scholarly journals Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

2021 ◽  
Vol 22 (S15) ◽  
Author(s):  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
Matteo Chiara ◽  
Giacinto Donvito ◽  
Marica Antonacci ◽  
...  
Keyword(s):  
Rapid Development ◽  
Use Cases ◽  
Bioinformatics Analyses ◽  
On Demand ◽  
Bioinformatics Tools ◽  
Global Pandemic ◽  
The Galaxy ◽  
Set Up ◽  
One Year ◽  
The Many

Abstract Background Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server’s initial configuration and deployment. Results “Laniakea@ReCaS”, the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. Conclusions During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers’ work.

scholarly journals Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage

2019 ◽  
Vol 35 (18) ◽  
pp. 3453-3460 ◽  
Author(s):  
Anastasia Tyryshkina ◽  
Nate Coraor ◽  
Anton Nekrutenko
Keyword(s):  
Random Forest ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Resource Requirement ◽  
Bioinformatics Analyses ◽  
Runtime Prediction ◽  
The Galaxy ◽  
Processing Resources ◽  
Resource Usage Prediction ◽  
The Many

Abstract Motivation One of the many technical challenges that arises when scheduling bioinformatics analyses at scale is determining the appropriate amount of memory and processing resources. Both over- and under-allocation leads to an inefficient use of computational infrastructure. Over allocation locks resources that could otherwise be used for other analyses. Under-allocation causes job failure and requires analyses to be repeated with a larger memory or runtime allowance. We address this challenge by using a historical dataset of bioinformatics analyses run on the Galaxy platform to demonstrate the feasibility of an online service for resource requirement estimation. Results Here we introduced the Galaxy job run dataset and tested popular machine learning models on the task of resource usage prediction. We include three popular forest models: the extra trees regressor, the gradient boosting regressor and the random forest regressor, and find that random forests perform best in the runtime prediction task. We also present two methods of choosing walltimes for previously unseen jobs. Quantile regression forests are more accurate in their predictions, and grant the ability to improve performance by changing the confidence of the estimates. However, the sizes of the confidence intervals are variable and cannot be absolutely constrained. Random forest classifiers address this problem by providing control over the size of the prediction intervals with an accuracy that is comparable to that of the regressor. We show that estimating the memory requirements of a job is possible using the same methods, which as far as we know, has not been done before. Such estimation can be highly beneficial for accurate resource allocation. Availability and implementation Source code available at https://github.com/atyryshkina/algorithm-performance-analysis, implemented in Python. Supplementary information Supplementary data are available at Bioinformatics online.

ENVIRONMENTAL EDUCATION FOR SCHOOLCHILDREN IN A SEAWATER POND FOR CREATING A SATOUMI

2017 ◽  
Author(s):  
Mari Maeda ◽  
Mari Maeda ◽  
Yasunori Kozuki ◽  
Yasunori Kozuki ◽  
Ken Hirai ◽  
...  
Keyword(s):  
Environmental Education ◽  
Food Chain ◽  
Tidal Flats ◽  
Reclaimed Land ◽  
Hyogo Prefecture ◽  
Set Up ◽  
One Year

In 2006, Hyogo prefecture opened the “Araihamakaze” park on reclaimed land leased with cooperation from some companies, and set up a seawater pond called “Konourafuna Ike” in the park. The initial plan was to make this seawater pond into a Satoumi, but since the water in the pond was stagnant, algae flourished making it uninhabitable for other living creatures. The authors conducted investigative research to implement activities for improving the environment and popularizing the park. This report is a summary of the results obtained and challenges faced while conducting these activities in the area over one year, which included involving the local schoolchildren in constructing tidal flats. The answers to the questionnaire revealed that schoolchildren understood that the nutrients in the seawater pond “go round and round” through the food chain and are utilized by living creatures. They realized that this process is called “circulation.”To the question, “Do you want to develop tidal flats?” 9 of the 10 children answered YES. However, only 50% of the children understood that a measure to prevent the degradation of the environment of the seawater pond is to “Construct tidal flats,” which suggested that there is a need to correlate the issues and the solutions to enhance their understanding.

The Union of Laughter and Forgetting? The European Union and the Construction of its own History

2006 ◽  
Author(s):  
Hernan Tesler-Mabe
Keyword(s):  
European Union ◽  
Great Part ◽  
The European Union ◽  
European Constitution ◽  
Close Study ◽  
Dramatic Shift ◽  
One Year ◽  
The Many ◽  
Teleological Interpretation ◽  
Compare And Contrast

As recently as one year ago, the European Union was seemingly on a direct path toward its avowed goal of "ever closer union." In numerous publications, EU authorities asserted that they had the confidence of European peoples desirous only of further integration. In the wake of the failed referenda for a European Constitution, however, enthusiasts of European Union can no longer be certain that their enterprise will succeed. The European Union, once strong and united, seems now an entity teetering on the edge of collapse. The reasons for such a dramatic shift are, of course, wide-ranging. Yet I would suggest that a great part of the general European disillusionment with European Union has come about as a result of the actions of the Europeanists themselves. Over the last decades, European officials have exhibited a frightfully high incidence of revisionism in their literature. This practice, I argue, has caused many Europeans to question the integrity of the project of European Union. For my presentation, I intend to undertake a close study of a selection of documents published by the European Communities. In this endeavour, I will compare and contrast the messages imparted in different editions of these works and consider the semiotic significance of the textual and non-textual language appearing therein. In this manner, I hope to achieve two aims. First, I mean to add a corrective element to a literature that, guided by a teleological interpretation of integration, endows integration with”logic" to be found only in hindsight. Second, I intend to examine the many meanings that the EU has had over its history and assess how closely policy has adhered to the ideological goals of prominent Europeanists. In sum, I hope to shed light on the fundamental disconnect between advocates of Europe and the "man on the street" and help establish a dialogue which may contribute to resolving the current impasse within the European Union. Full text available: https://doi.org/10.22215/rera.v2i4.178

scholarly journals Licorice: A Potential Herb in Overcoming SARS-CoV-2 Infections

2021 ◽  
Vol 26 ◽  
pp. 2515690X2199666
Author(s):  
Swee Li Ng ◽  
Kooi-Yeong Khaw ◽  
Yong Sze Ong ◽  
Hui Poh Goh ◽  
Nurolaini Kifli ◽  
...  
Keyword(s):  
Treatment Guidelines ◽  
Food Ingredient ◽  
Active Immunisation ◽  
Reference Guide ◽  
Global Pandemic ◽  
Biological Potential ◽  
Set Up ◽  
Surprising Fact ◽  
Epidemic Diseases ◽  
Roll Out

The management of the global pandemic outbreak due to the coronavirus disease (COVID-19) has been challenging with no exact dedicated treatment nor established vaccines at the beginning of the pandemic. Nonetheless, the situation seems to be better controlled with the recent COVID-19 vaccines roll-out globally as active immunisation to prevent COVID-19. The extensive usage and trials done in recent outbreak in China has shown the effectiveness of traditional Chinese Medicines (TCM) in improving the wellbeing of COVID-19 patients. Therefore, COVID-19 Prevention and Treatment guidelines has listed a number of recommended concoctions meant for COVID-19 patients. Licorice, more commonly known as Gancao in Chinese Pinyin, is known as one of the most frequently used ingredients in TCM prescriptions for treatment of epidemic diseases. Interestingly, it is deemed as food ingredient as well, where it is normally used in Western cuisines’ desserts and sweets. The surprising fact that licorice appeared in the top 10 main ingredients used in TCM prescriptions in COVID-19 has drawn great attention from researchers in revealing its biological potential in overcoming this disease. To date, there are no comprehensive review on licorice and its benefits when used in COVID-19. Thus, in this current review, the possible benefits, mechanism of actions, safety and limitations of licorice were explored in hope to provide a quick reference guide for its preclinical and clinical experimental set-up in this very critical moment of pandemic.

scholarly journals COVID-19 in conflict border regions: a case of South Kordofan, Sudan

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Quraish Sserwanja ◽  
Mohammed Bashir Adam ◽  
Joseph Kawuki ◽  
Emmanuel Olal
Keyword(s):  
Case Fatality ◽  
Mechanical Ventilators ◽  
Governmental Organizations ◽  
Non Governmental Organizations ◽  
Bed Capacity ◽  
Displaced People ◽  
Set Up ◽  
One Year ◽  
Novel Coronavirus ◽  
South Kordofan

AbstractThe novel coronavirus disease (COVID-19) was first reported in Sudan on 13 March 2020. Since then, Sudan has experienced one of the highest rates of COVID-19 spread and fatalities in Africa. One year later, as per 22 March 2021, Sudan had registered 29,661 confirmed cases and 2,028 deaths with a case fatality rate (CFR) of 6.8 %. By 12 December 2020, of the 18 states in Sudan, South Kordofan had the fifth highest CFR of 17.4 %, only surpassed by the other conflict affected North (57.5 %), Central (50.0 %) and East (31.8 %) Darfur States. By late March 2021, just three months from December 2020, the number of cases in South Kordofan increased by 100 %, but with a significant decline in the CFR from 17.4 to 8.5 %. South Kordofan is home to over 200,000 poor and displaced people from years of destructive civil unrests. To date, several localities such as the Nubba mountains region remain under rebel control and are not accessible. South Kordofan State Ministry of Health in collaboration with the federal government and non-governmental organizations set up four isolation centres with 40 total bed capacity, but with only two mechanical ventilators and no testing centre. There is still need for further multi-sectoral coalition and equitable allocation of resources to strengthen the health systems of rural and conflict affected regions. This article aims at providing insight into the current state of COVID-19 in South Kordofan amidst the second wave to address the dearth of COVID-19 information in rural and conflict affected regions.

scholarly journals William James and the Sustainable Transformation of Values, with a Case Study for Rethinking the American Dream

Human Arenas ◽  
2021 ◽  
Author(s):  
Paul Croce
Keyword(s):  
Economic Growth ◽  
Social Transformation ◽  
American Dream ◽  
William James ◽  
Social Issues ◽  
Virus Spread ◽  
Global Pandemic ◽  
The Face ◽  
The Many

AbstractThis article addresses the call of the Psychology of Global Crises conference for linkage of academic work with social issues in three parts: First, examples from conference participants with their mix of bold calls for social transformation and realization of limits, a combination that generated few clear paths to achieving them. Second, presentation of Jamesian practical idealism with psychological insights for moving past impediments blocking implementation of ideals. And third, a case study of impacts from the most recent prominent crisis, the global pandemic of 2020, which threatens to exacerbate the many crises that had already been plaguing recent history. The tentacles of COVID’s impact into so many problems, starting with economic impacts from virus spread, present an opportunity to rethink the hope for constant economic growth, often expressed as the American Dream, an outlook that has driven so many of the problems surging toward crises. Jamesian awareness of the construction of ideological differences and encouragement of listening to those in disagreement provide not political solutions, but psychological preludes toward improvements in the face of crises.

scholarly journals Architecture for integrating vertical customer’s programmability control of network functions and connectivity in a slice-as-a-service schema

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Luis M. Contreras ◽  
Samier Barguil ◽  
Ricard Vilalta ◽  
Victor López
Keyword(s):  
Business Model ◽  
Use Cases ◽  
Network Slicing ◽  
On Demand ◽  
Network Functions ◽  
End To End ◽  
Operational Networks ◽  
Potential Use ◽  
Telecom Infrastructure ◽  
As If

AbstractNetwork slicing will permit offering to vertical customers tailored end-to-end logical networks in an on-demand fashion, on top of a common telecom infrastructure, achieving a Slices-as-a-Service (SlaaS) business model. This is possible due to the progressive introduction of network softwarization techniques, such as programmability and virtualization, into existing operational networks, enabling dynamic and flexible provision of slices. Those vertical customers could require the control not only of the network functions composing the end-to-end service, but also of the connectivity among them, e.g., for influencing the paths for steering traffic among function instances. However, this can be problematic since decisions from one vertical customer can collide with decisions from others. One aspect not yet sufficiently investigated is how to permit vertical customers to jointly control the service functions and the underlay connectivity, in such a way that could operate the allocated slice as if it was actually a dedicated network entirely for them. This paper explores some architectural proposition in this respect illustrated with some potential use cases and it provides an example of the provision of SlaaS for a vertical customer.

scholarly journals Catalyst Twenty-Twenty: Post-Traumatic Growth at Scales of Person, Place and Planet

Challenges ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 9
Author(s):  
Alan C. Logan ◽  
Susan H. Berman ◽  
Richard B. Scott ◽  
Brian M. Berman ◽  
Susan L. Prescott
Keyword(s):  
Resource Depletion ◽  
Mass Trauma ◽  
Planetary Health ◽  
Post Traumatic Growth ◽  
Global Pandemic ◽  
Assumptive World ◽  
Post Traumatic ◽  
Discrimination And Oppression ◽  
The Many ◽  
Seismic Impact

Planetary health is a broad multidisciplinary effort that attempts to address what has been described as “Anthropocene Syndrome”—the wicked, interrelated challenges of our time. These include, but are not limited to, grotesque biodiversity losses, climate change, environmental degradation, resource depletion, the global burden of non-communicable diseases (NCDs), health inequalities, social injustices, erosion of wisdom and civility, together with the many structural underpinnings of these grand challenges. The ultimate aim of planetary health is flourishing along every link in the person, place and planet continuum. The events of “2020” have illuminated the consequences of “mass trauma” and how sub-threshold anxiety and/or depressive symptoms erase the rigid lines between mental “health” and mental “disorders”, and unmasked the systemic forms of injustice, discrimination, and oppression that have too often escaped discourse. Here, we query the ways in which post-traumatic growth research might inform the larger planetary health community, especially in the context of a global pandemic, broadening socioeconomic inequalities, a worsening climate crisis, and the rise of political authoritarianism. The available research would suggest that “2020” fulfills the trauma criteria of having a “seismic impact on the assumptive world”, and as such, provides fertile ground for post-traumatic growth. Among the many potential positive changes that might occur in response to trauma, we focus on the value of new awareness, perspective and greater wisdom.

Effects of high and low doses of methimazole in patients with Graves' thyrotoxicosis

1987 ◽  
Vol 116 (1_Suppl) ◽  
pp. S312-S317 ◽  
Author(s):  
G. Benker ◽  
D. Reinwein ◽  
H. Creutzig ◽  
H. Hirche ◽  
W. D. Alexander ◽  
...  
Keyword(s):  
Antithyroid Drug ◽  
Drug Dosage ◽  
Antithyroid Drugs ◽  
Graves Disease ◽  
Duration Of Treatment ◽  
Disease Heterogeneity ◽  
Remission Rates ◽  
Set Up ◽  
The Many ◽  
The Impact

Abstract. In spite of the long-established use of antithyroid drugs, there are many unsettled questions connected with this treatment of Graves' disease. There is a lack of controlled prospective trials studying the results of antithyroid drug therapy while considering the many variables such as disease heterogeneity, regional differences, drug dosage and duration of treatment. Therefore, a multicenter study has been set up in order to compare the effects of two fixed doses of methimazole (10 vs 40 mg) with thyroid hormone supplementation on the clinical, biochemical and immunological course of Graves' disease and on remission rates. Experience accumulated so far suggests that treatment is safe using either 10 or 40 mg of methimazole. While there is a tendency for an advantage of the higher dose within the first weeks (higher effectiveness in controlling hyperthyroidism), this difference is not significant. The impact of dosage on remission rates remains to be shown.

On-demand Electrohydrodynamic Jetting of an Ethylene Glycol and Water Mixture—System of Controlled Picoliter Fluid Deposition

2021 ◽  
Author(s):  
J. F. Dijksman ◽  
U. Stachewicz
Keyword(s):  
Fluid Flow ◽  
Power Amplifier ◽  
Large Diameter ◽  
Electrical Circuit ◽  
Viscous Drag ◽  
Water Mixture ◽  
Electrical Field ◽  
On Demand ◽  
Flat Substrate ◽  
Set Up

On-demand electrohydrodynamic jetting also called electrohydrodynamic atomization (EHDA) is a method to jet small amounts of fluid out of a nozzle with a relatively large diameter by switching on and off an electrical field between the nozzle and the substrate. The total amount of volume deposited is up to 5 pL. The set-up consists of a vertically placed glass pipette with a small nozzle directed downward and a flat substrate placed close to the end of the nozzle. Inside the pipette, an electrode is mounted close to the entrance of the nozzle. The electrode is connected to a high voltage power amplifier. Upon switching on the electrical field, the apparent surface tension drops, the meniscus deforms into a cone and fluid starts to flow toward the nozzle deforming the meniscus. At a certain moment the cone reaches the Taylor cone dimensions and from its tip a jet emerges that decomposes into a stream of charged fL droplets that fly toward the substrate. This process stops when the pulse is switched off. After switching off, the meniscus returns slowly to its equilibrium position. The process is controlled by different time constants, such as the slew rate of the power amplifier and the RC time of the electrical circuit composed of the electrical resistance in the fluid contained in the nozzle between the electrode and the meniscus, and the capacitance of the gap between the meniscus and the flat substrate. Another time constant deals with the fluid flow during the growth of the meniscus, directly after switching on the pulse. This fluid flow is driven by hydrostatic pressure and opposed by a viscous drag in the nozzle. The final fluid flow during droplet formation is governed by the balance between the drag of the charge carriers inside the fluid, caused by the current associated with the charged droplets leaving the meniscus and the viscous drag. These different phenomena will be discussed theoretically and compared to experimental results.

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