Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Design considerations for representing systems biology information with the Systems Biology Graphical Notation

Visual representations are commonly used to explore, analyse, and communicate information and knowledge in systems biology and beyond. Such visualisations not only need to be accurate but should also be aesthetically pleasing and informative. Using the example of the Systems Biology Graphical Notation (SBGN) we will investigate design considerations for graphically presenting information from systems biology, in particular regarding the use of glyphs for types of information, the style of graph layout for network representation, and the concept of bricks for visual network creation.

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.

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Specifications of standards in systems and synthetic biology: status and developments in 2020

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.

Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods

Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data. These data have different types (discrete, real, string, etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data (copy number variation, single nucleotide polymorphisms), annotations, interactions, and association data are some of the commonly used biological datasets to study various cellular mechanisms of living organisms. Each of them provides a unique, complementary and partly independent view of the genome and hence embed essential information about the regulatory mechanisms of genes and their products. Therefore, integrating these data and inferring regulatory interactions from them offer a system level of biological insight in predicting gene functions and their phenotypic outcomes. To study genome functionality through regulatory networks, different methods have been proposed for collective mining of information from an integrated dataset. We survey here integration methods that reconstruct regulatory networks using state-of-the-art techniques to handle multi-omics (i.e., genomic, transcriptomic, proteomic) and other biological datasets.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

[This corrects the article DOI: 10.4056/sigs.5279417.].

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.

SBMLPkgSpec: a LaTeX style file for SBML package specification documents

OBJECTIVE

The Systems Biology Markup Language (SBML) is a popular open format for storing and exchanging computational models in biology. The definition of SBML is captured in formal specification documents. SBMLPkgSpec is a LaTeX document style intended to fill the need for a standard format for writing such specification documents.

RESULTS

Specification documents for SBML Level 3 extensions (known as packages in SBML) are made more uniform with the use of a standard template. SBMLPkgSpec is a LaTeX class that provides a document framework for SBML Level 3 package specifications, to simplify the work of document authors while improving the overall quality of the family of SBML specifications.

Toward Community Standards and Software for Whole-Cell Modeling

OBJECTIVE

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.

METHODS

We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.

RESULTS

Our analysis revealed several challenges to representing WC models using the current standards.

CONCLUSION

We, therefore, propose several new WC modeling standards, software, and databases.

SIGNIFICANCE

We anticipate that these new standards and software will enable more comprehensive models.

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

OBJECTIVE

Only reproducible results are of significance to science. The lack of suitable standards and appropriate support of standards in software tools has led to numerous publications with irreproducible results. Our objectives are to identify the key challenges of reproducible research and to highlight existing solutions.

RESULTS

In this paper, we summarize problems concerning reproducibility in systems biology and systems medicine. We focus on initiatives, standards, and software tools that aim to improve the reproducibility of simulation studies.

CONCLUSIONS

The long-term success of systems biology and systems medicine depends on trustworthy models and simulations. This requires openness to ensure reusability and transparency to enable reproducibility of results in these fields.

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.

Modeling and Simulation Tools: From Systems Biology to Systems Medicine

Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of "Software as a Medical Device" and what this may imply for the migration of research-oriented, simulation software into the domain of human health.In our second perspective, we see how in practice hundreds of computational tools already accompany drug discovery and development at every stage of the process. Standardized exchange formats are required to streamline the model exchange between tools, which would minimize translation errors and reduce the required time. With the emergence, almost 15 years ago, of the SBML standard, a large part of the domain of interest is already covered and models can be shared and passed from software to software without recoding them. Until recently the last stage of the process, the pharmacometric analysis used in clinical studies carried out on subject populations, lacked such an exchange medium. We describe a new emerging exchange format in Pharmacometrics which covers the non-linear mixed effects models, the standard statistical model type used in this area. By interfacing these two formats the entire domain can be covered by complementary standards and subsequently the according tools.

Improving collaboration by standardization efforts in systems biology

Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology.