scholarly journals Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

2020 ◽  
Author(s):  
Anna Niarakis ◽  
Martin Kuiper ◽  
Marek Ostaszewski ◽  
Rahuman S Malik Sheriff ◽  
Cristina Casals-Casas ◽  
...  
Keyword(s):  
Best Practices ◽  
Regulatory Networks ◽  
Computational Models ◽  
Biological Data ◽  
Future Directions ◽  
Logical Models ◽  
Key Topics ◽  
Biological Entities ◽  
Model Annotation ◽  
Integration Analysis

Abstract The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled ‘Annotation and curation of computational models in biology’, organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements.

scholarly journals Semi-automatic model revision of Boolean regulatory networks: confronting time-series observations with (a)synchronous dynamics

2020 ◽  
Author(s):  
Filipe Gouveia ◽  
Inês Lynce ◽  
Pedro T. Monteiro
Keyword(s):  
Time Series ◽  
Regulatory Networks ◽  
Computational Models ◽  
Optimal Solutions ◽  
Biological Models ◽  
Logical Models ◽  
Manual Task ◽  
Cellular Processes ◽  
Biological Regulatory Networks ◽  
Boolean Regulatory Networks

AbstractMotivationComplex cellular processes can be represented by biological regulatory networks. Computational models of such networks have successfully allowed the reprodution of known behaviour and to have a better understanding of the associated cellular processes. However, the construction of these models is still mainly a manual task, and therefore prone to error. Additionally, as new data is acquired, existing models must be revised. Here, we propose a model revision approach of Boolean logical models capable of repairing inconsistent models confronted with time-series observations. Moreover, we account for both synchronous and asynchronous dynamics.ResultsThe proposed tool is tested on five well known biological models. Different time-series observations are generated, consistent with these models. Then, the models are corrupted with different random changes. The proposed tool is able to repair the majority of the corrupted models, considering the generated time-series observations. Moreover, all the optimal solutions to repair the models are produced.Contact{[email protected],[email protected]}

Formalization and Semantic Integration of Heterogeneous Omics Annotations for Exploratory Searches

2020 ◽  
Vol 15 ◽  
Author(s):  
Omer Irshad ◽  
Muhammad Usman Ghani Khan
Keyword(s):  
Data Integration ◽  
Semantic Integration ◽  
Biological Data ◽  
Cellular System ◽  
Formal Specifications ◽  
Integration Model ◽  
Geographically Dispersed ◽  
Proposed Model ◽  
Data Heterogeneity ◽  
Biological Entities

Aim: To facilitate researchers and practitioners for unveiling the mysterious functional aspects of human cellular system through performing exploratory searching on semantically integrated heterogeneous and geographically dispersed omics annotations. Background: Improving health standards of life is one of the motives which continuously instigates researchers and practitioners to strive for uncovering the mysterious aspects of human cellular system. Inferring new knowledge from known facts always requires reasonably large amount of data in well-structured, integrated and unified form. Due to the advent of especially high throughput and sensor technologies, biological data is growing heterogeneously and geographically at astronomical rate. Several data integration systems have been deployed to cope with the issues of data heterogeneity and global dispersion. Systems based on semantic data integration models are more flexible and expandable than syntax-based ones but still lack aspect-based data integration, persistence and querying. Furthermore, these systems do not fully support to warehouse biological entities in the form of semantic associations as naturally possessed by the human cell. Objective: To develop aspect-oriented formal data integration model for semantically integrating heterogeneous and geographically dispersed omics annotations for providing exploratory querying on integrated data. Method: We propose an aspect-oriented formal data integration model which uses web semantics standards to formally specify its each construct. Proposed model supports aspect-oriented representation of biological entities while addressing the issues of data heterogeneity and global dispersion. It associates and warehouses biological entities in the way they relate with Result: To show the significance of proposed model, we developed a data warehouse and information retrieval system based on proposed model compliant multi-layered and multi-modular software architecture. Results show that our model supports well for gathering, associating, integrating, persisting and querying each entity with respect to its all possible aspects within or across the various associated omics layers. Conclusion: Formal specifications better facilitate for addressing data integration issues by providing formal means for understanding omics data based on meaning instead of syntax

scholarly journals BioNetLink - An Architecture for Working with Network Data

2014 ◽  
Vol 11 (2) ◽  
pp. 68-79
Author(s):  
Matthias Klapperstück ◽  
Falk Schreiber
Keyword(s):  
Experimental Data ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Large Data ◽  
Biological Data ◽  
Network Data ◽  
Data Sets ◽  
Dynamic Views ◽  
Gene Regulatory ◽  
Multiple Network

Summary The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks. This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.

scholarly journals Genomics, bio specimens, and other biological data: Current status and future directions

2018 ◽  
Vol 45 (10) ◽  
pp. e829-e833 ◽  
Author(s):  
Barry S. Rosenstein ◽  
Arvind Rao ◽  
Jean M. Moran ◽  
Daniel E. Spratt ◽  
Marc S. Mendonca ◽  
...  
Keyword(s):  
Biological Data ◽  
Current Status ◽  
Future Directions

scholarly journals 2018: A Streaming Video Odyssey

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Anali Perry ◽  
Karen Grondin
Keyword(s):  
Best Practices ◽  
Lessons Learned ◽  
Streaming Video ◽  
Library Services ◽  
Implementation Plan ◽  
Future Directions ◽  
Environmental Scan ◽  
Training Materials ◽  
Navigation Strategies

In this case study, we reflect on our journey through a major revision of our streaming video reserve guidelines, informed by an environmental scan of comparable library services and current copyright best practices. Once the guidelines were revised, we developed an implementation plan for communicating changes and developing training materials to both instructors and internal library staff. We share our navigation strategies, obstacles faced, lessons learned, and ongoing challenges. Finally, we map out some of our future directions for improving and streamlining our services.  

scholarly journals Chapter 9 - Theory of Mind and Joint Attention - The Handbook on Socially Interactive Agents

2021 ◽  
Author(s):  
Jairo Pérez-Osorio ◽  
Eva Wiese ◽  
Agnieszka Wykowska
Keyword(s):  
Theory Of Mind ◽  
Joint Attention ◽  
Cognitive Neuroscience ◽  
Computational Models ◽  
Social Cognitive ◽  
Virtual Agents ◽  
Artificial Agents ◽  
Future Directions ◽  
Social Cognitive Neuroscience ◽  
Intelligent Virtual Agents

The present chapter provides an overview from the perspective of social cognitive neuroscience (SCN) regarding theory of mind (ToM) and joint attention (JA) as crucial mechanisms of social cognition and discusses how these mechanisms have been investigated in social interaction with artificial agents. In the final sections, the chapter reviews computational models of ToM and JA in social robots (SRs) and intelligent virtual agents (IVAs) and discusses the current challenges and future directions.

scholarly journals EVALUATION OF PHOTOGRAMMETRIC BLOCK ORIENTATION USING QUALITY DESCRIPTORS FROM STATISTICALLY FILTERED TIE POINTS

2018 ◽  
Vol XLII-2 ◽  
pp. 185-191 ◽  
Author(s):  
A. Calantropio ◽  
M. P. Deseilligny ◽  
F. Rinaudo ◽  
E. Rupnik
Keyword(s):  
Best Practices ◽  
Quality Assessment ◽  
Graphical User Interface ◽  
3D Model ◽  
Low Cost ◽  
Relative Orientation ◽  
Model Reconstruction ◽  
Future Directions ◽  
3D Model Reconstruction ◽  
Data Quality Assessment

Due to the increasing number of low-cost sensors, widely accessible on the market, and because of the supposed granted correctness of the semi-automatic workflow for 3D reconstruction, highly implemented in the recent commercial software, more and more users operate nowadays without following the rigorousness of classical photogrammetric methods. This behaviour often naively leads to 3D products that lacks metric quality assessment. This paper proposes and analyses an approach that gives the users the possibility to preserve the trustworthiness of the metric information inherent in the 3D model, without sacrificing the automation offered by modern photogrammetry software. At the beginning, the importance of Data Quality Assessment is outlined, together with some recall of photogrammetry best practices. With the purpose of guiding the user through a correct pipeline for a certified 3D model reconstruction, an operative workflow is proposed, focusing on the first part of the object reconstruction steps (tie-points extraction, camera calibration, and relative orientation). A new GUI (Graphical User Interface) developed for the open source MicMac suite is then presented, and a sample dataset is used for the evaluation of the photogrammetric block orientation using statistically obtained quality descriptors. The results and the future directions are then presented and discussed.

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