scholarly journals SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Fengkai Zhang ◽  
Martin Meier-Schellersheim
Keyword(s):  
Plasma Membrane ◽  
Spatial Information ◽  
Reaction Networks ◽  
Rule Based ◽  
Fine Grained ◽  
Multiple Components ◽  
Level 3 ◽  
Type Concept ◽  
Definition Of ◽  
Molecular Components

AbstractRule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains (components) and the states such as phosphorylation and binding status of the involved components. Fine-grained spatial information such as the locations of the molecular components relative to a membrane (e.g. whether a modeled molecular domain is embedded into the inner leaflet of the cellular plasma membrane) can also be provided. Through wildcards representing component states entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states and multiple compartments. The SBML Level 3 Multi Package (Multistate, Multicomponent and Multicompartment Species Package for SBML Level 3) extends the SBML Level 3 core with the “type” concept in the Species and Compartment classes and therefore reaction rules may contain species that can be patterns and be in multiple locations in reaction rules. Multiple software tools such as Simmune and BioNetGen support the SBML Level 3 Multi package that thus also becomes a medium for exchanging rule-based models.

scholarly journals Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Fengkai Zhang ◽  
Lucian P. Smith ◽  
Michael L. Blinov ◽  
James Faeder ◽  
William S. Hlavacek ◽  
...  
Keyword(s):  
Systems Biology ◽  
Spatial Information ◽  
Markup Language ◽  
Rule Based ◽  
Fine Grained ◽  
Multiple Components ◽  
Design Changes ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Definition Of

AbstractRule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.

Diagnosis Rule Discovery Based on Causality in the Context of Fault Diagnosis in Rotating Machinery

2014 ◽  
Vol 532 ◽  
pp. 113-117
Author(s):  
Zhou Jin ◽  
Ru Jing Wang ◽  
Jie Zhang
Keyword(s):  
Fault Diagnosis ◽  
General Framework ◽  
Complex Structure ◽  
Rotating Machinery ◽  
Massive Data ◽  
Formal Definition ◽  
Rule Discovery ◽  
Rule Based ◽  
Simple Implementation ◽  
Definition Of

The rotating machineries in a factory usually have the characteristics of complex structure and highly automated logic, which generated a large amounts of monitoring data. It is an infeasible task for uses to deal with the massive data and locate fault timely. In this paper, we explore the causality between symptom and fault in the context of fault diagnosis in rotating machinery. We introduce data mining into fault diagnosis and provide a formal definition of causal diagnosis rule based on statistic test. A general framework for diagnosis rule discovery based on causality is provided and a simple implementation is explored with the purpose of providing some enlightenment to the application of causality discovery in fault diagnosis of rotating machinery.

scholarly journals Evaluation of International Competitiveness

Ekonomika ◽  
2004 ◽  
Vol 68 ◽  
Author(s):  
Gediminas Ramanauskas
Keyword(s):  
International Competitiveness ◽  
International Level ◽  
Successful Performance ◽  
Common Definition ◽  
Country Level ◽  
Level 3 ◽  
Cross Country ◽  
Definition Of ◽  
Or Organization ◽  
A Company

Competitiveness can be defined in a number of ways. We can think of it as of a successful performance of a company or organization; or we may talk about competitiveness in a macro context such as a favourable exchange rate of a national currency. Can we also talk about competitiveness of a nation? What is it and how can it be evaluated?There does not seem to be a common definition of what the international competitiveness of nations is. Some feel that the very notion of international competitiveness of nations is unfair and unacceptable. They argue that the nations themselves do not compete, their enterprises do. For others the notion of international competitiveness of nations is fair. They believe that creating appropriate measures of international competitiveness is central for tracking and understanding the sources of competitiveness of countries.In this paper I classify and compare the measures developed by various authors. I suggest that the studies on the measurement of competitiveness can be classified into five groups:1. Particular sector studies.2. Competitiveness studies at the regional / country level.3. Particular competitiveness indicator studies.4. Competitiveness studies at an international level.5. Cross-country economic policy studies.Since the competitiveness studies serve a different audience and purpose, we cannot discuss which is best without first asking: best at what?

scholarly journals Non-Entrepreneurial Legal Entity: The Theoretical And Legal Analysis Of The Concept And Characteristics

2019 ◽  
pp. 22-33
Author(s):  
O.I. Zozuliak
Keyword(s):  
Social Life ◽  
Scientific Work ◽  
Legal Analysis ◽  
Legal Entity ◽  
Legal Model ◽  
Level 3 ◽  
Business Entities ◽  
Legal Forms ◽  
Definition Of ◽  
Legal Entities

The article is devoted to the theoretical and legal analysis of issues related to the range of problems connected with development of such legal model as ‘nonentrepreneurial legal entity’. In the scientific work the author makes an analysis of those concepts which are submitted by the leading Ukrainian scholars and concern the formation of civil-law terminology in general and that is applied to the nonentrepreneurial legal entities, in particular. The author has concluded that it is expedient to apply the set of criteria during formation of the non-entrepreneurial legal entity. The article gives the definition of non-entrepreneurial legal entity in the narrow and broad meanings. It is proved that a non-business entity should be singled out as a separate category according to the non-distribution of profit (income) rather than to the specifics of its business activity. The author demonstrates the feasibility to change classification criteria and levels while classifying the legal entities and on the mentioned ground she has singled out: 1) procedure for establishment of the legal entity; 2) structure of the legal entity as a criterion of the second classification level; 3) specific character of the profit distribution as a criterion of the third level of classification. It is based on the argument that non-business entities are an independent group of the legal entities, which is divided into subgroups: the non-business entities of corporate type and the non-business entities of unitary type. Each subgroup of the non-business legal entity distinguishes several legal forms within of which specific types of non-business entities are allocated. The author presents one’s own definition of the non-entrepreneurial legal entity, as a legal entity of public or private law, whether of corporate or unitary type, which is specially established in the different areas of social life and endowed with a special legal capacity. The non-entrepreneurial legal entity shall be entitled to carry out activities with a view to profit but it doesn’t distribute it among participants (members).

scholarly journals Unrestricted Bridging Resolution

2018 ◽  
Vol 44 (2) ◽  
pp. 237-284 ◽  
Author(s):  
Yufang Hou ◽  
Katja Markert ◽  
Michael Strube
Keyword(s):  
High Reliability ◽  
Class Imbalance ◽  
Collective Classification ◽  
Fine Grained ◽  
Joint Inference ◽  
Second Stage ◽  
Information Status ◽  
Novel Method ◽  
Definition Of ◽  
Marginal Reliability

In contrast to identity anaphors, which indicate coreference between a noun phrase and its antecedent, bridging anaphors link to their antecedent(s) via lexico-semantic, frame, or encyclopedic relations. Bridging resolution involves recognizing bridging anaphors and finding links to antecedents. In contrast to most prior work, we tackle both problems. Our work also follows a more wide-ranging definition of bridging than most previous work and does not impose any restrictions on the type of bridging anaphora or relations between anaphor and antecedent. We create a corpus (ISNotes) annotated for information status (IS), bridging being one of the IS subcategories. The annotations reach high reliability for all categories and marginal reliability for the bridging subcategory. We use a two-stage statistical global inference method for bridging resolution. Given all mentions in a document, the first stage, bridging anaphora recognition, recognizes bridging anaphors as a subtask of learning fine-grained IS. We use a cascading collective classification method where (i) collective classification allows us to investigate relations among several mentions and autocorrelation among IS classes and (ii) cascaded classification allows us to tackle class imbalance, important for minority classes such as bridging. We show that our method outperforms current methods both for IS recognition overall as well as for bridging, specifically. The second stage, bridging antecedent selection, finds the antecedents for all predicted bridging anaphors. We investigate the phenomenon of semantically or syntactically related bridging anaphors that share the same antecedent, a phenomenon we call sibling anaphors. We show that taking sibling anaphors into account in a joint inference model improves antecedent selection performance. In addition, we develop semantic and salience features for antecedent selection and suggest a novel method to build the candidate antecedent list for an anaphor, using the discourse scope of the anaphor. Our model outperforms previous work significantly.

Visuospatial Reasoning

2020 ◽  
pp. 81-91
Author(s):  
Stephen K. Reed
Keyword(s):  
Spatial Information ◽  
Visual Images ◽  
Geographic Education ◽  
Rule Based ◽  
New Information ◽  
Visuospatial Reasoning ◽  
Map Design ◽  
Human Thinking ◽  
Everyday Reasoning ◽  
Algebraic Solutions

Visual thinking has aided many scientific discoveries and is also useful in everyday reasoning. The Animation Tutor provides animation feedback to help students improve their ability to estimate and calculate answers to problems. Examples include calculating the average speed of a round trip and using spatial relationships as a substitute for deriving algebraic solutions. Computer simulations of human thinking have emphasized rule-based reasoning, but these simulations now include a visual buffer to model visuospatial reasoning. It is often difficult to discover new information in visual images such as reinterpreting an ambiguous figure although people are more successful in mentally combining figures to create useful objects. Applications of research on cognitive geography include improving spatial information, geographic education, map design, urban planning, and landscape design.

scholarly journals SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems

2019 ◽  
Vol 36 (7) ◽  
pp. 2165-2172 ◽  
Author(s):  
F Maggioli ◽  
T Mancini ◽  
E Tronci
Keyword(s):  
State Of The Art ◽  
General Purpose ◽  
Heterogeneous Model ◽  
Simulation Languages ◽  
Experimental Campaign ◽  
Heterogeneous Models ◽  
Open Standard ◽  
Level 3 ◽  
Model Networks ◽  
Definition Of

Abstract Motivation SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g. enable in silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models. Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems. Results In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2—compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialized SBML simulators. Availability and implementation SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica.

Rule-Based Data-Driven Thematic Mapping Technique

2013 ◽  
Vol 756-759 ◽  
pp. 4476-4481
Author(s):  
Hong Yun Zeng ◽  
Lv Hua Wang ◽  
Zhi Qiang Xie ◽  
Wei Bo Zeng
Keyword(s):  
Information Science ◽  
Spatial Information ◽  
Engineering Application ◽  
Data Driven ◽  
Mapping Technique ◽  
River Channels ◽  
Computer Mapping ◽  
Rule Based ◽  
Thematic Mapping ◽  
Representation Technique

Mapping automation is not only a key objective of cartology, but also a study hotspot of geo-spatial information science at present. Here, we take thematic mapping of river channels (pipelines) passing through Yunnan in Kunming City for example to study and discuss, with regard to the effect required by complicated mapping encountering in the process of project implementation and the requirements on high quality of mapping data, the representation of rule-based data-driven computer mapping by the Representation technique of Arcgis9.3 to partly accomplish such mapping task that needs a lot of manual editing in traditional mapping mode, especially achieve the some kinds of mapping effect that cannot be achieved by traditional mapping without destructing GIS spatial information. The findings indicate that, the representation technique of rule-based driven computer mapping can reflect the advantages of both GIS spatial database establishment and mapping. This technique can make map rapidly according to different data requirements, and achieve the effect of traditional mapping. Due to less demand on manpower and financial capacity, such technique has a broad prospect of promotion and engineering application.

scholarly journals Compartmentalization of intracellular membrane glycocomponents is revealed by fracture-label.

1984 ◽  
Vol 98 (1) ◽  
pp. 29-34 ◽  
Author(s):  
M R Torrisi ◽  
P Pinto da Silva
Keyword(s):  
Endoplasmic Reticulum ◽  
Plasma Membrane ◽  
Binding Sites ◽  
Wheat Germ Agglutinin ◽  
Wheat Germ ◽  
Secretory Granules ◽  
The Other ◽  
Rat Tissues ◽  
Intracellular Membrane ◽  
Definition Of

We used thin-section fracture-label to determine the distribution of wheat-germ agglutinin binding sites in intracellular membranes of secretory and nonsecretory rat tissues as well as in human leukocytes. In all cases, analysis of the distribution of wheat germ agglutinin led to the definition of two endomembrane compartments: one, characterized by absence of the label, includes the membranes of mitochondria and peroxisomes as well as those of the endoplasmic reticulum and nuclear envelope; the other, strongly labeled, comprises the membrane of lysosomes, phagocytic vacuoles, and secretory granules, as well as the plasma membrane. The Golgi apparatus was weakly labeled in all studied tissues.

Sign in / Sign up

Export Citation Format

Share Document