistic expression of the key concepts of culture is among the paramount programs of modern linguistics, need for the linguoculturological approach towards analysis of euphemisms in the languages, viewing it in light of the current sociocultural transformations, which are refer to euphemisms and values reflected by them. The subject of this research is the euphemisms in the English and Buryat languages, representing the semiosphere “corporeal and spiritual”. The scientific novelty consists in introduction of the previously unexamined euphemism in Buryat language that comprise semiosphere “corporeal and spiritual” into the scientific discourse. The analysis of language material testifies to the fact that in various cultures the topic of intimacy and sex is euphemized differently. The lexis indicating the intimate parts of the body is vividly presented in the West, while in Buryat language – rather reserved. The author also determines the common, universal, and nationally marked components elucidating the linguistic worldview of different ethnoses and cultures.


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