This quick tour provides a brief introduction to EMBL-EBI’s resource of mathematical models of biological/biomedical systems.

A tutorial on how to create kinetic models with COPASI. Covers the basics of creating models, including definition of new rate laws, etc.

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...

1. Introduction

2. Many Views of A Pathway(Lecture)

3. Pathway Models & Pathway Types (Lecture)

4. Sources of ‘Pathway Data’ (Lecture)

5. Issues (Lecture)

6. SBGN (Lecture)

7. mEPN (Lecture)

8. Practical Session: Pathway to Pathway Construction - yED(1)

9. Practical...

A tutorial on Metabolic Control Analysis and how to apply it to kinetic models with the software COPASI.

A short tutorial on how to carry out time course simulations based on ODEs with the software COPASI.

A video tutorial for the simulation software COPASI, showing how to create sequences of simulations that scan values of various parameters, or that sample those parameters at random.

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),...

This tutorial explains how to use a collection of R regression tools for estimating the optimal model via a fully validated procedure.

1. Introduction

2. What Are Mixed Models?

3. Potential Advantages of Mixed Models

4. Historical Perspective

5. Example 1: Biological & Technical Replicates

6. Example 2: Rabbit Inspiration Time – Sources of Variation

7. Non-Normal Data

8. Example 3: Non-normal data

9....

1. Introduction

2. One-Way Analysis of Variance (ANOVA) Recap

3. Two-Way ANOVA - Assessing Two Effects in Same Model

4. Two-Way ANOVA - Allowing for Structure in The Data

5. Paired T-Test Using Two-Way ANOVA & ANOVA With More Effects

6. Regression Recap

7. General Linear...

1. Introduction

2. Many Views of A Pathway(Lecture)

3. Pathway Models & Pathway Types (Lecture)

4. Sources of ‘Pathway Data’ (Lecture)

5. Issues (Lecture)

6. SBGN (Lecture)

7. mEPN (Lecture)

8. Practical Session: Pathway to Pathway Construction - yED(1)

9. Practical...

This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data...

The goal of this course is to expose the participants to 3-dimensional structures of proteins. Analysis and visualization software (DeepView) will be used to display, analyze, compare and interpret protein structures. The second part of the course is dedicated to protein structure prediction...

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,...

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

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,...

BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR.

Wikidata
fairification

Genome Properties allows you to infer the presence of pathways and systems within a species, based on the occurrence of a set of underlying molecular markers.

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

This course provides an introduction to the concepts of modelling biological systems. It is intended for biologists who have no experience in modelling but would like to know how it might apply to their area of research. The course provides a complete background to the history of modelling and...

Poster presented at 3rd BiVi in April 2017.InterMine is an open source data warehouse based in the University of Cambridge. We integrate data from disparate sources and provide a single unified interface, allowing you to access your data via an easy-to-use webapp or API. InterMine has over 30...

What is the course about?
Signalling pathways and networks are very important to regulate and control cellular processes, cell fate, and their malfunctions often lead to diseases, such as cancer or diabetes. This course provides an introductory overview of the most useful resources and tools to...

Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the...

This course will provide participants with an introduction and hands-on training on modelling approaches, tools and resources used in systems biology as well as touch on network analysis.

Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the...

Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, attendees learned how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file.

Jaqpot is a computational platform for in silico...

COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base...

The questions this addresses are:
- How to build & evaluate a niche model, visualize and project it ?

The objectives are:
- Find and download occurrences data from GBIF
- Find and download environmental data
- Process both occurrences and environmental
- Partition occurrence data
-...