scholarly journals nf-core: Community curated bioinformatics pipelines

2019 ◽  
Author(s):  
Philip A Ewels ◽  
Alexander Peltzer ◽  
Sven Fillinger ◽  
Johannes Alneberg ◽  
Harshil Patel ◽  
...  
Keyword(s):  
Best Practice ◽  
High Quality ◽  
Practice Analysis ◽  
Tightly Coupled ◽  
The Creation ◽  
Research Facilities ◽  
Bioinformatics Community ◽  
Software Dependencies

AbstractThe standardization, portability, and reproducibility of analysis pipelines is a renowned problem within the bioinformatics community. Most pipelines are designed for execution on-premise, and the associated software dependencies are tightly coupled with the local compute environment. This leads to poor pipeline portability and reproducibility of the ensuing results - both of which are fundamental requirements for the validation of scientific findings. Here, we introduce nf-core: a framework that provides a community-driven, peer-reviewed platform for the development of best practice analysis pipelines written in Nextflow. Key obstacles in pipeline development such as portability, reproducibility, scalability and unified parallelism are inherently addressed by all nf-core pipelines. We are also continually developing a suite of tools that assist in the creation and development of both new and existing pipelines. Our primary goal is to provide a platform for high-quality, reproducible bioinformatics pipelines that can be utilized across various institutions and research facilities.

scholarly journals Immune Checkpoint Inhibitors in Urothelial Carcinoma: Recommendations for Practical Approaches to PD-L1 and Other Potential Predictive Biomarker Testing

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1424
Author(s):  
Antonio Lopez-Beltran ◽  
Fernando López-Rios ◽  
Rodolfo Montironi ◽  
Sophie Wildsmith ◽  
Markus Eckstein
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Best Practice ◽  
Checkpoint Inhibitors ◽  
Predictive Biomarker ◽  
High Quality ◽  
The Status ◽  
Biomarker Testing ◽  
Novel Biomarkers ◽  
Scoring Algorithms

Immuno-oncology (IO) agents (anti–programmed cell death 1 (PD-1) and anti–programmed cell death-ligand 1 (PD-L1)) are approved as first- and second-line treatments for metastatic UC. PD-L1 expression levels in UC tumors help clinicians determine which patients are more likely to respond to IO therapies. Assays for approved IO agents use different antibodies, immunohistochemical protocols, cutoffs (defining “high” vs. “low” PD-L1 expression), and scoring algorithms. The robust control of pre-analytical and analytical standards is needed to obtain high-quality PD-L1 results. To better understand the status and perspectives of biomarker-guided patient selection for anti–PD-1 and anti–PD-L1 agents in UC, three workshops were held from December 2018 to December 2019 in Italy, Malaysia, and Spain. The primary goal was to develop recommendations for best practice approaches to PD-L1 testing in UC. Recommendations pertaining to the interpretation and reporting of the results of PD-L1 assays from experienced pathologists and oncologists from around the globe are included. A test request form for pathology laboratories was developed as a critical first step for oncologists/urologists to encourage communication between clinicians and pathologists, ensuring fast and high-quality test results. In this era of personalized medicine, we briefly discuss novel biomarkers being evaluated for IO agents in UC.

An authoring tool for democratizing the creation of high-quality VR experiences

2021 ◽  
Author(s):  
Dimitrios Ververidis ◽  
Panagiotis Migkotzidis ◽  
Efstathios Nikolaidis ◽  
Eleftherios Anastasovitis ◽  
Anastasios Papazoglou Chalikias ◽  
...  
Keyword(s):  
Authoring Tool ◽  
High Quality ◽  
The Creation

scholarly journals Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix

GigaScience ◽  
2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Justin Bedő ◽  
Leon Di Stefano ◽  
Anthony T Papenfuss
Keyword(s):  
Best Practice ◽  
Software Dependencies

Abstract Motivation A challenge for computational biologists is to make our analyses reproducible—i.e. to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers. Results We present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. Availability and Implementation BioNix is implemented in the Nix expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662).

Creating effective illustrations for pictorial assembly instructions

2007 ◽  
Vol 15 (2) ◽  
pp. 97-109 ◽  
Author(s):  
Peter Schumacher
Keyword(s):  
Developing Countries ◽  
Sri Lanka ◽  
Practice Guidelines ◽  
Best Practice ◽  
Diagnostic Testing ◽  
Consumer Products ◽  
Common Element ◽  
Best Practice Guidelines ◽  
Assembly Instructions ◽  
The Creation

Pictorial assembly instructions are a common element of many consumer products however there is very little research published about their design, particularly regarding the creation of effective illustrations. This paper reviews published work that offers best practice guidelines for the design of pictorial assembly instructions. The application of the guidelines is discussed in the context of a project to design assembly instructions for a flat pack wheelchair for distribution in developing countries. The paper will present findings from diagnostic testing with users in Sri Lanka.

scholarly journals OPEN URBAN AND FOREST DATASETS FROM A HIGH-PERFORMANCE MOBILE MAPPING BACKPACK – A CONTRIBUTION FOR ADVANCING THE CREATION OF DIGITAL CITY TWINS

2021 ◽  
Vol XLIII-B1-2021 ◽  
pp. 125-131
Author(s):  
S. Blaser ◽  
J. Meyer ◽  
S. Nebiker
Keyword(s):  
High Performance ◽  
City Centre ◽  
Data Sets ◽  
High Quality ◽  
Mobile Mapping ◽  
Street Level ◽  
Localization And Mapping ◽  
Digital Twins ◽  
Potential Applications ◽  
The Creation

Abstract. With this contribution, we describe and publish two high-quality street-level datasets, captured with a portable high-performance Mobile Mapping System (MMS). The datasets will be freely available for scientific use. Both datasets, from a city centre and a forest represent area-wide street-level reality captures which can be used e.g. for establishing cloud-based frameworks for infrastructure management as well as for smart city and forestry applications. The quality of these data sets has been thoroughly evaluated and demonstrated. For example, georeferencing accuracies in the centimetre range using these datasets in combination with image-based georeferencing have been achieved. Both high-quality multi sensor system street-level datasets are suitable for evaluating and improving methods for multiple tasks related to high-precision 3D reality capture and the creation of digital twins. Potential applications range from localization and georeferencing, dense image matching and 3D reconstruction to combined methods such as simultaneous localization and mapping and structure-from-motion as well as classification and scene interpretation. Our dataset is available online at: https://www.fhnw.ch/habg/bimage-datasets

scholarly journals The Multimedia Nature of Modern Literary Discourse

2018 ◽  
pp. 40-43
Author(s):  
Margarita G. Bogatkina ◽  
Elena S. Doroschuk ◽  
Tatiana S. Staroverova
Keyword(s):  
Modern Science ◽  
Literary Discourse ◽  
Classical Literature ◽  
High Quality ◽  
External Context ◽  
Degree Of Certainty ◽  
Information And Communication ◽  
The Creation ◽  
Multimedia Product ◽  
Dialogic Interaction

Today the convergence processes determine the most promising areas of modern science. This methodological setting in the field of journalism is implemented in a variety of multimedia forms, which has led to the creation of the fundamentally new information and communication environment and the emergence of a variety of multimedia projects. The question about the criteria and methods for creating a high-quality multimedia product remains open. The multimedia method of perception and presentation of materials require special philological preparation and mastering of the interdisciplinary technique of interpretation of the source materials, which would help to create its qualitative multimedia variation. To transfer the literary discourse into a multimedia projection, it is necessary to identify its semantic channels, contexts that can be implemented in the cross-media content using various technical means. In this regard, it is important to substantiate the basic principles of the contextual method of interpreting literary discourse. It is also proposed to highlight contexts that are present in the discourse and are actualized by the perceiving recipient including historical, biographical, literary, linguistic, philosophical, mythological, literary critical, as well as those of various types of art - painting, music, etc., and the scientific context. The structure-forming principle that allows comprehending these contexts as an integral system is the process of dialogic interaction of their intra- and extra-textual existence. The nature of the functioning of this context system is based on the implementation of the following factors: 1) the degree to which authorial/reader determinism manifests itself in the process of implementation of a specific context; 2) the degree of awareness/unconsciousness of the context embodiment in the work; 3) the degree of relative stiffness/probability of the context functioning; and 4) the degree of certainty/uncertainty of the implementation of the external context in the literary discourse. Considering an example of the story by Sholokhov, “The Fate of Man”, it is considered as the development of the context system in the form of a substantive basis for the further transfer of this text into a multimedia projection. It is revealed that the literary discourse is born at the junction of information and communication approaches to the text. The disclosure of the multimedia nature of literary discourse helps to restore the very process of its functioning and its dialogical nature. The contextual methodology for the interpretation of literary discourse also allows determining the dialogue channels - the context system that are the basis for the creation of high-quality multimedia content in the future. Since the multimedia method of material perception and presentation requires special preparation, it is advisable to develop the skills of multimedia thinking using the example of classical literature, based on the principles of contextual methodology. A philological literacy can also play an important role in the process of training future journalists.

scholarly journals Analysis on the Conformity between the Closed-Circuit Embroidery Elements of Different Widths and the Digitally Designed Elements

2019 ◽  
Vol 19 (3) ◽  
pp. 250-256
Author(s):  
Žaneta Juchnevičienė ◽  
Milda Jucienė ◽  
Vaida Dobilaitė ◽  
Virginija Sacevičienė ◽  
Svetlana Radavičienė
Keyword(s):  
Closed Circuit ◽  
Dynamic Loads ◽  
Geometrical Parameters ◽  
High Quality ◽  
Quality Requirements ◽  
Textile Materials ◽  
The Creation

Abstract The embroidery process is one of the means of joining textile materials into a system, which is widely applied in the creation of products of special destinations. The development of the functionality of embroidery systems is indissoluble from high-quality requirements for the accuracy of the form of the element. In the embroidery process, the system of textile materials experiences various dynamic loads, multiple stretching, and crushing; therefore, the geometrical parameters of the embroidery element change. The objective of this paper was to analyze the widths of the different square-form closed-circuit embroidery elements and also to perform their analysis with the purpose to evaluate the embroidery accuracy of the embroidered elements. Test samples were prepared in the form of square-form closed-circuit embroidery elements of five different contour widths: 6 mm, 10 mm, 14 mm, 18 mm, and 22 mm. During the investigation, it has been determined that in most cases the contour widths of the five closed-circuit square-form embroidery elements were obtained, smaller than the size of the digitally designed element.

Silicon Based System-in-Package : Breakthroughs in Miniaturization and ‘Nano’-integration Supported by Very High Quality Passives and System Level Design Tools

2006 ◽  
Vol 969 ◽  
Author(s):  
Franck Murray ◽  
François LeCornec ◽  
Serge Bardy ◽  
Catherine Bunel ◽  
Jan Verhoeven ◽  
...  
Keyword(s):  
New Technologies ◽  
Test System ◽  
System Level ◽  
Design Tools ◽  
Design Environment ◽  
High Quality ◽  
Silicon Chips ◽  
The Creation ◽  
Silicon Based ◽  
Very High

AbstractThe very large development of home and domestic electronic appliances as well as portable device has led the microelectronics industry to evolve in two complimentary directions : “More Moore” with the continuous race towards extremely small dimensions hence the development of SoCs (System on Chip) and more recently a new direction that we could name “More than Moore” with the integration of devices that were laying outside the chips and here the creation of SiPs (System in Package).These two approaches are not in competition one with the other: the paper will show some examples of integrated nano systems that use several SoCs.The technology we have developed is called Silicon Based System in Package. The first products using this technology are now in volume production and used mainly in the field of wireless communications.This new technology relies on four pillars. Passive integration is the first. Very efficient and high quality factor capacitors and inductors have been integrated, allowing the creation of complete modules including active devices, filters and decoupling capacitors. High-density MOS capacitors with 1-1000 nF capacitance, and as high values as 25-250+ nF/mm2 specific capacitance have been fabricated in macroporous Si-wafers, containing over 1 billion macropores. Typically an ESR less than 100 mÙ and an ESL less than 25 pH were found for capacitors over 10 nF. This novel concept is an important step forward in improving the stability of power-amplifier modules by replacing conventional SMD technology.Whereas generations with capacitors density of up to 100 nF/mm2 will be using “conventional” materials and structures, the next steps in the roadmap will call for new 3D structures and materials such as high-k dielectrics.The second element is advanced packaging. New technologies, such as the assembly of Silicon chips onto other Silicon chips, also named “double flip chip” have been developed. This has been made possible thanks to the combination of the most advanced microbumping and die placement techniques. In addition to a tremendous reduction of size (up to a factor of 10 to 20) these techniques have also brought a better repeatability of system performance.The third element has been the development of design tools that allow a seamless system design for engineers used to IC design tools and flows. Our Design Environment allows co design of multiple technologies chips and their integration in a single system. This IC-like Design Environment has contributed a lot to the adoption of the technology.Testing is the fourth element and is one of the economical enablers of the technology. The key words are: “known good die”, RF test, system test? Some innovative RF probing and full on wafer subsystem test will be shown. Even though efficient test is not vital for the technical feasibility of this system integration, it becomes very quickly one of the most important enablers, especially when we deal with very high volumes of production. The conclusion of the paper will be an open door to the future. Some innovations like the integration of light or even energy storage inside our SiPs will be presented.

In memoriam fundraising: An empirical exploration of donor motivations

2021 ◽  
Author(s):  
Sara Penner ◽  
Kelley Main
Keyword(s):  
Consumer Choice ◽  
Charitable Giving ◽  
Best Practice ◽  
Consumer Behaviour ◽  
Empirical Support ◽  
Process Models ◽  
Grieving Process ◽  
Nonprofit Organisations ◽  
In Memoriam ◽  
The Creation

Purpose: This research explores in memoriam fundraising from the perspective of the donor, providing empirical support for what motivates people to make permanent in memoriam donations and how making such donations assists them in the grieving process. These insights then provide guidance to aid nonprofit organisations (herein referred to as nonprofits) in building relationships with bereaved donors.Methodology: Study one collected data using a purposive criterion sampling, with 10 in-depth interviews that were analysed using thematic analysis. Study two used an experimental design that collected data using a convenience-based sampling, with 184 participants (53.6% male, mean age 38 years). T-tests and Process models were utilised for analysis. Findings: This research demonstrates that charitable donations can play a role in bereavement and that the value they provide is to both the nonprofit, with monetary outcomes and increased donor loyalty, and to the donor, with the creation of a continued bond with the deceased. This research provides the first empirical evidence that people use in memoriam donations, which include a permanent memorial, to create a symbolic continuing bond with the deceased and that such symbolic donations increase the giver’s desire to visit the memorial. Using the findings of this research, we provide a set of recommendations that fundraisers can follow in order to best meet the needs of both their donors and their organisation. Recommendations include ways to provide the value that donors are looking for which will aid them in their bereavement along with best practices for the organization to allow for the most effective in memoriam fundraising program.Implications: Providing evidence that the creation of a continued bond is a motivator for charitable giving connects the literature on charitable giving, bereavement and consumer behaviour. This research deepens our understanding of consumer behaviour by examining why people spend money to help themselves through the grieving process, thus building on the mood, decision making, and consumer-choice literatures that can be used in both for profit and nonprofit marketing domains. Providing empirical support for the industry best practice of providing permanent memorial opportunities is of significant importance, as doing so can provide relationship building opportunities. This research shows that there are societal benefits to in memoriam giving, demonstrating that it can provide value to people in their grieving process. Contribution: This is the first empirical study that looks at motivations for in memoriam fundraising, providing evidence of continued bonds as a motivator for in memoriam donations, and the role that charitable giving can play in bereavement.

Abstract 247: STEMI 365: Creating a Yearlong Program to Reduce Cardiac Recidivism After STEMI

2016 ◽  
Vol 9 (suppl_2) ◽  
Author(s):  
Daniel Ryczek ◽  
David Burt
Keyword(s):  
Myocardial Infarction ◽  
Practice Guidelines ◽  
Relapse Prevention ◽  
Best Practice ◽  
The United States ◽  
Post Myocardial Infarction ◽  
Care Hospital ◽  
Evaluation Tool ◽  
Best Practice Guidelines ◽  
The Creation

Survivors of myocardial infarctions are at increased risk of recurrent infarctions and have an annual death rate of 5%, six times that in people of the same age who do not have coronary heart disease. Despite the existence of published interventions and clinical recommendations aimed at secondary and tertiary prevention their application and adherence statistics in post-myocardial infarction patients are woeful. The objective of this paper is to detail the creation of a template curriculum that gives best practice recommendations to post STEMI patients in an effort to reduce recidivism by combining current medical methodology with lessons learned from other fields currently addressing the problem of recidivism and relapse. STEMI 365 is a yearlong program that aims to reduce cardiac recidivism in STEMI survivors. STEMI 365 is composed of three parts: best practice guidelines, evaluation toolkit, and template curriculum. The best practice guidelines document is broken into sections on cardiac rehabilitation, lifestyle modification, drug therapy, patient follow-up and screening, and patient education. All guidelines are informed by the latest recommendations and research in the fields of medicine and relapse prevention. The evaluation toolkit is composed of the cardiac recidivism risk tool, the self-evaluation tool, and the global evaluation tool. The goal of the toolkits is to guide resource allocation by understanding a patient’s unique cardiac recidivism risk, internal sources of potential relapse, and external sources of potential relapse. The Federal Post Conviction Risk Assessment developed by the Administrative Office of the United States Courts informs the toolkits’ construction. The template curriculum is a summation of the programs and interventions that can be utilized by a health system to decrease cardiac recidivism in STEMI survivors. The curriculum addresses one year of time divided into three phases: inpatient, outpatient, and maintenance. The interventions rage in scope from training a patient’s family members in bystander CPR to the creation of a centralized patient monitoring program and post-myocardial infarction clinic. Each phase combines the best modalities in treatment found in the fields of post-myocardial infarction care, hospital re-admission prevention, substance abuse relapse prevention, scholastic dropout prevention, and criminal justice. Personal interviews were conducted with leaders in each field to ensure the correct application of their methodologies. STEMI 365 provides tools to identify patients at highest risk of cardiovascular relapse, to apply local and regional resources in an effective way based on patient risk, and to customize interventions to a health system’s available resources. STEMI 365 is beginning an application phase at this institution, and will be available to other health systems in the near future.

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