UNIFIED MODELING OF SEVERAL PERTURBATION EXPERIMENTS IN SYSTEMS BIOLOGY - A Case Study on the Glucose Uptake of Lactococcus Lactis

2008 ◽  
Vol 6 (7) ◽  
pp. 520-528 ◽  
Author(s):  
Douglas Young ◽  
Jaroslav Stark ◽  
Denise Kirschner

Author(s):  
Haider Boudjemline ◽  
Mohamed Touahria ◽  
Abdelhak Boubetra ◽  
Hamza Kaabeche

Purpose The development of context-aware applications in ubiquitous environments depends not only on the user interactions but also on several context parameters. The handling of these parameters is a fundamental problem in these systems. The key purpose of this work is to enrich the unified modeling language (UML) class diagram with new constructs to provide a universal model capable of coping with the context-awareness concerns. Design/methodology/approach The authors provide a review of existing context handling approaches. Afterward, they relied on the UML extensibility mechanisms to propose a heavyweight extension for the UML class diagram. This generic approach allows describing the different context parameters since the modeling phase. Findings Existing solutions for context handling apply the contextual constraints on finished applications or tend to be dependent on a specific development process. This paper presents a solution based on UML, which allows dealing with context since the modeling phase, and independently of development processes. This proposal is implemented as an eclipse editor and illustrated through a case study in the healthcare field. Originality/value This paper addresses the problem of context handling, and it presents a review of the foremost existing solutions. The paper also presents a heavyweight extension for the UML class diagram, which consists in enriching it with additional constructs, capable of monitoring how applications are linked to context parameters and how the values of these parameters may affect the application behavior.


2014 ◽  
Author(s):  
Alexander Franks ◽  
Florian Markowetz ◽  
Edoardo Airoldi

Building better models of cellular pathways is one of the major challenges of systems biology and functional genomics. There is a need for methods to build on established expert knowledge and reconcile it with results of high-throughput studies. Moreover, the available data sources are heterogeneous and need to be combined in a way specific for the part of the pathway in which they are most informative. Here, we present a compartment specific strategy to integrate edge, node and path data for the refinement of a network hypothesis. Specifically, we use a local-move Gibbs sampler for refining pathway hypotheses from a compendium of heterogeneous data sources, including novel methodology for integrating protein attributes. We demonstrate the utility of this approach in a case study of the pheromone response MAPK pathway in the yeast S. cerevisiae.


2020 ◽  
Vol 2 (1) ◽  
pp. 15-28
Author(s):  
Irwandi Rizki Putra ◽  
Muh. Rasyid Ridha

Along with the times, technology and information are developing rapidly in various sectors in terms of human life. In the business world, technological development is very helpful in many ways. The phenomenon that occurs at this time is the increasingly widespread competition in the business world, especially in the field of marketplace in getting consumers to the emergence of various online marketplace sites. So far, Tembilahan online shop business is only known through social media such as Facebook, Whatsapp and Instagram or verbally to the public. Therefore, researchers are interested in taking a title, namely Marketpleace Q-Store Market Analysis and planning. Tembilahan Case Study aims to become a media promotion, and can make it easier for people to find goods that they want. In designing this Marketplace, the analysis used is PIECES and UML (Unified Modeling Language) as modeling and using the Framework code igniter to facilitate researchers in building systems. With the implementation of the Marketplace Q-Store, it provides a platform for seller to market their products.


2018 ◽  
Vol 30 (12) ◽  
pp. e4488 ◽  
Author(s):  
Patricia González ◽  
David R. Penas ◽  
Xoan C. Pardo ◽  
Julio R. Banga ◽  
Ramón Doallo

2020 ◽  
pp. 549-573
Author(s):  
Mario Tulenan Parinsi ◽  
Keith Francis Ratumbuisang

As a developing country, Indonesia continues to improve its quality as a state, in which the attempt to optimize all of its potential both in terms of economic, political, social, cultural, technological, educational, health, etc. This modern era, all aspects of life are depending on technology. This makes the technology becomes one of necessary in people's life. The utilization of technology has been used by all people in all aspects of life. Specifically, this paper tries to offer an innovation that has never been designed before, namely a platform of M-Learning in form of social media related to the development of technology for learning. Nowadays, internet users and smartphone ownership in Indonesia increased dramatically, then writers took initiative to design an innovation related to this case. Social media technologies provide the opportunity for teachers to engage students in online classes, thereby supporting the development of skills and learners to achieve competency. In addition to students, the opportunity is also open to outside the community to get information that can add knowledge. This case study provides a platform for M-Learning based learning that facilitate student learning also helps society size to obtain information more easily. The design of this platform using models UML (Unified Modeling Language) to design a visual model of this platform.


2020 ◽  
pp. 369-389
Author(s):  
Sara Montagna ◽  
Andrea Omicini

This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.


2010 ◽  
Vol 192 (21) ◽  
pp. 5806-5812 ◽  
Author(s):  
Daniel M. Linares ◽  
Jan Kok ◽  
Bert Poolman

ABSTRACT Lactococcus lactis NZ9000 and its parent MG1363 are the most commonly used lactic acid bacteria for expression and physiological studies. We noted unexpected but significant differences in the growth behaviors of both strains. We sequenced the entire genomes of the original NZ9000 and MG1363 strains using an ultradeep sequencing strategy. The analysis of the L. lactis NZ9000 genome yielded 79 differences, mostly point mutations, with the annotated genome sequence of L. lactis MG1363. Resequencing of the MG1363 strain revealed that 73 out of the 79 differences were due to errors in the published sequence. Comparative transcriptomic studies revealed several differences in the regulation of genes involved in sugar fermentation, which can be explained by two specific mutations in a region of the ptcC promoter with a key role in the regulation of cellobiose and glucose uptake.


Sign in / Sign up

Export Citation Format

Share Document