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17 materials found

Scientific topics: Computational biology 


Data-driven modelling of intercellular interactions in the tumour microenvironment

Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumours, recent studies have uncovered complex macrophage populations, including tumour-associated macrophages, which support tumorigenesis through cancer hallmarks such as...

Scientific topics: Computational biology, Oncology, Personalised medicine

Resource type: Recorded webinar

Introducing PerMedCoE Building Blocks and Workflows to streamline biological analysis pipelines

Analysing biological datasets is nearly always a multi-step process involving many interconnected stages. Even so, the lack of transparent approaches to managing complex data analysis pipelines remains a common challenge in the life sciences. Another limiting factor is that completing such...

Scientific topics: Computational biology, Personalised medicine, Workflows

Resource type: Recorded webinar

The environmental impact of computational biology

The environmental impact of (scientific) computing, computational biology in particular, is a growing concern in light of the urgency of the climate crisis, and there is widespread interest in the research community; so what can we all do about it? Tackling this issue and making it easier for...

Scientific topics: Computational biology

Resource type: Recorded webinar

Croupier, an user-centric meta-orchestrator for cross-platform workflow delivery and execution

The orchestration of complex application workflows executed in the context of High Performance Computing (HPC) infrastructures requires the joint collaboration of application designers/developers, HPC engineers and application consumers (i.e. end-users). In the context of HPC, complex workflows...

Scientific topics: Computational biology, Personalised medicine, Simulation experiment

Resource type: Recorded webinar

HPC boosts mathematical models’ promises of personalised medicine

Mathematical models of the biological processes that are deregulated in diseases show a high complexity not only because of the number of genes and pathways involved, but also because of the numerous patients or samples to include in the simulations in order to be predictive. One way to address...

Scientific topics: Computational biology, Personalised medicine, Simulation experiment

Resource type: Recorded webinar

The PerMedCoE competency framework to guide training and career development

PerMedCoE aims at providing an efficient and sustainable infrastructure to support personalised medicine, adapting cell-level simulation methods to pre-exascale systems to translate omics data into molecular disease models. One of the activities to achieve this consists of a training programme to...

Scientific topics: Computational biology, Personalised medicine

Resource type: Recorded webinar

Mathematical modelling as knowledge mapping in PhysiCell: a guided tour

Tissues are complex multiscale biological systems where cells communicate to modulate their behaviour in response to dynamical microenvironmental conditions. Small perturbations to cells—such as injuries or therapy—can have unanticipated "ripple effects" that percolate through the system. We can...

Scientific topics: Computational biology, Personalised medicine

Resource type: Recorded webinar

Computer-assisted functional precision medicine in cancer

Biological mechanisms provide a link between anti cancer compounds and therapy responses. Insight to biological mechanisms is central for tomorrow’s clinical decision support systems and personalised cancer therapy. I will present the NTNU DrugLogics software that combines cancer signalling prior...

Scientific topics: Computational biology, Personalised medicine, Simulation experiment

Resource type: Recorded webinar

Steady State Analysis in COPASI

A short tutorial on how to carry out steady state simulations with the software COPASI.

COPASI logo

Scientific topics: Systems biology, Computational biology, Simulation experiment

Operations: Modelling and simulation, Visualisation

Resource type: Video

WEBINAR: Getting started with command line bioinformatics

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.

Bioinformatics skills are in demand like never before and biologists are stepping up to the challenge of...

Scientific topics: Computational biology

Keywords: Command line

runBioSimulations tutorial and help

runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...

Scientific topics: Systems biology, Computational biology, Simulation experiment

Operations: Modelling and simulation

Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL

Resource type: Tutorial, Documentation

BioSimulators tutorial and help

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...

Scientific topics: Systems biology, Computational biology, Simulation experiment

Operations: Modelling and simulation

Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL

Resource type: Tutorial, Documentation

DE-Sim examples, tutorials, and documentation

DE-Sim is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as NumPy, Scipy,...

Scientific topics: Simulation experiment, Computer science, Mathematics, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

BioSimulations tutorial and help

BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and...

Scientific topics: Computational biology, Systems biology, Simulation experiment

Operations: Visualisation, Modelling and simulation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE

Resource type: Documentation

bio.tools documentation

bio.tools provides essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences.

Some notable bio.tools documentation links:
- About bio.tools
- [Installing bio.tools on your...

Scientific topics: Bioinformatics, Data submission, annotation, and curation, Computational biology, Ontology and terminology

Operations: Data retrieval

Keywords: Tools, Curation, Software, Sofware curation, Tool curation

Resource type: Documentation, API reference

MATHEMATICS BOOT CAMP: Introduction to Complex Systems Tools

This intensive course is to provide students with the prerequisites - some conceptual background and sufficient working knowledge of mathematics - necessary to master the mathematically based graduate courses at the Center for Complex Systems & Brain Sciences. By no means it is intended to...

Scientific topics: Mathematics, Computational biology

Keywords: ComputationalBiology, Neuroscience, complex systems, Mathematics

Resource type: Notes, Scripts

Train the trainer

Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics Training hub. The five slide decks cover pedagogical theory, trainer...

Scientific topics: Computational biology, Bioinformatics

Keywords: training, pedagogy