Specifications of standards in systems and synthetic biology: status and developments in 2021

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards.

Pengaruh Penambahan Perasan Paprika Merah (Capsicum annuum) dalam Pakan Terhadap Tingkat Kecerahan Warna Ikan Koi (Cyprinus carpio L.) [The Influence of Additional Red Pepper (Capsicum annuum) Juice in Fish Feed to Koi (Cyprinus Carpio L.) Color Brightness Level]

Koi fish (Cyprinus carpio L.) is high economical fish and has some type of color and pattern on its body. Koi fish (C. carpio L.) is particularly prone to unstable water quality so the fish with prime condition is very limited. To get the fish with the prime condition required several supporting factors such as the genetic, environment and nutritional feed. In this research the used of red pepper (Capsicum annuum) juice as an additional ingredient in fish feed. The aim of this research is to know about the influence of additional red pepper juice (C. annuum) to the brightness of the color of koi fish (C. carpio L.) and the optimal concentration. There are six treatment used in this research, which are treatment A just given by pelet as a control, B treatment is adding red pepper juice by concentration of 1%, C by concentration of 3% and D by concentration of 5%. E treatment is adding carrot juice by concentrations of 4.5% and F treatment is adding astaxanthin by concentration of 1%. Each treatment given to fish with the level of color brightness that has score 2. The result of color scoring tested by experiment description method that in the end of research on A treatment (control) didn’t increase with the same score 2. B treatment (red pepper 1%) increased from score 2 to score 3 started from day 28. C treatment (red pepper 3%) increased from score 2 to score 3 started from day 21. D treatment (red pepper 5%) increased from score 2 to score 4 started from day 21. E treatment (carrot 4,5%) increased from score 2 to score 4 started from day 28. F treatment (astaxanthin 1%) increased from score 2 to score 4 started from day 21.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats. Availability and Implementation: sysbioapps.dyndns.org/SED-ML_Web_Tools.

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats. Availability and Implementation: sysbioapps.dyndns.org/SED-ML_Web_Tools.