scholarly journals Ki MoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

2014 ◽  
Vol 8 (1) ◽  
Author(s):  
Rafael S Costa ◽  
André Veríssimo ◽  
Susana Vinga
Keyword(s):  
Experimental Data ◽  
Kinetic Models ◽  
Biological Systems ◽  
Web Based

Systems biology model databases and resources

2008 ◽  
Vol 45 ◽  
pp. 223-236 ◽  
Author(s):  
Carel van Gend ◽  
Jacky L. Snoep
Keyword(s):  
Experimental Data ◽  
Systems Biology ◽  
Kinetic Models ◽  
Complete System ◽  
Kinetic Modelling ◽  
Biological Systems ◽  
Standard Form ◽  
Computer Models ◽  
Data Sets ◽  
Quantitative Understanding

Systems biology aims at a quantitative understanding of systemic behaviour as a function of its components and their interactions. In systems biology studies computer models play an important role: (i) to integrate the components’ behaviour and (ii) to analyse experimental data sets. With the growing number of kinetic models that are being constructed for parts of biological systems, it has become important to store these models and make them available in a standard form, such that these models can be combined, eventually leading to a model of a complete system. In the present chapter we describe database initiatives that contain kinetic models for biological systems, together with a number of other systems biology resources related to kinetic modelling.

scholarly journals Web-based applications for building, managing and analysing kinetic models of biological systems

2008 ◽  
Vol 10 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D.-Y. Lee ◽  
R. Saha ◽  
F. N. K. Yusufi ◽  
W. Park ◽  
I. A. Karimi
Keyword(s):  
Kinetic Models ◽  
Biological Systems ◽  
Web Based

A New Adsorption Rate Equation in Batch Systems

2018 ◽  
Author(s):  
yongson hong ◽  
Kye-Ryong Sin ◽  
Jong-Su Pak ◽  
Chol-Min Pak
Keyword(s):  
Experimental Data ◽  
Kinetic Analysis ◽  
Adsorption Kinetics ◽  
Rate Equation ◽  
Kinetic Models ◽  
Adsorption Kinetic ◽  
Adsorption Rate ◽  
Batch Systems ◽  
New View

<p><b>In this paper, the deficiencies and cause of previous adsorption kinetic models were revealed, new adsorption rate equation has been proposed and its validities were verified by kinetic analysis of various experimental data.</b> <b>This work is a new view on the adsorption kinetics rather than a comment on the previous adsorption papers.</b></p>

scholarly journals Kinetics study on non-isothermal thermochemical liquefaction of corncobs in ethanol-water solution: Effect of ethanol concentration

2018 ◽  
Vol 197 ◽  
pp. 09005
Author(s):  
Bregas Siswahjono Tatag Sembodo ◽  
Hary Sulistyo ◽  
Wahyudi Budi Sediawan ◽  
Mohammad Fahrurrozi
Keyword(s):  
Experimental Data ◽  
Kinetic Models ◽  
Ethanol Concentration ◽  
Water Solution ◽  
Reaction Products ◽  
Gaseous Products ◽  
Bio Oil ◽  
Volatile Products ◽  
Calculation Results ◽  
Oil Gas

Corncobs are potentially processed into bio-oil through thermochemical liquefaction processes. It is difficult to construct kinetics models based on the compounds involved in the reaction. It would be made four kinetic models based on four reaction products, i.e., solids, bio-oil, gas and volatile products. The purposes of the study were to seek kinetics model of thermochemical liquefaction of corncobs in ethanol-water solution and to study the effect of ethanol concentration. The experiment of liquefaction processes of corncobs in ethanol-water solution using sodium carbonate catalyst was performed in the 150 ml autoclave equipped with a magnetic stirrer in the temperature up to 280°C. Four kinetic models were applied to predict the yield of four reaction product lumps. The calculation results were compared to the experimental data. Compared to the others, model 4 was the most realistic and closely matching to the experimental data. In model 4 the reaction mechanism was assumed that biomass (corncobs) first decomposed into bio-oil, followed by decomposition of bio-oil into volatile products reversibly and, finally, volatile products decomposed into gaseous products. The yield of bio-oil increased from 42.05% to 54.93% by increasing to ethanol concentration of 0% to 40%.

scholarly journals KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Hugo Mochão ◽  
Pedro Barahona ◽  
Rafael S Costa
Keyword(s):  
Experimental Data ◽  
Metabolic Networks ◽  
Model Simulation ◽  
Web Interface ◽  
Concentration Data ◽  
Web Based ◽  
Share Data ◽  
Visualization Tools ◽  
Filter Mechanism ◽  
Machine Readable

Abstract The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data. It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data. In addition, it also supplies tools to simplify the construction process of ODE (Ordinary Differential Equations)-based models of metabolic networks. In this release, we present an update of KiMoSys with new data and several new features, including (i) an improved web interface, (ii) a new multi-filter mechanism, (iii) introduction of data visualization tools, (iv) the addition of downloadable data in machine-readable formats, (v) an improved data submission tool, (vi) the integration of a kinetic model simulation environment and (vii) the introduction of a unique persistent identifier system. We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL:  www.kimosys.org

Complementing corpus analysis with web-based experimentation in research on World Englishes

2019 ◽  
Vol 40 (1) ◽  
pp. 24-52 ◽  
Author(s):  
Stephanie Horch
Keyword(s):  
Experimental Data ◽  
Open Source Software ◽  
Previous Analysis ◽  
Experimental Methods ◽  
World Englishes ◽  
Corpus Analysis ◽  
Maze Task ◽  
Web Based ◽  
Corpus Linguistic ◽  
Large Corpus

Abstract Usage-based research in linguistics has to a large extent relied on corpus data. However, a feature’s “failure to appear in even a very large corpus (such as the Web) is not evidence for ungrammaticality, nor is appearance evidence for grammaticality” (Schütze and Sprouse 2013: 29). It is therefore advisable to complement corpus-based analyses with experimental data, so as to (ideally) obtain converging evidence. This paper reviews reasons for combining corpus linguistic with psycholinguistic experimental methods, and demonstrates how research on varieties of English can profit from experimentation. For a study of conversion in Asian Englishes, the maze task (Forster, Guerrera, and Elliot 2009; Forster 2010) was implemented with a web-based, open-source software. The results of the experiment dovetail with a previous analysis of the Corpus of Global Web-based English (Davies 2013). These results should encourage researchers not to base findings exclusively on corpus evidence, but corroborate them by means of experimental data.

scholarly journals Removal of Malachite Green from Aqueous Solution by Activated Carbon Developed from Cocoa (Theobroma Cacao) Shell - A Kinetic and Equilibrium Studies

2011 ◽  
Vol 8 (s1) ◽  
pp. S363-S371 ◽  
Author(s):  
C. Theivarasu ◽  
S. Mylsamy
Keyword(s):  
Experimental Data ◽  
Activated Carbon ◽  
Malachite Green ◽  
Kinetic Models ◽  
Theobroma Cacao ◽  
Second Order ◽  
Order Kinetic ◽  
Equilibrium Studies ◽  
Initial Ph ◽  
Pseudo Second Order

The removal of malachite green (MG) by cocoa (Theobroma cacao) shell activated carbon (CSAC) was investigated in present study. Adsorption studies were performed by batch experiments as a function of process parameters such as initial pH, contact time, initial concentration and adsorbent dose. A comparison of kinetic models applied to the adsorption of MG on CSAC was evaluated for the pseudo-first order and pseudo-second order kinetic models. Results showed that the pseudo-second order kinetic model was found to correlate the experimental data well. The experimental equilibrium adsorption data was represented with Langmuir, Freundlich, Tempkin, Dubinin-Radushkevich and Flory-Huggins isotherms. The experimental data obtained in the present study indicated that activated carbon developed from cocoa shell can be attractive options for dye removal from waste water.

scholarly journals Applications of the Twinning CIF Dictionary 1.0 for Twinned Crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C1031-C1031
Author(s):  
Victor Young ◽  
James Hester ◽  
Ian Brown
Keyword(s):  
Experimental Data ◽  
Web Site ◽  
Web Based ◽  
Future Developments ◽  
Chemical Crystallography ◽  
The Web

Version 1.0 of the Twinning CIF Dictionary was posted on the IUCr web site in February 2014.[1] The purpose of this presentation is to illustrate the application of these definitions in many common situations relevant to chemical crystallography. Within these definitions are tools to describe all known twin types as defined by the monograph by Nespolo.[2] Tools are available to describe a single twin law or combinations of unrelated twin laws. These definitions were developed mindful that experimental data should have a set format for deposition and validation through future developments of the web-based IUCr CheckCIF software. Several examples of twins will be presented to illustrate the functionality of these definitions.

Soot Formation Reaction Effect in Modeling Thermal Partial Oxidation of Jet-A

2014 ◽  
Author(s):  
Richard Scenna ◽  
Ashwani K. Gupta
Keyword(s):  
Experimental Data ◽  
Carbon Monoxide ◽  
Partial Oxidation ◽  
Kinetic Models ◽  
Soot Formation ◽  
Radical Formation ◽  
Fuel Reforming ◽  
Chemical Modeling ◽  
Formation Reaction ◽  
One Dimensional

The results obtained from the modeling of thermal partial oxidation of kerosene based Jet-A fuel are presented using one dimensional chemical modeling. Two detailed kinetic models for alkenes chemistry ranging between C8 to C16 were evaluated and compared against experimental data of thermal partial oxidation of Jet-A fuel. The key difference between these two kinetic models was the inclusion of model for soot formation reactions. Chemical modeling was performed using dodecane to represent Jet-A fuel. The results showed that the model with soot reactions was significantly more accurate in predicting reformate products from Jet-A. In particular, the formation of carbon monoxide, methane and acetylene closely followed the experimental data with the model that included soot formation reactions. The results revealed that the soot formation reactions promoted the smaller hydrocarbons to decompose via the alternate kinetic pathways and from additional radical formation. The results also reveal that the inclusions of soot formation reactions are critical in the modeling of thermal partial oxidation of fuels for fuel reforming.

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