scholarly journals TeachOpenCADD 2021: Open Source and FAIR Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research

2021 ◽  
Author(s):  
Dominique Sydow ◽  
Jaime Rodríguez-Guerra ◽  
Talia B. Kimber ◽  
David Schaller ◽  
Corey J. Taylor ◽  
...  
Keyword(s):  
Best Practices ◽  
Open Source ◽  
Theoretical Background ◽  
Structural Bioinformatics ◽  
Research Projects ◽  
Domain Specific ◽  
Modern Drug ◽  
Hands On ◽  
Novice Scientists ◽  
Crucial Part

Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming --- especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks and based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that each cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with an automated continuous integration and adhering to a more idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub.

Polytechnic to Business Project (P2B) a Case of Innovation and Knowledge Transference

2019 ◽  
Vol 6 (1) ◽  
pp. 40-49
Author(s):  
Teresa Paiva
Keyword(s):  
Knowledge Transfer ◽  
Best Practices ◽  
Education Institution ◽  
Theoretical Background ◽  
Transfer Model ◽  
Case Study Method ◽  
Multiple Sources ◽  
The Subject ◽  
Manage Innovation

Background: The theoretical background of this article is on the model developed of knowledge transfer between universities and the industry in order to access the best practices and adapt to the study case in question regarding the model of promoting and manage innovation within the universities that best contribute with solution and projects to the business field. Objective: The development of a knowledge transfer model is the main goal of this article, supported in the best practices known and, also, to reflect in the main measurement definitions to evaluate the High Education Institution performance in this area. Methods: The method for this article development is the case study method because it allows the fully understanding of the dynamics present within a single setting, and the subject examined to comprehend what is being done and what the dynamics mean. The case study does not have a data collection method, as it is a research that may rely on multiple sources of evidence and data which should be converged. Results: Since it’s a case study this article present a fully description of the model proposed and implemented for the knowledge transfer process of the institution. Conclusion: Still in a discussion phase, this article presents as conclusions some questions and difficulties that could be pointed out, as well as some good perspectives of performed activity developed.

scholarly journals WORCS: A workflow for open reproducible code in science

Data Science ◽  
2021 ◽  
pp. 1-21
Author(s):  
Caspar J. Van Lissa ◽  
Andreas M. Brandmaier ◽  
Loek Brinkman ◽  
Anna-Lena Lamprecht ◽  
Aaron Peikert ◽  
...  
Keyword(s):  
Best Practices ◽  
Source Code ◽  
R Package ◽  
Open Science ◽  
Research Projects ◽  
Tabular Data ◽  
Step Procedure ◽  
Starting Point ◽  
Conducting Research ◽  
And Training

Adopting open science principles can be challenging, requiring conceptual education and training in the use of new tools. This paper introduces the Workflow for Open Reproducible Code in Science (WORCS): A step-by-step procedure that researchers can follow to make a research project open and reproducible. This workflow intends to lower the threshold for adoption of open science principles. It is based on established best practices, and can be used either in parallel to, or in absence of, top-down requirements by journals, institutions, and funding bodies. To facilitate widespread adoption, the WORCS principles have been implemented in the R package worcs, which offers an RStudio project template and utility functions for specific workflow steps. This paper introduces the conceptual workflow, discusses how it meets different standards for open science, and addresses the functionality provided by the R implementation, worcs. This paper is primarily targeted towards scholars conducting research projects in R, conducting research that involves academic prose, analysis code, and tabular data. However, the workflow is flexible enough to accommodate other scenarios, and offers a starting point for customized solutions. The source code for the R package and manuscript, and a list of examplesof WORCS projects, are available at https://github.com/cjvanlissa/worcs.

From Academic to Practitioner: Tips for Increasing Engagement With Your Research (Essay on Best Practices)

2021 ◽  
Vol 37 (2) ◽  
pp. 244-256
Author(s):  
Ava T. Carcirieri
Keyword(s):  
Domestic Violence ◽  
Best Practices ◽  
Lessons Learned ◽  
Family Court ◽  
Academic Training ◽  
Research Projects ◽  
Data Analyst ◽  
Systemic Improvement

Academics and practitioners all too often have little or no contact with each other; the practitioner does not know what research exists that can inform their practices, and the academic does not know enough about the institutions they primarily study to make recommendations that are specific enough to inform a concrete practice or policy. I leverage my experiences both as an academic and as a data analyst and domestic violence coordinator at Family Court to outline lessons learned in the field. I detail how my academic training hindered my work as a practitioner, and how practitioners differ in terms of conducting internal research and presenting data and findings. I use my lessons learned and subsequently list several concrete practices that academics can begin to work into their work to increase communication with important stakeholders, and tailor their work to practical systemic improvement. Bridging the gap between academics and practitioners will lead to better research projects, and findings that will be able to actively enact changes within systems that academics focus on.

A Framework for Engineering Dissection Exercise Creation and Implementation

2009 ◽  
Author(s):  
Kathleen M. Hart ◽  
Steven B. Shooter ◽  
Charles J. Kim
Keyword(s):  
Active Learning ◽  
Best Practices ◽  
Reverse Engineering ◽  
Engineering Education ◽  
Learning Outcomes ◽  
Positive Impact ◽  
Rigorous Approach ◽  
Engineering Activity ◽  
Hands On ◽  
Different Levels

Hands-on product dissection and reverse engineering exercises have been shown to have a positive impact on engineering education, and many universities have incorporated such exercises in their curriculum. The CIBER-U project seeks to examine the potential to utilize cyberinfrastructure to enhance these active-learning exercises. We have formulated a framework for product dissection and reverse engineering activity creation to support a more rigorous approach to assessing other exercises for satisfaction of the CIBER-U project goals and adapting the best practices. This framework is driven by the fulfillment of learning outcomes and considers the maturity of students at different levels. Prototype exercises developed with the framework are presented. The approach is sufficiently general that it can be applied to the consideration and adaption of other types of exercises while ensuring satisfaction of the established goals.

scholarly journals Strengthening the SSTC NRS Scientific and Technical Potential through Participation in the IAEA Coordinated Research Projects

2021 ◽  
pp. 5-13
Author(s):  
Yu. Balashevska ◽  
D. Gumenyuk ◽  
Iu. Ovdiienko ◽  
O. Pecherytsia ◽  
I. Shevchenko ◽  
...  
Keyword(s):  
Best Practices ◽  
Safety Assessment ◽  
Radiation Safety ◽  
Research Projects ◽  
Spent Fuel ◽  
Research Activities ◽  
Technical Potential ◽  
Technical Issues ◽  
Fuel Characterization ◽  
Definition Of

The State Scientific and Technical Center for Nuclear and Radiation Safety (SSTC NRS), a Ukrainian enterprise with a 29-year experience in the area of scientific and technical support to the national nuclear regulator (SNRIU), has been actively involved in international research activities. Participation in the IAEA coordinated research activities is among the SSTC NRS priorities. In the period of 2018–2020, the IAEA accepted four SSTC NRS proposals for participation in respective Coordinated Research Projects (CRPs). These CRPs address scientific and technical issues in different areas such as: 1) performance of probabilistic safety assessment for multi-unit/multi-reactor sites; 2) use of dose projection tools to ensure preparedness and response to nuclear and radiological emergencies; 3) phenomena related to in-vessel melt retention; 4) spent fuel characterization. This article presents a brief overview of the abovementioned projects with definition of scientific contributions by the SSTC NRS (participation in benchmarks, development of methodological documents on implementing research stages and of IAEA technical documents (TECDOC) for demonstration of best practices and results of research carried out by international teams).

scholarly journals Towards Growth-Mindset Mathematics Teaching in the Netherlands

10.29007/gdgh ◽  
2019 ◽  
Author(s):  
Greg Alpar ◽  
Marloes van Hoeve
Keyword(s):  
Best Practices ◽  
Personal Growth ◽  
Mathematics Teaching ◽  
Time Pressure ◽  
Deep Understanding ◽  
Growth Mindset ◽  
The Other ◽  
Research Projects ◽  
New Era ◽  
Collaboration And Communication

Mathematics is the foundation of sciences and it is important in a learner’s career success. Growth mindset in mathematics teaching is essential to reach a broader student population effectively. Shifting the focus from performance and time pressure to deep understanding and personal growth, unnecessary competition vanishes among learners. As a result, they develop a better relation with their own thinking and they gain insights into the thinking of others. At the same time, collaboration and communication emerge naturally. The fear of mathematics and making mistakes disappear, while students learn by connecting ideas and applying the already learned study material.In the academic years of 2017-2018 and 2018-2019, two Dutch research projects dealt with the application of a growth mindset in mathematics teaching. One was in secondary schools, the other one at universities. In this article, we briefly report about and reflect on the exciting results of these studies and suggest further directions for research and the development of best practices.The ideas and experiences described in this paper are urgent as currently we are at the threshold of a new era in which education and learning are (and should be) really open for everyone; with low floor and without ceilings.

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