Related Experiment Video
Updated: Jul 5, 2026
10:41
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
Published on: May 9, 2017
SYCAMORE--a systems biology computational analysis and modeling research environment.
Andreas Weidemann1, Stefan Richter, Matthias Stein
1Scientific Databases and Visualization Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.
Bioinformatics (Oxford, England)
|May 9, 2008
Summary
SYCAMORE is a browser-based tool for systems biology, enabling users to build, simulate, and analyze kinetic models. It supports database-driven modeling and parameter estimation, making computational biology accessible to non-experts.
Area of Science:
- Systems Biology
- Computational Biology
- Biophysics
Background:
- Kinetic modeling is crucial for understanding biological systems.
- Existing tools may have limitations for non-expert users.
- SYCAMORE addresses these challenges with a user-friendly interface.
Purpose of the Study:
- To introduce SYCAMORE, a novel browser-based application.
- To facilitate the construction, simulation, and analysis of kinetic models.
- To empower non-expert users in computational biology tasks.
Main Methods:
- Web-based application development.
- Integration of database support for modeling.
- Implementation of model checking algorithms.
- Methods for kinetic parameter estimation using protein structures.
Main Results:
- SYCAMORE enables database-supported kinetic model construction.
- The application allows for basic model checking and simulation.
- It facilitates the estimation of unknown kinetic parameters.
- User guidance is provided for non-expert users.
Conclusions:
- SYCAMORE simplifies complex kinetic modeling tasks.
- It enhances accessibility to computational systems biology.
- The tool supports advanced analyses like parameter estimation.
Related Concept Videos
02:55Synthetic Biology
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
01:29Mathematical Modeling: Problem Solving
Mathematical modeling transforms real-world scenarios into mathematical expressions, allowing for structured problem-solving and analysis. This process involves defining the situation, assigning variables to measurable quantities, selecting an appropriate model, and solving the resulting equation. Such models are invaluable in finance, providing precise methods to evaluate investments, loans, and repayment structures.A widely used example is the calculation of fixed monthly payments on a loan,...
02:00Molecular Models
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
01:26Classification of Systems-I
Linearity is a system property characterized by a direct input-output relationship, combining homogeneity and additivity.
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:
01:14Statistical Analysis System (SAS)
SAS, short for Statistical Analysis System, is a powerful data analysis, management, and visualization tool. Developed by the SAS Institute in the early 1970s, SAS has evolved into a comprehensive software suite used across various industries for statistical analysis, business intelligence, and predictive modeling.
Applications: SAS finds applications in numerous fields, including healthcare for clinical trial analysis, finance for risk assessment, marketing for customer data analysis, and...
Applications: SAS finds applications in numerous fields, including healthcare for clinical trial analysis, finance for risk assessment, marketing for customer data analysis, and...
01:25Control Systems: Applications
Electrical engineering plays a pivotal role in our daily lives, with control systems at the heart of many applications, from home appliances to sophisticated space shuttles. Control systems manage and regulate the behavior of devices and processes, ensuring they function safely, correctly, and efficiently.
In modern vehicles, control systems manage various functions to enhance performance and safety. The steering wheel and accelerator are primary inputs in a car's control system. The direction...
In modern vehicles, control systems manage various functions to enhance performance and safety. The steering wheel and accelerator are primary inputs in a car's control system. The direction...