Meeting highlight: BioVision

With 125 speakers, 30 thematic debates, 8 debate dinners and over 3000 participants, BioVision 2009 (March 8–11, 2009, Lyon, France) offered ample food for thoughts for scientists and policy makers alike. BioVision fosters the dialogue between scientists, civil society, industrialists and policy makers for concrete solutions concerning major issues in Life Sciences.     

RightField: embedding ontology annotation in spreadsheets

MOTIVATION: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation. RESULTS: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is 'semantic annotation by stealth', with an annotation process that is less error-prone, more efficient, and more consistent with community standards. Availability and implementation: RightField is open source under a BSD license and freely available from http://www.rightfield.org.uk     

Improving biodiversity monitoring

Effective biodiversity monitoring is critical to evaluate, learn from, and ultimately improve conservation practice. Well conceived, designed and implemented monitoring of biodiversity should: (i) deliver information on trends in key aspects of biodiversity (e.g. population changes); (ii) provide early warning of problems that might otherwise be difficult or expensive to reverse; (iii) generate quantifiable evidence of conservation successes (e.g. species recovery following management) and conservation failures; (iv) highlight ways to make management more effective; and (v) provide information on return on conservation investment. The importance of effective biodiversity monitoring is widely recognized (e.g. Australian Biodiversity Strategy). Yet, while everyone thinks biodiversity monitoring is a good idea, this has not translated into a culture of sound biodiversity monitoring, or widespread use of monitoring data. We identify four barriers to more effective biodiversity monitoring in Australia. These are: (i) many conservation programmes have poorly articulated or vague objectives against which it is difficult to measure progress contributing to design and implementation problems; (ii) the case for long‐term and sustained biodiversity monitoring is often poorly developed and/or articulated; (iii) there is often a lack of appropriate institutional support, co‐ordination, and targeted funding for biodiversity monitoring; and (iv) there is often a lack of appropriate standards to guide monitoring activities and make data available from these programmes. To deal with these issues, we suggest that policy makers, resource managers and scientists better and more explicitly articulate the objectives of biodiversity monitoring and better demonstrate the case for greater investments in biodiversitymonitoring. There is an urgent need for improved institutional support for biodiversity monitoring in Australia, for improved monitoring standards, and for improved archiving of, and access to, monitoring data. We suggest that more strategic financial, institutional and intellectual investments in monitoring will lead to more efficient use of the resources available for biodiversity conservation and ultimately better conservation outcomes.     

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases

MOTIVATION: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. RESULTS: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. AVAILABILITY: http://www.molgenis.nl     

Issues on research integrity: a perspective

This paper discusses several key issues that are relevant to the integrity and success of the biomedical research enterprise. Attention to these issues will improve research outcomes and reduce negative consequences in research. Subjects addressed include normative practices in research; the importance of quality data; mentoring of young scientists; how to proceed when a member of the scientific community discovers misconduct or other breaches of integrity; and the level of harm to public confidence in research due to misconduct and lack of transparency in research findings.     

Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias

Science China Life Sciences - Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However, the lack of a uniform format and dispersed...     

A blueprint for success: integration of neglected tropical disease control programmes

The rapid expansion of chemotherapy-based control programmes for neglected tropical diseases has been catalysed by funding from the Bill and Melinda Gates Foundation, donations of several drugs from pharmaceutical manufacturers, and the reduced price of the drug praziquantel. Focussing on lymphatic filariasis, schistosomiasis and soil-transmitted helminthiasis, we review here the progress made to date with the implementation and integration of large-scale control programmes. Unresolved issues include a means for rapid identification of communities at highest risk of co-morbidity, cost-effective approaches for integrating the technical interventions into setting-specific packages, and determination of the most appropriate and sustainable delivery systems.     

Evaluating sustainable forest management

The concepts underlying the post-Brundtland drive towards sustainable forest management (SFM) have been relatively well defined since 1995. While substantial progress has been made in the science and policy fields related to SFM internationally, a number of significant challenges remain. Inter-jurisdictional examples include determining the appropriate sampling frequencies required to obtain meaningful trends or develop well-founded opinions, the correlation of indicators from different jurisdictions, and problems associated with extrapolation to varying scales of application. More specifically, issues related to monitoring and information reporting (including incentives, funding, the level of streamlined data and information systems, linkages between organizations, critical analyses designed to identify indicators, structured reports and the effectiveness of extension services), remain as challenges for policy makers and forest managers internationally. The papers included in this Special Issue of Ecological Indicators describe a range of innovative approaches to developing forest-related indicator frameworks at varying scales of management, and mark some significant developments in the science underlying indicator utility.     

Bridging the Gap: How Can Information Access and Exchange Between Conservation Biologists and Field Practitioners be Improved for Better Conservation Outcomes?

It is widely accepted that there is a considerable gap between the science of conservation biology and the design and execution of biodiversity conservation projects in the field and science is failing to inform the practice of conservation. There are many reasons why this implementation gap exists. A high proportion of papers published in scientific journals by conservation biologists are seldom read outside of the academic world and there are few incentives for academics to convert their science into practice. In turn, field practitioners rarely document their field experiences and experiments in a manner that can meaningfully inform conservation scientists. Issues related to access to scientific literature, scientific relevance in multidisciplinary environments, donor expectations and a lack of critical analysis at all levels of conservation theory and practice are factors that exacerbate the divide. The contexts in which conservation biologists and field practitioners operate are also often highly dissimilar, and each has differing professional responsibilities and expectations that compromise the ability to learn from each other's expertise. Building on recent debate in the literature, and using case studies to illustrate the issues that characterize the divide, this paper draws on the authors' experiences of project management as well as academic research. We identify five key issues related to information exchange: access to scientific literature, levels of scientific literacy, lack of interdisciplinarity, questions of relevance and lack of sharing of conservation-related experiences and suggest new ways of working that could assist in bridging the gap between conservation scientists and field practitioners.     

Natural Resource Management: The Need for Interdisciplinary Collaboration

Human influence is now so pervasive that every ecosystem on Earth is being managed, whether intentionally or inadvertently. It is therefore imperative for scientists and managers to work together so that appropriate management regimes can be put in place wherever possible. However, it is not always clear what is appropriate, and the difficulties that often arise when scientists and managers work together can be even further compounded by the inclusion of lay stakeholders in the decision-making process. The expansion of interdisciplinary undergraduate and graduate programs would help both scientists and managers to deal more effectively with sociological issues and to understand how economic and demographic changes impact on natural resources. In addition, continuing education programs in these areas should be made available to established professionals to help them deal with new challenges. The concept of ecosystem services should be used to communicate the importance of various ecosystem components and processes to a broader audience. Consensus on a management regime can often be achieved through adaptive management. The process by which interdisciplinary collaboration can lead to new insights and research initiatives is exemplified by a resource management study on the island of Kosrae, Federated States of Micronesia. As a paradigm of natural resource management, microcosms like this small island community offer a unique opportunity for training and education. Received 4 October 2000; accepted 20 March 2001.     

The user's view on biodiversity data sharing — Investigating facts of acceptance and requirements to realize a sustainable use of research data —

Data sharing has become an important issue in modern biodiversity research to address large scale questions. Despite the steadily growing scientific demand, data are not easily accessed. Why is this the case? This study explores the reasons for the reluctance to share data on the one hand and the motivations for sharing on the other by summarising results from > 60 interviews and > 700 survey participants within the biodiversity science community. As result, there is a clear commitment to share biodiversity data, but also a reluctance to actually do so due to a mixture of social and technical impediments, such as loss of control over data and lack of professional reward for sharing. This exploratory study summarises the formal and technical requirements for data sharing and reuse, stated by voluntarily participating scientists worldwide. To ensure sustainable data use, user friendly data infrastructure have to be expanded or newly designed, data management plans for all scientific investigations have to be promoted, training for the users has to be provided and motivational aspects at all stages of data submission and re-use have to be considered.     

siRNA therapeutics: a clinical reality

Since the revolutionary discovery of RNA interference(RNAi), a remarkable progress has been achieved in understanding and harnessing gene silencing mechanism; especially in small interfering RNA(siRNA) therapeutics. Despite its tremendous potential benefits, major challenges in most siRNA therapeutics remains unchanged—safe, efficient and target oriented delivery of siRNA. Twenty years after the discovery of RNAi, siRNA therapeutics finally charts its way into clinics. As we journey through the decades, we reminisce the history of siRNA discovery and its application in a myriad of disease treatments. Herein,we highlight the breakthroughs in si RNA therapeutics, with special feature on the first FDA approved RNAi therapeutics Onpattro(Patisiran) and the consideration of effective siRNA delivery system focusing on current siRNA nanocarrier in clinical trials. Lastly, we present some challenges and multiple barriers that are yet to be fully overcome in siRNA therapeutics.     

Biodiversity information platforms: From standards to interoperability

One of the most serious bottlenecks in the scientific workflows of biodiversity sciences is the need to integrate data from different sources, software applications, and services for analysis, visualisation and publication. For more than a quarter of a century the TDWG Biodiversity Information Standards organisation has a central role in defining and promoting data standards and protocols supporting interoperability between disparate and locally distributed systems.Although often not sufficiently recognized, TDWG standards are the foundation of many popular Biodiversity Informatics applications and infrastructures ranging from small desktop software solutions to large scale international data networks. However, individual scientists and groups of collaborating scientist have difficulties in fully exploiting the potential of standards that are often notoriously complex, lack non-technical documentations, and use different representations and underlying technologies. In the last few years, a series of initiatives such as Scratchpads, the EDIT Platform for Cybertaxonomy, and biowikifarm have started to implement and set up virtual work platforms for biodiversity sciences which shield their users from the complexity of the underlying standards. Apart from being practical work-horses for numerous working processes related to biodiversity sciences, they can be seen as information brokers mediating information between multiple data standards and protocols.The ViBRANT project will further strengthen the flexibility and power of virtual biodiversity working platforms by building software interfaces between them, thus facilitating essential information flows needed for comprehensive data exchange, data indexing, web-publication, and versioning. This work will make an important contribution to the shaping of an international, interoperable, and user-oriented biodiversity information infrastructure.     

COVID-19 threatens faculty diversity: postdoctoral scholars call for action

Despite substantial investment and effort by federal agencies and institutions to improve the diversity of the professoriate, progress is excruciatingly slow. One program that aims to enhance faculty diversity is the Institutional Research and Academic Career Development Award (IRACDA) funded by the National Institutes of Health/National Institute of General Medical Sciences. IRACDA supports the training of a diverse cohort of postdoctoral scholars who will seek academic research and teaching careers. The San Diego IRACDA program has trained 109 postdoctoral scholars since its inception in 2003; 59% are women and 63% are underrepresented (UR) Black/African-American, Latinx/Mexican-American, and Indigenous scientists. Sixty-four percent obtained tenure-track faculty positions, including a substantial 32% at research-intensive institutions. However, the COVID-19 pandemic crisis threatens to upend IRACDA efforts to improve faculty diversity, and academia is at risk of losing a generation of diverse, talented scholars. Here, a group of San Diego IRACDA postdoctoral scholars reflects on these issues and discusses recommendations to enhance the retention of UR scientists to avoid a “lost generation” of promising UR faculty scholars.     

A plan of life science education programs in the Japanese Society for Biological Sciences in Space]

The Future Plan Committee of the Japanese Society for Biological Sciences in Space drafted a Life Science Education Programs. The program consists of preparation of teaching materials for elementary and high school teachers and of summer course of the gravitational and space biology for university students and young scientists. The outline of the programme are presented.     

The Barcode of Life Data Portal: bridging the biodiversity informatics divide for DNA barcoding

With the volume of molecular sequence data that is systematically being generated globally, there is a need for centralized resources for data exploration and analytics. DNA Barcode initiatives are on track to generate a compendium of molecular sequence-based signatures for identifying animals and plants. To date, the range of available data exploration and analytic tools to explore these data have only been available in a boutique form--often representing a frustrating hurdle for many researchers that may not necessarily have resources to install or implement algorithms described by the analytic community. The Barcode of Life Data Portal (BDP) is a first step towards integrating the latest biodiversity informatics innovations with molecular sequence data from DNA barcoding. Through establishment of community driven standards, based on discussion with the Data Analysis Working Group (DAWG) of the Consortium for the Barcode of Life (CBOL), the BDP provides an infrastructure for incorporation of existing and next-generation DNA barcode analytic applications in an open forum.     

城市生态基础设施管理研究进展

城市生态基础设施作为城市生态系统的重要组成部分,在维持自然生态过程稳定、促进社会经济发展、保障人居环境质量方面发挥着重要的作用。在快速城市化进程中,对城市生态基础设施进行科学的管理显得尤为重要。在重新明确城市生态基础设施管理概念和内涵的基础上,归纳提炼了4项管理原则,并对现有管理类型进行了梳理。对生态基础设施管理涉及的3个关键问题的常见解决方法进行了总结、分类,并对每类方法的优劣进行了分析讨论。针对此领域的工作做了展望。对于现有城市生态基础设施管理问题与方法的整合研究既有利于明确今后研究重点,也为城市生态基础设施管理提供了科学依据和案例参考。     

Calculating life? Duelling discourses in interdisciplinary systems biology

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences.     

Practical Issues in the Use of Probabilistic Risk Assessment

Probabilistic risk assessment (PRA) represents an important step in the evolution of risk assessment methodology to assist decision-making at hazardous waste sites. Despite considerable progress in the development of PRA techniques, regulatory acceptance of PRA has been limited, in part because a number of practical issues in its use must yet be resolved. A recent workshop on PRA identified several areas to be addressed, including the need for: (1) better demonstration of the value of PRA in risk management; (2) PRA training and education opportunities; (3) the development of technical criteria for acceptability of a PRA; (4) policy decisions on acceptable risk distributions; (5) ways to deal with risk communication issues; and (6) a variety of technical issues, including ways to include estimates of variability and uncertainty associated with toxicity values. Solutions to many of these issues will require better dialog between risk assessors and risk managers than has existed in the past.