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PyBioNetFit and the Biological Property Specification Language.

ABSTRACT: In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations. To help modelers perform these steps, we developed the software PyBioNetFit, which in addition supports checking models against known system properties and solving design problems. PyBioNetFit introduces Biological Property Specification Language (BPSL) for the formal declaration of system properties. BPSL allows qualitative data to be used alone or in combination with quantitative data. PyBioNetFit performs parameterization with parallelized metaheuristic optimization algorithms that work directly with existing model definition standards: BioNetGen Language (BNGL) and Systems Biology Markup Language (SBML). We demonstrate PyBioNetFit's capabilities by solving various example problems, including the challenging problem of parameterizing a 153-parameter model of cell cycle control in yeast based on both quantitative and qualitative data. We demonstrate the model checking and design applications of PyBioNetFit and BPSL by analyzing a model of targeted drug interventions in autophagy signaling.

SUBMITTER: Mitra ED

PROVIDER: S-EPMC6744527 | biostudies-literature |

REPOSITORIES: biostudies-literature

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PyBioNetFit and the Biological Property Specification Language

Project description: Not available

| S-BSST240 | biostudies-other

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Project description:Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

| S-EPMC5451324 | biostudies-other

Context Definition and Query Language: Conceptual Specification, Implementation, and Evaluation.

Project description:As IoT grows at a staggering pace, the need for contextual intelligence is a fundamental and critical factor for IoT intelligence, efficiency, effectiveness, performance, and sustainability. As the standardisation efforts for IoT are fast progressing, efforts in standardising context management platforms led by the European Telecommunications Standards Institute (ETSI) are gaining more attention from both academic and industrial research organizations. These standardisation endeavours will enable intelligent interactions between 'things', where things could be devices, software components, web-services, or sensing/actuating systems. Therefore, having a generic platform to describe and query context is crucial for the future of IoT applications. In this paper, we propose Context Definition and Query Language (CDQL), an advanced approach that enables things to exchange, reuse and share context between each other. CDQL consists of two main parts, namely: context definition model, which is designed to describe situations and high-level context; and Context Query Language (CQL), which is a powerful and flexible query language to express contextual information requirements without considering details of the underlying data structures. An important feature of the proposed query language is its ability to query entities in IoT environments based on their situation in a fully dynamic manner where users can define situations and context entities as part of the query. We exemplify the usage of CDQL on three different smart city use cases to highlight how CDQL can be utilised to deliver contextual information to IoT applications. Performance evaluation has demonstrated scalability and efficiency of CDQL in handling a fairly large number of concurrent context queries.

| S-EPMC6470624 | biostudies-literature

PeptideBERT: A Language Model Based on Transformers for Peptide Property Prediction.

Project description:Recent advances in language models have enabled the protein modeling community with a powerful tool that uses transformers to represent protein sequences as text. This breakthrough enables a sequence-to-property prediction for peptides without relying on explicit structural data. Inspired by the recent progress in the field of large language models, we present PeptideBERT, a protein language model specifically tailored for predicting essential peptide properties such as hemolysis, solubility, and nonfouling. The PeptideBERT utilizes the ProtBERT pretrained transformer model with 12 attention heads and 12 hidden layers. Through fine-tuning the pretrained model for the three downstream tasks, our model is state of the art (SOTA) in predicting hemolysis, which is crucial for determining a peptide's potential to induce red blood cells as well as nonfouling properties. Leveraging primarily shorter sequences and a data set with negative samples predominantly associated with insoluble peptides, our model showcases remarkable performance.

| S-EPMC10683064 | biostudies-literature

Simultaneity as an Emergent Property of Efficient Communication in Language: A Comparison of Silent Gesture and Sign Language.

Project description:Sign languages use multiple articulators and iconicity in the visual modality which allow linguistic units to be organized not only linearly but also simultaneously. Recent research has shown that users of an established sign language such as LIS (Italian Sign Language) use simultaneous and iconic constructions as a modality-specific resource to achieve communicative efficiency when they are required to encode informationally rich events. However, it remains to be explored whether the use of such simultaneous and iconic constructions recruited for communicative efficiency can be employed even without a linguistic system (i.e., in silent gesture) or whether they are specific to linguistic patterning (i.e., in LIS). In the present study, we conducted the same experiment as in Slonimska et al. with 23 Italian speakers using silent gesture and compared the results of the two studies. The findings showed that while simultaneity was afforded by the visual modality to some extent, its use in silent gesture was nevertheless less frequent and qualitatively different than when used within a linguistic system. Thus, the use of simultaneous and iconic constructions for communicative efficiency constitutes an emergent property of sign languages. The present study highlights the importance of studying modality-specific resources and their use for linguistic expression in order to promote a more thorough understanding of the language faculty and its modality-specific adaptive capabilities.

| S-EPMC9287048 | biostudies-literature

The Centre for Speech, Language and the Brain (CSLB) concept property norms.

Project description:Theories of the representation and processing of concepts have been greatly enhanced by models based on information available in semantic property norms. This information relates both to the identity of the features produced in the norms and to their statistical properties. In this article, we introduce a new and large set of property norms that are designed to be a more flexible tool to meet the demands of many different disciplines interested in conceptual knowledge representation, from cognitive psychology to computational linguistics. As well as providing all features listed by 2 or more participants, we also show the considerable linguistic variation that underlies each normalized feature label and the number of participants who generated each variant. Our norms are highly comparable with the largest extant set (McRae, Cree, Seidenberg, & McNorgan, 2005) in terms of the number and distribution of features. In addition, we show how the norms give rise to a coherent category structure. We provide these norms in the hope that the greater detail available in the Centre for Speech, Language and the Brain norms should further promote the development of models of conceptual knowledge. The norms can be downloaded at www.csl.psychol.cam.ac.uk/propertynorms.

| S-EPMC4237904 | biostudies-literature

Modeling and simulation of biological systems using SPICE language.

Project description:The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology).

| S-EPMC5546598 | biostudies-other

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

Project description:MOTIVATION: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. RESULTS: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. AVAILABILITY AND IMPLEMENTATION: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

| S-EPMC4382901 | biostudies-other

PyBEL: a computational framework for Biological Expression Language.

Project description:SummaryBiological Expression Language (BEL) assembles knowledge networks from biological relations across multiple modes and scales. Here, we present PyBEL; a software package for parsing, validating, converting, storing, querying, and visualizing networks encoded in BEL.Availability and implementationPyBEL is implemented in platform-independent, universal Python code. Its source is distributed under the Apache 2.0 License at https://github.com/pybel.Contactcharles.hoyt@scai.fraunhofer.de.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC5860616 | biostudies-literature

Investigating data-driven biological subtypes of sychiatric disorders using specification-curve analysis.

Project description:BackgroundCluster analyses have become popular tools for data-driven classification in biological psychiatric research. However, these analyses are known to be sensitive to the chosen methods and/or modelling options, which may hamper generalizability and replicability of findings. To gain more insight into this problem, we used Specification-Curve Analysis (SCA) to investigate the influence of methodological variation on biomarker-based cluster-analysis results.MethodsProteomics data (31 biomarkers) were used from patients (n = 688) and healthy controls (n = 426) in the Netherlands Study of Depression and Anxiety. In SCAs, consistency of results was evaluated across 1200 k-means and hierarchical clustering analyses, each with a unique combination of the clustering algorithm, fit-index, and distance metric. Next, SCAs were run in simulated datasets with varying cluster numbers and noise/outlier levels to evaluate the effect of data properties on SCA outcomes.ResultsThe real data SCA showed no robust patterns of biological clustering in either the MDD or a combined MDD/healthy dataset. The simulation results showed that the correct number of clusters could be identified quite consistently across the 1200 model specifications, but that correct cluster identification became harder when the number of clusters and noise levels increased.ConclusionSCA can provide useful insights into the presence of clusters in biomarker data. However, SCA is likely to show inconsistent results in real-world biomarker datasets that are complex and contain considerable levels of noise. Here, the number and nature of the observed clusters may depend strongly on the chosen model-specification, precluding conclusions about the existence of biological clusters among psychiatric patients.

| S-EPMC9069352 | biostudies-literature

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