LM-Merger: A workflow for merging logical models with an application to gene regulation.

Motivation: Gene regulatory network (GRN) models provide mechanistic understanding of genetic interactions that regulate gene expression and, consequently, influence cellular behavior. Dysregulated gene expression plays a critical role in disease progression and treatment response, making GRN models a promising tool for precision medicine. While researchers have built many models to describe specific subsets of gene interactions, more comprehensive models that cover a broader range of genes are challenging to build.

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.

Motivation: Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface. However, as with the development of complex software, text-based representations of models provide many benefits for advanced model development.

An automated model annotation system (AMAS) for SBML models.

Motivation: Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations, or the annotations provide insufficient detail to understand the limitations of the model. The quality and quantity of annotations can be improved by developing tools that recommend annotations.

An Automated Model Annotation System (AMAS) for SBML Models.

Motivation: Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations, or the annotations provide insufficient detail to understand the limitations of the model. The quality and quantity of annotations can be improved by developing tools that recommend annotations.

Replenishing Alkali During Hemodialysis: Physiology-Based Approaches.

The acid-base goal of intermittent hemodialysis is to replenish buffers consumed by endogenous acid production and expansion acidosis in the period between treatments. The amount of bicarbonate needed to achieve this goal has traditionally been determined empirically with a goal of obtaining a reasonable subsequent predialysis blood bicarbonate concentration ([HCO ]). This approach has led to very disparate hemodialysis prescriptions around the world.

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface.

NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.

Semantic annotation is a crucial step to assure reusability and reproducibility of biosimulation models in biology and physiology. For this purpose, the COmputational Modeling in BIology NEtwork (COMBINE) community recommends the use of the Resource Description Framework (RDF). This grounding in RDF provides the flexibility to enable searching for entities within models (e.

OMEX metadata specification (version 1.2).

A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. This document details version 1.

libOmexMeta: enabling semantic annotation of models to support FAIR principles.

Summary: As the number and complexity of biosimulation models grows, so do demands for tools that can help users better understand models and make those models more findable, shareable and reproducible. Consistent model annotation is a step toward these goals. Both models and tools are written in a variety of different languages; thus, the community has recognized the need for standard, language-independent methods for annotation.

Hemodialysis using a low bicarbonate dialysis bath: Implications for acid-base homeostasis.

The low bath bicarbonate concentration ([ ]) used by a nephrology group in Japan (25.5 mEq/L), coupled with a bath [acetate] of 8 mEq/L, provided an opportunity to study the acid-base events occurring during hemodialysis when flux is from the patient to the bath. We used an analytic tool that allows calculation of delivery during hemodialysis and the physiological response to it in 17 Japanese outpatients with an average pre-dialysis blood [ ] of 25 mEq/L.

Deep phenotyping of cardiac function in heart transplant patients using cardiovascular system models.

Key Points: Right heart catheterization data from clinical records of heart transplant patients are used to identify patient-specific models of the cardiovascular system. These patient-specific cardiovascular models represent a snapshot of cardiovascular function at a given post-transplant recovery time point. This approach is used to describe cardiac function in 10 heart transplant patients, five of which had multiple right heart catheterizations allowing an assessment of cardiac function over time.

Model annotation and discovery with the Physiome Model Repository.

Background: Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such models help to ensure that such models are accessible, discoverable, and reusable. To this end, researchers have developed tools and standards to encode mathematical models of biological systems enabling reproducibility and reuse, tools and guidelines to facilitate semantic description of mathematical models, and repositories in which to archive, share, and discover models.

Synthetic Biology Open Language (SBOL) Version 2.3.

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems is to improve the exchange of information about designed systems between laboratories.

Predicting instances of pathway ontology classes for pathway integration.

Background: To improve the outcomes of biological pathway analysis, a better way of integrating pathway data is needed. Ontologies can be used to organize data from disparate sources, and we leverage the Pathway Ontology as a unifying ontology for organizing pathway data. We aim to associate pathway instances from different databases to the appropriate class in the Pathway Ontology.

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information.

Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent information about genetic circuits, and it is based on capturing data using graphs. The language provides the syntax using a free text document that is accessible to humans only.

Changing dialysate composition to optimize acid-base therapy.

In response to rapid alkali delivery during hemodialysis, hydrogen ions (H ) are mobilized from body buffers and from stimulation of organic acid production in amounts sufficient to convert most of the delivered bicarbonate to CO and water. Release of H from nonbicarbonate buffers serves to back-titrate them to a more alkaline state, readying them to buffer acids that accumulate in the interval between treatments. By contrast, stimulation of organic acid production only serves to remove added bicarbonate (HCO ) from the body; the organic anions produced by this process are lost into the dialysate, irreversibly acidifying the patient as well as diverting metabolic activity from normal homeostasis.

Harmonizing semantic annotations for computational models in biology.

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent.

SemGen: a tool for semantics-based annotation and composition of biosimulation models.

Summary: As the number and complexity of biosimulation models grows, so do demands for tools that can help users understand models and compose more comprehensive and accurate systems from existing models. SemGen is a tool for semantics-based annotation and composition of biosimulation models designed to address this demand. A key SemGen capability is to decompose and then integrate models across existing model exchange formats including SBML and CellML.

Acid-base homeostasis during hemodialysis: New insights into the mystery of bicarbonate disappearance during treatment.

In patients receiving hemodialysis, it has long been recognized that much more bicarbonate is delivered during treatment than ultimately appears in the blood. To gain insight into this mystery, we developed a model that allows a quantitative analysis of the patient's response to rapid alkalinization during hemodialysis. Our model is unique in that it is based on the distribution of bicarbonate in the extracellular fluid and assesses its removal from this compartment by mobilization of protons (H ) from buffers and other sources.

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories.

Acid-base assessment of patients receiving hemodialysis. What are our management goals?

Acid-base assessment of patients receiving conventional hemodialysis (HD) has been based solely on predialysis serum [total CO ], and treatment is currently driven by the KDOQI guideline from 2000. This guideline was directed solely at minimizing metabolic acidosis and thereby improving bone and muscle metabolism. In 2000, no data were available to assess the effects of acid-base status on morbidity and mortality.

Qualitative causal analyses of biosimulation models.

We describe an approach for performing qualitative, systems-level causal analyses on biosimulation models that leverages semantics-based modeling formats, formal ontology, and automated inference. The approach allows users to quickly investigate how a qualitative perturbation to an element within a model's network (an increment or decrement) propagates throughout the modeled system. To support such analyses, we must interpret and annotate the semantics of the models, including both the physical properties modeled and the dependencies that relate them.