scholarly journals The roles of code in biology

2021 ◽  
Vol 104 (2) ◽  
pp. 003685042110105
Author(s):  
Brendan Lawlor ◽  
Roy D Sleator
Keyword(s):  
Research Team ◽  
Life Science ◽  
Life Sciences ◽  
Three Dimensional ◽  
Science Research ◽  
Computer Code ◽  
Biological Research ◽  
Sweet Spot ◽  
Optimal Outcomes ◽  
Software Engineers

The way in which computer code is perceived and used in biological research has been a source of some controversy and confusion, and has resulted in sub-optimal outcomes related to reproducibility, scalability and productivity. We suggest that the confusion is due in part to a misunderstanding of the function of code when applied to the life sciences. Code has many roles, and in this paper we present a three-dimensional taxonomy to classify those roles and map them specifically to the life sciences. We identify a “sweet spot” in the taxonomy—a convergence where bioinformaticians should concentrate their efforts in order to derive the most value from the time they spend using code. We suggest the use of the “inverse Conway maneuver” to shape a research team so as to allow dedicated software engineers to interface with researchers working in this “sweet spot.” We conclude that in order to address current issues in the use of software in life science research such as reproducibility and scalability, the field must reevaluate its relationship with software engineering, and adapt its research structures to overcome current issues in bioinformatics such as reproducibility, scalability and productivity.

scholarly journals Educational Challenges of Molecular Life Science: Characteristics and Implications for Education and Research

2010 ◽  
Vol 9 (1) ◽  
pp. 25-33 ◽  
Author(s):  
Lena A.E. Tibell ◽  
Carl-Johan Rundgren
Keyword(s):  
Applied Sciences ◽  
Pure Sciences ◽  
Life Science ◽  
Daily Life ◽  
Life Sciences ◽  
Science Research ◽  
Technical Innovation ◽  
Research And Teaching ◽  
Educational Challenges ◽  
Starting Point

Molecular life science is one of the fastest-growing fields of scientific and technical innovation, and biotechnology has profound effects on many aspects of daily life—often with deep, ethical dimensions. At the same time, the content is inherently complex, highly abstract, and deeply rooted in diverse disciplines ranging from “pure sciences,” such as math, chemistry, and physics, through “applied sciences,” such as medicine and agriculture, to subjects that are traditionally within the remit of humanities, notably philosophy and ethics. Together, these features pose diverse, important, and exciting challenges for tomorrow's teachers and educational establishments. With backgrounds in molecular life science research and secondary life science teaching, we (Tibell and Rundgren, respectively) bring different experiences, perspectives, concerns, and awareness of these issues. Taking the nature of the discipline as a starting point, we highlight important facets of molecular life science that are both characteristic of the domain and challenging for learning and education. Of these challenges, we focus most detail on content, reasoning difficulties, and communication issues. We also discuss implications for education research and teaching in the molecular life sciences.

scholarly journals Proceedings of the “Think Tank Hackathon’’, Big Data Training School for Life Sciences Follow-up, Ljubljana 6th – 7th February 2018

2018 ◽  
Vol 24 ◽  
pp. e912
Author(s):  
Sabrina K. Schulze ◽  
Živa Ramšak ◽  
Yen Hoang ◽  
Eftim Zdravevski ◽  
Juliane Pfeil ◽  
...  
Keyword(s):  
Big Data ◽  
Life Science ◽  
Life Sciences ◽  
Science Research ◽  
Recent Experience ◽  
Think Tank ◽  
Training School ◽  
Big Data Technologies ◽  
The Cost

On 6th and 7th February 2018, a Think Tank took place in Ljubljana, Slovenia. It was a follow-up of the “Big Data Training School for Life Sciences” held in Uppsala, Sweden, in September 2017. The focus was on identifying topics of interest and optimising the programme for a forthcoming “Advanced” Big Data Training School for Life Science, that we hope is again supported by the COST Action CHARME (Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research - CA15110). The Think Tank aimed to go into details of several topics that were - to a degree - covered by the former training school. Likewise, discussions embraced the recent experience of the attendees in light of the new knowledge obtained by the first edition of the training school and how it comes from the perspective of their current and upcoming work. The 2018 training school should strive for and further facilitate optimised applications of Big Data technologies in life sciences. The attendees of this hackathon entirely organised this workshop.

scholarly journals Exploring emerging topics

2017 ◽  
Vol 1 (1) ◽  
pp. e1-e2
Author(s):  
Colin Kleanthous
Keyword(s):  
Life Science ◽  
Life Sciences ◽  
Science Research ◽  
Life Science Research ◽  
Aims And Scope ◽  
Emerging Topics

Life science research is becoming increasingly interdisciplinary in nature, and therefore there is a need for a journal that will support researchers, covering the latest thinking and newest concepts. Emerging Topics in Life Sciences is a new journal that fulfils this need, covering rapidly-moving areas of life science research, and providing a link between the established record and the latest research. Here, Colin Kleanthous, the Editor-in-Chief, provides an introduction to the journal, its aims and scope, and highlights the first featured topics.

scholarly journals Regulatory brokerage: Competitive advantage and regulation in the field of regenerative medicine

2019 ◽  
Vol 49 (3) ◽  
pp. 355-380 ◽  
Author(s):  
Margaret Sleeboom-Faulkner
Keyword(s):  
Regenerative Medicine ◽  
Competitive Advantage ◽  
Life Science ◽  
Social Science Research ◽  
Life Sciences ◽  
Science Research ◽  
Regulatory Reform ◽  
Political Debate ◽  
Political Consequences ◽  
The Uk

This article concerns the roles of entrepreneurial scientists in the co-production of life science research and regulation. Regulatory brokerage, defined as a mode of strategic planning and as the negotiation of regulation based on comparative advantage and competition, is expressed in scientific activities that take advantage of regulatory difference. This article is based on social science research in Japan, Thailand, India and the UK. Using five cases related to Japan’s international activities in the field of regenerative medicine, I argue that, driven by competitive advantage, regulatory brokerage at lower levels of managerial organization and governance is emulated at higher levels. In addition, as regulatory brokerage affects the creation of regulation at national, bilateral and global levels, new regulation may be based on competition in regulatory advantage rather than on ethical and scientific values. I argue that regulatory brokerage as the basis for regulatory reform bypasses issues that need to be decided by a broader public. More space is needed for international and political debate about the socio-political consequences of the global diversity of regulation in the field of the life sciences.

scholarly journals From intent to implementation: Factors affecting public involvement in life science research

2019 ◽  
Author(s):  
John. A. Burns ◽  
Kora Korzec ◽  
Emma R. Dorris
Keyword(s):  
Public Involvement ◽  
Life Science ◽  
Life Sciences ◽  
Science Research ◽  
Early Career ◽  
Top Down ◽  
Life Science Research ◽  
The Public ◽  
Research Production ◽  
Time Required

AbstractPublic involvement is key to closing the gap between research production and research use, and the only way to achieving ultimate transparency in science. The majority of life science research is not public-facing, but is funded by the public and impacts the community. We undertook a survey of researchers within the life sciences to better understand their views and perceived challenges to involving the public in their research. We had a valid response cohort of n=110 researchers, of whom 90% were primarily laboratory based. Using a mixed methods approach, we demonstrate that a top-down approach is key to motivate progression of life scientists from feeling positive towards public involvement to actually engaging in it. Researchers who viewed public involvement as beneficial to their research were more likely to have direct experience of doing it. We demonstrate that the systemic flaws in the way life sciences research enterprise is organised, including the promotion system, hypercompetition, and time pressures are major barriers to involving the public in the scientific process. Scientists are also apprehensive of being involuntarily involved in the current politicized climate, misinformation and publicity hype surrounding science nowadays makes them hesitant to share their early and in-progress research. The time required to deliberate study design and relevance, plan and build relationships for sustained involvement, provide and undertake training, and improve communication in the current research environment is often considered nonpragmatic, particularly for early career researchers. In conclusion, a top-down approach involving institutional incentives and infrastructure appears most effective at transitioning researchers from feeling positive towards public involvement to actually implementing it.

scholarly journals Report on the “Big Data Training School for Life Sciences”, 18-22 September 2017, Uppsala, Sweden

2018 ◽  
Vol 23 ◽  
pp. e905
Author(s):  
Juliane Pfeil ◽  
Sabrina Kathrin Schulze ◽  
Eftim Zdravevski ◽  
Yen Hoang
Keyword(s):  
Big Data ◽  
Personal Experience ◽  
Life Science ◽  
Life Sciences ◽  
Science Research ◽  
Training School ◽  
Intensive Courses ◽  
Hands On ◽  
Diverse Backgrounds ◽  
The Cost

In September 2017 a "Big Data Training School for Life Sciences" took place in Uppsala, Sweden, jointly organised by EMBnet and the COST Action CHARME (Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research - CA15100). The week programme was divided into hands-on sessions and lectures. In both cases, insights into dealing with big amounts of data were given. This paper describes our personal experience as students’ by providing also some suggestions that we hope can help the organisers as well as other trainers to further increase the efficiency of such intensive courses for students with diverse backgrounds.

Systems biology–the transformative approach to integrate sciences across disciplines

2022 ◽  
Vol 0 (0) ◽  
Author(s):  
Maya Madhavan ◽  
Sabeena Mustafa
Keyword(s):  
Biological Sciences ◽  
Life Science ◽  
Current Knowledge ◽  
Science Research ◽  
Biological Research ◽  
Computer Tools ◽  
Interdisciplinary Approaches ◽  
Basic And Applied Research ◽  
Living Organisms ◽  
Transformative Approach

Abstract Life science is the study of living organisms, including bacteria, plants, and animals. Given the importance of biology, chemistry, and bioinformatics, we anticipate that this chapter may contribute to a better understanding of the interdisciplinary connections in life science. Research in applied biological sciences has changed the paradigm of basic and applied research. Biology is the study of life and living organisms, whereas science is a dynamic subject that as a result of constant research, new fields are constantly emerging. Some fields come and go, whereas others develop into new, well-recognized entities. Chemistry is the study of composition of matter and its properties, how the substances merge or separate and also how substances interact with energy. Advances in biology and chemistry provide another means to understand the biological system using many interdisciplinary approaches. Bioinformatics is a multidisciplinary or rather transdisciplinary field that encourages the use of computer tools and methodologies for qualitative and quantitative analysis. There are many instances where two fields, biology and chemistry have intersection. In this chapter, we explain how current knowledge in biology, chemistry, and bioinformatics, as well as its various interdisciplinary domains are merged into life sciences and its applications in biological research.

scholarly journals Construction, comparison and evolution of networks in life sciences and other disciplines

2020 ◽  
Vol 17 (166) ◽  
pp. 20190610 ◽  
Author(s):  
Deisy Morselli Gysi ◽  
Katja Nowick
Keyword(s):  
Social Sciences ◽  
Life Science ◽  
Life Sciences ◽  
Science Research ◽  
Comprehensive Understanding ◽  
Network Analyses ◽  
Research Fields ◽  
Complex Relationships ◽  
Network Approaches ◽  
Computational Gastronomy

Network approaches have become pervasive in many research fields. They allow for a more comprehensive understanding of complex relationships between entities as well as their group-level properties and dynamics. Many networks change over time, be it within seconds or millions of years, depending on the nature of the network. Our focus will be on comparative network analyses in life sciences, where deciphering temporal network changes is a core interest of molecular, ecological, neuropsychological and evolutionary biologists. Further, we will take a journey through different disciplines, such as social sciences, finance and computational gastronomy, to present commonalities and differences in how networks change and can be analysed. Finally, we envision how borrowing ideas from these disciplines could enrich the future of life science research.

scholarly journals From intent to implementation: Factors affecting public involvement in life science research

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250023
Author(s):  
John A. Burns ◽  
Sinead Holden ◽  
Kora Korzec ◽  
Emma R. Dorris
Keyword(s):  
Public Involvement ◽  
Life Science ◽  
Life Sciences ◽  
Science Research ◽  
Early Career ◽  
Top Down ◽  
Life Science Research ◽  
The Public ◽  
Research Production ◽  
Time Required

Public involvement is key to closing the gap between research production and research use, and the only way to achieving ultimate transparency in science. The majority of life science research is not public-facing, but is funded by the public and impacts communities. We undertook an exploratory survey of researchers within the life sciences to better understand their views and perceived challenges to involving the public in their research. As survey response rate could not be determined, interpretation of the results must be cautious. We had a valid response cohort of n = 110 researchers, of whom 90% were primarily laboratory based. Using a mixed methods approach, we demonstrate that a top-down approach is key to motivate progression of life scientists from feeling positive towards public involvement to actually engaging in it. Researchers who viewed public involvement as beneficial to their research were more likely to have direct experience of doing it. We demonstrate that the systemic flaws in the way life sciences research enterprise is organised, including the promotion system, hyper-competition, and time pressures are major barriers to involving the public in the scientific process. Scientists are also apprehensive of being involuntarily involved in the current politicized climate; misinformation and publicity hype surrounding science nowadays makes them hesitant to share their early and in-progress research. The time required to deliberate study design and relevance, plan and build relationships for sustained involvement, provide and undertake training, and improve communication in the current research environment is often considered nonpragmatic, particularly for early career researchers. In conclusion, a top-down approach involving institutional incentives and infrastructure appears most effective at transitioning researchers from feeling positive towards public involvement to actually implementing it.

scholarly journals Identifying ELIXIR Core Data Resources

F1000Research ◽  
2017 ◽  
Vol 5 ◽  
pp. 2422 ◽  
Author(s):  
Christine Durinx ◽  
Jo McEntyre ◽  
Ron Appel ◽  
Rolf Apweiler ◽  
Mary Barlow ◽  
...  
Keyword(s):  
Life Science ◽  
Life Sciences ◽  
Life Cycles ◽  
Biological Data ◽  
Biological Information ◽  
Biological Research ◽  
Scientific Quality ◽  
Data Resource ◽  
Core Data

The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

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