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841.
Frank T Bergmann Richard Adams Stuart Moodie Jonathan Cooper Mihai Glont Martin Golebiewski Michael Hucka Camille Laibe Andrew K Miller David P Nickerson Brett G Olivier Nicolas Rodriguez Herbert M Sauro Martin Scharm Stian Soiland-Reyes Dagmar Waltemath Florent Yvon Nicolas Le Novère 《BMC bioinformatics》2014,15(1)
Background
With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result.Results
We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software.Conclusions
The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0369-z) contains supplementary material, which is available to authorized users. 相似文献842.
This article examines issues relating to ethics decision‐making in clinical trials. The overriding concern is to ensure that the well being and the interests of human subjects are adequately safeguarded. In this respect, this article will embark on a critical analysis of the ICH‐GCP Guideline. The purpose of such an undertaking is to highlight areas of concern and the shortcomings of the existing ICH‐GCP Guideline. Particular emphasis is made on how ethics committees perform their duties and responsibilities in line with the principles outlined in the ICH‐GCP Guideline. This article will draw attention to the need for a new approach to addressing the weaknesses of the ICH‐GCP Guideline in its present form. 相似文献
843.
JANINE GIBERT DAVID C. CULVER MARIE-JOSE DOLE-OLIVIER FLORIAN MALARD MARY C. CHRISTMAN LOUIS DEHARVENG 《Freshwater Biology》2009,54(4):930-941
1. This paper is a synthesis of a special issue on groundwater biodiversity with a focus on obligate subterranean species, the stygobionts. The series of papers constitutes a great leap forward in assessing and understanding biodiversity patterns because of the use of large quantitative data sets obtained over a broad geographic scale. They also represent a conceptual shift, away from a purely taxonomic and phylogenetic focus to the analysis of whole groundwater assemblages.
2. The general patterns emerging for groundwater fauna are: very high levels of endemism, low local diversity relative to regional diversity, a limited number of lineages, occurrence of many relicts, and truncated food webs with very few predators.
3. β-Diversity is at least as important as α-diversity in determining total richness at different scales (aquifer, basin and region) and overall taxa richness increases across spatial scales.
4. Advances in understanding groundwater biodiversity patterns further include identification of several important factors related to geology and hydrology that determine the composition of European stygobiotic assemblages.
5. Important challenges for future research include improving sampling strategies, filling gaps in sampling coverage, intensifying research on theoretical and statistical models, and including functional and genetic diversity components in biodiversity assessments.
6. Strategies are proposed for protecting groundwater biodiversity and an argument is made to integrate biodiversity in groundwater management. Applying principles such as complementarity and flexibility for groundwater biodiversity conservation is a major step toward delineating a reserve network that maximise species representation at the European scale. 相似文献
2. The general patterns emerging for groundwater fauna are: very high levels of endemism, low local diversity relative to regional diversity, a limited number of lineages, occurrence of many relicts, and truncated food webs with very few predators.
3. β-Diversity is at least as important as α-diversity in determining total richness at different scales (aquifer, basin and region) and overall taxa richness increases across spatial scales.
4. Advances in understanding groundwater biodiversity patterns further include identification of several important factors related to geology and hydrology that determine the composition of European stygobiotic assemblages.
5. Important challenges for future research include improving sampling strategies, filling gaps in sampling coverage, intensifying research on theoretical and statistical models, and including functional and genetic diversity components in biodiversity assessments.
6. Strategies are proposed for protecting groundwater biodiversity and an argument is made to integrate biodiversity in groundwater management. Applying principles such as complementarity and flexibility for groundwater biodiversity conservation is a major step toward delineating a reserve network that maximise species representation at the European scale. 相似文献
844.
中国孢粉学的研究进展与展望 总被引:1,自引:0,他引:1
中国古生物学会孢粉学分会今年迎来了学会成立30周年纪念.本文就中国孢粉学的发展历程作了简要的回顾,重点列举中国孢粉学在地层孢粉学、第四纪孢粉学、孢粉形态学和应用孢粉学等方面所取得的成就和研究进展,并对中国孢粉学的今后发展提出展望,呼吁中国孢粉工作者不断开拓,利用当前孢粉学良好的发展机遇,开创新的辉煌. 相似文献
845.
探讨了在植物考据研究中如何应用进化思想。我们认为在确定中国古籍文献中记载植物的学名时,对部分植物宜采用集合种(或复合种)的概念。 相似文献
846.
International research enrolling human subjects has raised an ethical concern regarding the just distribution of benefits between the countries that design the research and the host communities. Although several universal declarations have expressed this concern, a gap between theory and practice continues to exist, as well as a significant divergence between the design of the research protocol and the social context where it will be implemented. Although institutional review boards have made a valuable effort to evaluate international research, their sensitivity to the just sharing of research benefits as well as their attention to the social context must be evaluated. This article analyzes the distribution of benefits in a review of international research in Mexico and produces an ethical reflection based on the results. 相似文献
847.
产河豚毒素(TTX)菌株ZY-23的分离与鉴定 总被引:3,自引:0,他引:3
从河豚卵巢中分离得到35株细菌,利用小鼠生物法检测获11株产河豚毒素(TTX)菌株,其中有6株菌产TTX含量达400ng/mL以上,对其中ZY-23菌株进行传统分类学方法鉴定,初步鉴定为液化沙雷氏菌(Serratia liquefaciens)。16SrRNA基因序列分析,ZY-23菌株与Serratiasp.Tp5的亲缘关系最近,相似度达99%。用荧光检测分析其发酵液,发现在423nm处与标准品具有相同的发射峰,初步证实发酵液含有TTX。 相似文献
848.
Olivier Danos Kay Davies Pierre Lehn Richard Mulligan 《The journal of gene medicine》2010,12(7):559-560
Here we introduce the ARRIVE (Animal Research: Reporting In Vivo Experiments) guidelines, produced by the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), which are published in this issue of the journal with our endorsement, and will be incorporated into our Instructions to Authors. Copyright © 2010 John Wiley & Sons, Ltd. 相似文献
849.
NICOLA BARSDORF SUZANNE MAMAN NANCY KASS CATHERINE SLACK 《Developing world bioethics》2010,10(2):78-87
Access to treatment, in HIV vaccine trials (HVTs), remains ethically controversial. In most prevention trials, including in South Africa, participants who seroconvert are referred to publicly funded programmes for treatment. This strategy is problematic when there is inadequate and uneven access to public sector antiretroviral therapy (ART) and support resources. The responsibilities, if any, of researchers, sponsors and public health authorities involved in HVTs has been hotly debated among academics, scholars, representatives of international organizations and sponsors. However, there is little published on community perceptions. Recent guidance asserts that communities should make inputs into treatment and care decisions. This qualitative study explored a South African community's perceptions of who should provide what to HVT participants as well as how and why this should be done. Twenty‐nine adults working at or attending five primary health care clinics in two rural areas in KwaZulu‐Natal participated in in‐depth interviews. Respondents expressed that researchers should ‘help participants to access’ treatment and care ‘because they are in a position to do so’ and ‘are in a relationship with’ trial participants. Respondents suggested that researchers could help by ‘facilitating referral’ until such time that participants can access care and treatment on their own. We highlight a series of implications for researchers in HVTs, including their need to be aware of prospective participants' considerable trust in and respect for researchers, the responsibility that this places on them, and the need for clear communication with communities so as not to erode community trust. 相似文献
850.
At the Crossroads of Human Rights and Anthropology: Toward a Critically Engaged Activist Research 总被引:1,自引:0,他引:1
SHANNON SPEED 《American anthropologist》2006,108(1):66-76
In this article, I consider anthropology's engagement with human rights today. Through the lens of my experience in a case brought before the International Labor Organization by a community in Chiapas, Mexico, I consider the ethical, practical, and epistemological questions that arise in research defined by rights activism. I argue that the critical engagement brought about by activist research is both necessary and productive. Such research can contribute to transforming the discipline by addressing the politics of knowledge production and working to decolonize our research process. Rather than seeking to avoid or resolve the tensions inherent in anthropological research on human rights, activist research draws them to the fore, making them a productive part of the process. Finally, activist research allows us to merge cultural critique with political action to produce knowledge that is empirically grounded, theoretically valuable, and ethically viable. 相似文献