Eliciting Expert Knowledge of Forest Succession Using an Innovative Software Tool

Author(s):  
Michael Drescher ◽  
Lisa J. Buse ◽  
Ajith H. Perera ◽  
Marc R. Ouellette
2008 ◽  
Vol 159 (10) ◽  
pp. 326-335 ◽  
Author(s):  
Niklaus E. Zimmermann ◽  
Harald Bugmann

New IPCC climate projections suggest drastic changes in future climate. We discuss two commonly used modeling approaches, statistical distribution models and dynamic forest succession models, as they are suitable for assessing expected effects of climate change on the tree species distribution in Switzerland and for assisting management decisions in forestry. We discuss the basic assumptions and the strengths and weaknesses of the two approaches, without an understanding of which it is impossible to fully judge the outcome of modeling exercises. We give an overview of results from applying these two modeling approaches in Switzerland and in the Alps and discuss their appropriate use. We believe that these models are an important basis for decision making in the face of highly uncertain development of future climate. Nonetheless, models do not represent an exact copy of reality. Plausibility analyses are necessary in order to assess the results' usefulness and precision. Sensitivity analyses and a critical comparison of model results with expert knowledge of current forests, long measurement time series and other data are important. Also, dialog with practitioners and managers is not only important for checking the plausibility of model predictions under current conditions, but may also serve to improve the evaluation of future projections. We propose to apply models to the whole of Switzerland and to many tree species. Such a concerted national analysis may serve the adaptive management of forests and may strengthen dialog between researchers and practitioners.


2021 ◽  
Author(s):  
Esther Heid ◽  
Samuel Goldman ◽  
Karthik Sankaranarayanan ◽  
Connor W. Coley ◽  
Christoph Flamm ◽  
...  

Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.


Author(s):  
Zdenek Dvorak ◽  
David Rehak ◽  
Andrej David ◽  
Zoran Cekerevac

The purpose of this paper is to present the development of a qualitative approach to environmental risk assessment (QAERA) in transport. The approach is described as a model developed for the future software tool which will be utilizable as a risk decision support system. The basic part is aimed on developing a quantitative environmental risk assessment. Thus, this paper describes a set of 6 pillars of safety and security. Accordingly, the paper contains both chosen safety and security indicators and selected criteria for assessing the risk of launching the environmental change of global model thinking in the transport sector. The environmental risk assessment as a global model of thinking was originally based on historical experience but, nowadays, it is changing. Based on new expert knowledge, more precisely, on input of new global data, paper displays an environmental risk assessment with actual interpretation. The discussion of the paper is oriented to support research results, a new knowledge-oriented approach to global climate changes, using suitable risk assessment methods and technics. The result of the paper is a new approach for the modeling of environmental risk assessment in the transport sector.


2021 ◽  
Author(s):  
Esther Heid ◽  
Samuel Goldman ◽  
Karthik Sankaranarayanan ◽  
Connor W. Coley ◽  
Christoph Flamm ◽  
...  

Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.


2021 ◽  
Vol 1 ◽  
Author(s):  
Jin Tao ◽  
Kelly A. Brayton ◽  
Shira L. Broschat

Advances in genome sequencing have accelerated the growth of sequenced genomes but at a cost in the quality of genome annotation. At the same time, computational analysis is widely used for protein annotation, but a dearth of experimental verification has contributed to inaccurate annotation as well as to annotation error propagation. Thus, a tool to help life scientists with accurate protein annotation would be useful. In this work we describe a website we have developed, the Protein Annotation Surveillance Site (PASS), which provides such a tool. This website consists of three major components: a database of homologous clusters of more than eight million protein sequences deduced from the representative genomes of bacteria, archaea, eukarya, and viruses, together with sequence information; a machine-learning software tool which periodically queries the UniprotKB database to determine whether protein function has been experimentally verified; and a query-able webpage where the FASTA headers of sequences from the cluster best matching an input sequence are returned. The user can choose from these sequences to create a sequence similarity network to assist in annotation or else use their expert knowledge to choose an annotation from the cluster sequences. Illustrations demonstrating use of this website are presented.


2022 ◽  
Vol 29 (3) ◽  
pp. 1-34
Author(s):  
Moritz Alexander Messerschmidt ◽  
Sachith Muthukumarana ◽  
Nur Al-Huda Hamdan ◽  
Adrian Wagner ◽  
Haimo Zhang ◽  
...  

We present ANISMA, a software and hardware toolkit to prototype on-skin haptic devices that generate skin deformation stimuli like pressure, stretch, and motion using shape-memory alloys (SMAs). Our toolkit embeds expert knowledge that makes SMA spring actuators more accessible to human–computer interaction (HCI) researchers. Using our software tool, users can design different actuator layouts, program their spatio-temporal actuation and preview the resulting deformation behavior to verify a design at an early stage. Our toolkit allows exporting the actuator layout and 3D printing it directly on skin adhesive. To test different actuation sequences on the skin, a user can connect the SMA actuators to our customized driver board and reprogram them using our visual programming interface. We report a technical analysis, verify the perceptibility of essential ANISMA skin deformation devices with 8 participants, and evaluate ANISMA regarding its usability and supported creativity with 12 HCI researchers in a creative design task.


Author(s):  
Catherine E. Bauby ◽  
Philippe Hai¨k ◽  
Emmanuel Remy ◽  
Benoiˆt Ricard

The long-term management of a production asset raises several major issues among which rank the technical management of the plant, its economics and the fleet level perspective one has to adopt. Decision-makers are therefore faced with the need to define long term policies (up to the end of asset operation), which take into account multiple criteria including safety (which is paramount) and performance. In this paper we remind the reader of the EDF three-level methodology for asset management. As introduced in PVP 2003, this methodology provides decision-makers with indicators to evaluate the status of a plant. The methodology addresses the component/technical level (how to safely operate daily and invest for the future), the plant level (how to translate technical decisions into plant-wide consequences including economic performance) and the fleet level (how to manage a large number of similar assets). Identifying what might occur to ageing plant components, how operations or maintenance decisions might influence these occurrences and what the consequences of these decisions and events might have on plant operation, is definitely an expert task. In order to gather, preserve, share, maintain and exploit this expert knowledge, we therefore relied on a “knowledge modeling” activity. This activity is used to support the asset management evaluation methodology. We detail the knowledge model — an entity/relation expert description of the plant life-management domain — on which our three-level methodology relies. Lastly, we focus on the software tool that implements this model in order to allow decision-makers to define, analyze and evaluate long-term plant operation and maintenance policies.


2021 ◽  
Author(s):  
Esther Heid ◽  
Samuel Goldman ◽  
Karthik Sankaranarayanan ◽  
Connor W. Coley ◽  
Christoph Flamm ◽  
...  

Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.


Author(s):  
Delphine Guillon ◽  
Christophe Merlo ◽  
Eric Villeneuve ◽  
Elise Vareilles ◽  
Michel Aldanondo

AbstractEarly phases of product development are critical for next phases and impact the product definition. During bid process, suppliers generate offers for a customer that must both meet customer's requirements and be realizable in terms of technical aspects, costs and due date. Our aim is to propose a methodology for implementing a generic bid model, composed of context parameters, customer's requirements, the product i.e. technical solution, its delivery process, and associated risks. Key Performance Indicators allow to evaluate different solutions. The bid model is exploited with two different approaches. First, we use Constraint Satisfaction Problems to formalize expert knowledge and identify variables/constraints and relations. Second, we use case database to reuse past experiences. This model and the methodology are applied with a company developing harbour cranes. An initialisation phase allows to define existing bid process. Then, the generic model is adapted through a specialisation phase, using specific knowledge from company's experts. Finally, the specific model is implemented and tested in an implementation phase. Future work will be focused on a software tool development.


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