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JSEDML: Java Library for Simulation Experiment Descriptions #101

Closed matthiaskoenig closed 3 years ago

matthiaskoenig commented 6 years ago

Background

The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for the description of simulation experiments. The number of computational models of biological systems is growing at an ever-increasing pace. At the same time, their size and complexity are also increasing. It is now generally accepted that one must be able to exchange the mathematical structure of such models, for instance, to build on existing studies by reusing models or for the reproduction of model results.

SED-ML describes in a computer-readable exchange format the information for the reproduction of simulation experiments. SED-ML is a software-independent format encoded in XML not specific to particular simulation tools and independent of the underlying model language.

With the recent publication of SED-ML L1V3, it is now possible to include and use data in simulation experiments, opening the door for better integration of data and models.

A major bottleneck for the adoption of SED-ML is that currently no dedicated Java library supporting SED-ML L1V3 exists. Multiple Java-based tools have already support for computational models in the systems biology language, but lack support for SED-ML L1V3. Open Source projects immediately profiting from this project would be among others

Implementing a dedicated Java library supporting SED-ML L1V3 would be an important step for the exchange, reproducibility, reusability, and interoperability of models and their simulations.

https://sed-ml.github.io/ https://sed-ml.github.io/documents/sed-ml-L1V3.pdf

Goal

The end result of the GSOC project should be a first version of a java based SED-ML library (JSEDML) supporting the SED-ML specification L1V3.

Difficulty Level 2

The project requires Java programming skills, understanding of SED-ML and basic knowledge of SBML. The project can reuse components and build on jlibsedml.

Skills

List skills/technologies that the student should be familiar with. Also tag the issue with these.

Public Repository

https://github.com/SED-ML/JSEDML https://github.com/sed-ml/

Potential Mentors

Matthias König Chris Myers

Contact

Matthias König

shalinshah1993 commented 5 years ago

I think this needs to be addressed as it will be helpful to any Java-based library that works with SED-ML files. Let me know if someone gets interested in working on this or if there is a need to mentor this (or related issue) for next GSoC year. I'll be happy to help!

draeger commented 3 years ago

@matthiaskoenig, I think this could still be of interest. I'd suggest to reopen this.

khanspers commented 3 years ago

@matthiaskoenig @draeger : This issue was closed as part of our preparation for GSoC 2021. In fact, all NRNB GSoC issues are closed for now. Stay tuned for more information coming shortly on how to reformat closed issues that are still of interest.