scholarly journals Contributions from the 2019 Literature on Bioinformatics and Translational Informatics

2020 ◽  
Vol 29 (01) ◽  
pp. 188-192
Author(s):  
Malika Smaïl-Tabbone ◽  
Bastien Rance ◽  
Keyword(s):  
Open Data ◽  
Leading Edge ◽  
Open Science ◽  
Editorial Committee ◽  
Cancer Pathways ◽  
Sequence Of Events ◽  
Independent Review ◽  
Logical Modeling ◽  
Translational Informatics ◽  
Selection Of

Objectives: Summarize recent research and select the best papers published in 2019 in the field of Bioinformatics and Translational Informatics (BTI) for the corresponding section of the International Medical Informatics Association Yearbook. Methods: A literature review was performed for retrieving from PubMed papers indexed with keywords and free terms related to BTI. Independent review allowed the section editors to select a list of 15 candidate best papers which were subsequently peer-reviewed. A final consensus meeting gathering the whole Yearbook editorial committee was organized to finally decide on the selection of the best papers. Results: Among the 931 retrieved papers covering the various subareas of BTI, the review process selected four best papers. The first paper presents a logical modeling of cancer pathways. Using their tools, the authors are able to identify two known behaviours of tumors. The second paper describes a deep-learning approach to predicting resistance to antibiotics in Mycobacterium tuberculosis. The authors of the third paper introduce a Genomic Global Positioning System (GPS) enabling comparison of genomic data with other individuals or genomics databases while preserving privacy. The fourth paper presents a multi-omics and temporal sequence-based approach to provide a better understanding of the sequence of events leading to Alzheimer’s Disease. Conclusions: Thanks to the normalization of open data and open science practices, research in BTI continues to develop and mature. Noteworthy achievements are sophisticated applications of leading edge machine-learning methods dedicated to personalized medicine.

scholarly journals Moving towards an Open Archaeology: projects, opportunities and challenges

2019 ◽  
Vol 72 (2) ◽  
pp. 538-554
Author(s):  
Edeltraud Aspöck
Keyword(s):  
Open Access ◽  
Open Data ◽  
Open Science ◽  
Science Practices ◽  
Archaeological Practice ◽  
Selection Of

Generally, open science practices are only slowly having an impact on mainstream archaeological practice. An exception is the open access to publications, which, together with open data and open methodologies may represent those practices most relevant for archaeological researchers. This article introduces a selection of archaeology projects that embrace and facilitate open science practices. Finally there will be a discussion of some of the questions and challenges the discipline is facing in its move towards an Open Archaeology.

scholarly journals Contributions from the 2018 Literature on Bioinformatics and Translational Informatics

2019 ◽  
Vol 28 (01) ◽  
pp. 190-193 ◽  
Author(s):  
Malika Smaïl-Tabbone ◽  
Bastien Rance ◽  
Keyword(s):  
Expression Profiles ◽  
Leading Edge ◽  
Computational Method ◽  
Omics Data ◽  
Neural Network Approach ◽  
Editorial Committee ◽  
Chemotherapy Drugs ◽  
Phenotype Classification ◽  
Translational Informatics

Objectives: To summarize recent research and select the best papers published in 2018 in the field of Bioinformatics and Translational Informatics (BTI) for the corresponding section of the International Medical Informatics Association (IMIA) Yearbook. Methods: A literature review was performed for retrieving from PubMed papers indexed with keywords and free terms related to BTI. Independent review allowed the two section editors to select a list of 14 candidate best papers which were subsequently peer-reviewed. A final consensus meeting gathering the whole IMIA Yearbook editorial committee was organized to finally decide on the selection of the best papers. Results: Among the 636 retrieved papers published in 2018 in the various subareas of BTI, the review process selected four best papers. The first paper presents a computational method to identify molecular markers for targeted treatment of acute myeloid leukemia using multi-omics data (genome-wide gene expression profiles) and in vitro sensitivity to 160 chemotherapy drugs. The second paper describes a deep neural network approach to predict the survival of patients suffering from glioma on the basis of digitalised pathology images and genomics biomarkers. The authors of the third paper adopt a pan-cancer approach to take benefit of multi-omics data for drug repurposing. The fourth paper presents a graph-based semi-supervised method to accurate phenotype classification applied to ovarian cancer. Conclusions: Thanks to the normalization of open data and open science practices, research in BTI continues to develop and mature. Noteworthy achievements are sophisticated applications of leading edge machine-learning methods dedicated to personalized medicine.

scholarly journals Total SciComm: A Strategy for Communicating Open Science

Publications ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 31
Author(s):  
Manh-Toan Ho ◽  
Manh-Tung Ho ◽  
Quan-Hoang Vuong
Keyword(s):  
Social Media ◽  
Science Communication ◽  
Scientific Community ◽  
Open Data ◽  
Open Science ◽  
Central Idea ◽  
Retracted Article ◽  
Scientific Ideas

This paper seeks to introduce a strategy of science communication: Total SciComm or all-out science communication. We proposed that to maximize the outreach and impact, scientists should use different media to communicate different aspects of science, from core ideas to methods. The paper uses an example of a debate surrounding a now-retracted article in the Nature journal, in which open data, preprints, social media, and blogs are being used for a meaningful scientific conversation. The case embodied the central idea of Total SciComm: the scientific community employs every medium to communicate scientific ideas and engages all scientists in the process.

scholarly journals The C-BIG Repository: an Institution-Level Open Science Platform

2021 ◽  
Author(s):  
Samir Das ◽  
Rida Abou-Haidar ◽  
Henri Rabalais ◽  
Sonia Denise Lai Wing Sun ◽  
Zaliqa Rosli ◽  
...  
Keyword(s):  
Neurological Diseases ◽  
Open Data ◽  
Open Science ◽  
Data Repository ◽  
Multiple Stakeholders ◽  
Montreal Neurological Institute ◽  
Multimodal Data ◽  
Small Patient ◽  
Clinical Data Repository ◽  
Access Data

AbstractIn January 2016, the Montreal Neurological Institute-Hospital (The Neuro) declared itself an Open Science organization. This vision extends beyond efforts by individual scientists seeking to release individual datasets, software tools, or building platforms that provide for the free dissemination of such information. It involves multiple stakeholders and an infrastructure that considers governance, ethics, computational resourcing, physical design, workflows, training, education, and intra-institutional reporting structures. The C-BIG repository was built in response as The Neuro’s institutional biospecimen and clinical data repository, and collects biospecimens as well as clinical, imaging, and genetic data from patients with neurological disease and healthy controls. It is aimed at helping scientific investigators, in both academia and industry, advance our understanding of neurological diseases and accelerate the development of treatments. As many neurological diseases are quite rare, they present several challenges to researchers due to their small patient populations. Overcoming these challenges required the aggregation of datasets from various projects and locations. The C-BIG repository achieves this goal and stands as a scalable working model for institutions to collect, track, curate, archive, and disseminate multimodal data from patients. In November 2020, a Registered Access layer was made available to the wider research community at https://cbigr-open.loris.ca, and in May 2021 fully open data will be released to complement the Registered Access data. This article outlines many of the aspects of The Neuro’s transition to Open Science by describing the data to be released, C-BIG’s full capabilities, and the design aspects that were implemented for effective data sharing.

scholarly journals Learning Open Science by doing Open Science. A reflection of a qualitative research project-based seminar

2020 ◽  
Vol 36 (3) ◽  
pp. 263-279
Author(s):  
Isabel Steinhardt
Keyword(s):  
Qualitative Research ◽  
Open Source ◽  
Knowledge Society ◽  
Open Data ◽  
Open Science ◽  
Research Project ◽  
Science Practices ◽  
Bachelor's Degrees ◽  
Participatory Technologies ◽  
Digital Knowledge

Openness in science and education is increasing in importance within the digital knowledge society. So far, less attention has been paid to teaching Open Science in bachelor’s degrees or in qualitative methods. Therefore, the aim of this article is to use a seminar example to explore what Open Science practices can be taught in qualitative research and how digital tools can be involved. The seminar focused on the following practices: Open data practices, the practice of using the free and open source tool “Collaborative online Interpretation, the practice of participating, cooperating, collaborating and contributing through participatory technologies and in social (based) networks. To learn Open Science practices, the students were involved in a qualitative research project about “Use of digital technologies for the study and habitus of students”. The study shows the practices of Open Data are easy to teach, whereas the use of free and open source tools and participatory technologies for collaboration, participation, cooperation and contribution is more difficult. In addition, a cultural shift would have to take place within German universities to promote Open Science practices in general.

The effect of low-solidity vaned diffusers on the performance of a turbocharger compressor

1997 ◽  
Vol 211 (5) ◽  
pp. 325-339 ◽  
Author(s):  
P A Eynon ◽  
A Whitfield
Keyword(s):  
Pressure Ratio ◽  
Leading Edge ◽  
Vaneless Diffuser ◽  
Peak Efficiency ◽  
Turning Angle ◽  
Edge Angle ◽  
Turbo Charger ◽  
Geometry Configuration ◽  
Vane Angle ◽  
Selection Of

The design of low-solidity diffuser vanes and the effect on the performance of a turbo-charger compressor is discussed. The effect of vane number and turning angle was investigated while maintaining a basic design with a solidity of 0.69 and a leading edge angle of 75°. This large leading edge angle was specifically chosen so that the vane would be aligned with the low flowrates close to surge. Tests were initially conducted with six, eight and ten vanes and a turning angle of 10°. Based on these results the ten-vane design was selected for further investigation with 15 and 20° of vane turning; this led to vane exit angles of 60 and 55° respectively. All results are compared with those obtained with the standard vaneless diffuser configuration and it was shown that all designs increased and shifted the peak pressure ratio to reduced flowrates. The peak efficiency was reduced relative to that obtained with the vaneless diffuser. Despite the low-solidity configuration none of the vane designs provided a broad operating range without the use of a variable geometry configuration. This was attributed to the selection of a large leading edge vane angle.

scholarly journals Methodology for mapping the average transaction prices of residential premises using GIS

2016 ◽  
Vol 48 (4) ◽  
pp. 161-171 ◽  
Author(s):  
Martyna Sosnowska ◽  
Izabela Karsznia
Keyword(s):  
Real Estate ◽  
Open Data ◽  
Transaction Prices ◽  
Residential Properties ◽  
Choropleth Maps ◽  
Presentation Methods ◽  
Real Estate Prices ◽  
Gis Software ◽  
The Impact ◽  
Selection Of

Abstract Geographic information systems (GIS) and their tools support the process of real estate trading. Of key importance is the ability to visualise information about real estate in the form of maps of average real estate transaction prices. The following study presents a methodology for mapping average real estate transaction prices using GIS. The map development process comprised three main stages. In the first stage, the input data was processed and statistically analysed. Official data came from the Register of Real Estate Prices and Values, and open data from the National Register of Boundaries. The second stage involved the visualization of the data in the form of maps of average apartment prices using the cartographic methods of choropleth maps and diagrams. The commercial tool ArcMap 10.3 and the free Quantum GIS software were used in the design of the maps of average real estate transaction prices, to check the options for using these types of programs. As a result, eight maps were designed presenting the average transaction prices for residential properties in the Warsaw district of Ursynów in 2015. The final stage was the analysis of the designed maps. The influence of the selection of the reference units on the visualization content, and the impact of combining cartographic presentation methods on the complexity of the presentation of real estate information, were also analysed.

scholarly journals An open toolkit for tracking open science partnership implementation and impact

2019 ◽  
Vol 3 ◽  
pp. 1442 ◽  
Author(s):  
E. Richard Gold ◽  
Sarah E. Ali-Khan ◽  
Liz Allen ◽  
Lluis Ballell ◽  
Manoel Barral-Netto ◽  
...  
Keyword(s):  
Annual Report ◽  
Open Data ◽  
Structured Interview ◽  
Open Science ◽  
Social Scientists ◽  
Policy Makers ◽  
Ethical Concerns ◽  
Research And Innovation ◽  
Survey Form ◽  
The Impact

Serious concerns about the way research is organized collectively are increasingly being raised. They include the escalating costs of research and lower research productivity, low public trust in researchers to report the truth, lack of diversity, poor community engagement, ethical concerns over research practices, and irreproducibility. Open science (OS) collaborations comprise of a set of practices including open access publication, open data sharing and the absence of restrictive intellectual property rights with which institutions, firms, governments and communities are experimenting in order to overcome these concerns. We gathered two groups of international representatives from a large variety of stakeholders to construct a toolkit to guide and facilitate data collection about OS and non-OS collaborations. Ultimately, the toolkit will be used to assess and study the impact of OS collaborations on research and innovation. The toolkit contains the following four elements: 1) an annual report form of quantitative data to be completed by OS partnership administrators; 2) a series of semi-structured interview guides of stakeholders; 3) a survey form of participants in OS collaborations; and 4) a set of other quantitative measures best collected by other organizations, such as research foundations and governmental or intergovernmental agencies. We opened our toolkit to community comment and input. We present the resulting toolkit for use by government and philanthropic grantors, institutions, researchers and community organizations with the aim of measuring the implementation and impact of OS partnership across these organizations. We invite these and other stakeholders to not only measure, but to share the resulting data so that social scientists and policy makers can analyse the data across projects.

scholarly journals Critérios para avaliação de ferramentas para repositório conforme a Ciência Aberta

2017 ◽  
Vol 6 (2) ◽  
Author(s):  
Angélica Conceição Dias Miranda ◽  
Milton Shintaku ◽  
Simone Machado Firme
Keyword(s):  
Open Access ◽  
Evaluation Criteria ◽  
Open Data ◽  
Open Science ◽  
Scientific Production ◽  
Open File ◽  
Research Institutes ◽  
Criteria For Evaluation ◽  
Science Movement ◽  
Bibliographic Study

Resumo: Os repositórios têm se tornado comum nas universidades e institutos de pesquisa, como forma de ofertar acesso à produção científica e, com isso, dar visibilidade à instituição. Entretanto, em muitos casos ainda estão restritos aos conceitos do movimento do arquivo aberto e acesso aberto, sendo que já se discute o Movimento da Ciência Aberta, revelando certo descompasso, requerendo estudos que apoiem a atualização dessa importante ferramenta. Nesse sentido, o presente estudo verifica os requisitos envolvidos nos movimentos abertos, de forma a apoiar a discussão técnica e tecnológica. Um estudo bibliográfico, que transforma as informações sobre os movimentos em critérios para avaliação de ferramentas para criação de repositórios, apresentando a implementação da interação como um novo desafio. Nas considerações procura-se contribuir com a discussão sobre a Ciência Aberta, de forma mais aplicada bem como o ajuste dos repositórios a esse movimento.Palavras-chave: Repositórios.  Critérios de avaliação. Arquivo aberto. Acesso aberto. Dados abertos. Ciência aberta.SURVEY OF CRITERIA FOR EVALUATION OF REPOSITORY TOOLS ACCORDING TO OPEN SCIENCE Abstract: Repositories have become common in universities and research institutes, as a way of offering access to scientific production, thereby giving visibility to the institution. Meanwhile, in many cases, repositories are restricted to the concepts of open movement and open access considering that the Open Science Movement is already being discussed. Regarding this matter, this study verifies the requirements involved in the open movements, in order to support a technical and technological discussion.  A bibliographic study that transforms information about movements into criteria to evaluate tools used to create repositories, presenting an implementation of interaction as a new challenge. In the considerations, we contribute with a discussion about an Open Science, in a more applied way, as well as the adjustment of the repositories to this movement.Keywords: Repositories. Evaluation Criteria. Open File. Open Access. Open Data. Open Science.

scholarly journals Open Developmental Science: An Overview and Annotated Reading List

2021 ◽  
Author(s):  
Tamara Kalandadze ◽  
Sara Ann Hart
Keyword(s):  
Open Access ◽  
Open Data ◽  
Open Science ◽  
Science Practices ◽  
The Core ◽  
Reading List ◽  
Annotated List ◽  
Developmental Science ◽  
Starting Point

The increasing adoption of open science practices in the last decade has been changing the scientific landscape across fields. However, developmental science has been relatively slow in adopting open science practices. To address this issue, we followed the format of Crüwell et al., (2019) and created summaries and an annotated list of informative and actionable resources discussing ten topics in developmental science: Open science; Reproducibility and replication; Open data, materials and code; Open access; Preregistration; Registered reports; Replication; Incentives; Collaborative developmental science.This article offers researchers and students in developmental science a starting point for understanding how open science intersects with developmental science. After getting familiarized with this article, the developmental scientist should understand the core tenets of open and reproducible developmental science, and feel motivated to start applying open science practices in their workflow.

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