SBSCL | Systems Biology Simulation Core Library

by draeger-lab HTML Version: v2.1 License: LGPL-3.0

X-Ray Key Features Code Snippets(2)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | SBSCL Summary

SBSCL is a HTML library. SBSCL has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. This library is based on the JSBML project. It can be used on every operating system for which a Java Virtual Machine is available. Please note that this project does not contain any user interface neither a command-line interface, nor a graphical user interface. This project has been developed as a pure programming library. To support the MIASE effort, it understands SED-ML files. Its abstract type and interface hierarchy facilitates the implementation of further community standards, such as CellML.

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Quality

Security

License

Reuse

Support

SBSCL has a low active ecosystem.

It has 19 star(s) with 11 fork(s). There are 9 watchers for this library.

It had no major release in the last 12 months.

There are 13 open issues and 39 have been closed. On average issues are closed in 73 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of SBSCL is v2.1

Quality

SBSCL has 0 bugs and 0 code smells.

Security

SBSCL has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

SBSCL code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

SBSCL is licensed under the LGPL-3.0 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

SBSCL releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

It has 741054 lines of code, 1866 functions and 2967 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

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SBSCL Key Features

No Key Features are available at this moment for SBSCL.

SBSCL Examples and Code Snippets

The Systems Biology Simulation Core Library ,File structure

HTML

Lines of Code : 15

License : Weak Copyleft (LGPL-3.0)

Copy

 /
 |- dev                 -> Contains the diagrams and fomatting-guidelines for the developers
 |- docs                -> Contains code for the maven built website
 |- modules             -> Contains the code for support of cellDesigner and

For developers

HTML

Lines of Code : 5

License : Weak Copyleft (LGPL-3.0)

Copy


  org.draegerlab
  sbscl
  2.1

Community Discussions

Trending Discussions on SBSCL

Simulating the SBML models with coupled compartment and species rate rules

QUESTION

Simulating the SBML models with coupled compartment and species rate rules

Asked 2020-Jul-02 at 19:40

I am working on the Simulation Biology Simulation Core Library (SBSCL) where we are currently simulating the SBML models from the SBML Test Suite. But I am having issues in simulating the SBML models where there are coupled compartment and species rate rules and the species are in concentration units (i.e. the species depends on the values of the compartment). The models with this property can be found in the SBML Test Suite with one of them being the test case 1198.

The series of discussions on this issue can also be found at the sbml-discuss google group [Link]. Even I have created an issue for this in SBSCL.

Can I get the best way of simulating this type of SBML models?

...

ANSWER

Answered 2020-Jul-02 at 19:40

If you can treat your species concentration like a parameter, this is the easiest solution: simply set the rate of change directly. If asked to compute the amount of the species, multiply that concentration by the compartment size.

If, however, your simulator is like most SBML simulators, your fundamental unit of change is the species amount. This makes this scenario particularly awkward, because the rate of change of the species amount must be derived from the rate of change of the species concentration as well as the rate of change of the compartment size.

However, it's still doable. If we use "S1" as the species amount, "[S1]" as the species concentration, and "C" as the compartment size:

Again, this applies in the scenario where dC/dt and d[S1]/dt are defined, and dS1/dt is unknown.

This can be derived as follows:

(via the chain rule)

Source https://stackoverflow.com/questions/62703123

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install SBSCL

You can download it from GitHub.

Support

Systems Biology Markup Language (L1V1 - L3V2)SBML models with FBC V1 and V2SBML models with comp extensionsSimulation Experiment Description Markup Language (L1V3)COMBINE archive and OMEX formatAll models from SBML Test Suite and BiGG modelsAll models from Stochastic Test Suite

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