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29 materials found

Scientific topics: Toxicology  or Statistics and probability 


Hands-on for 'A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy' tutorial

The questions this addresses are:
- How to use Jupyterlab and it several features?
- How to use it for creating input datasets and writing artificial intelligence (AI) algorithms?

\nThe objectives are:
- Learn to use Jupyterlab - an online Python editor designed for developing AI algorithms
...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools, machine-learning, deep-learning, jupyter-lab, image-segmentation, protein-3D-structure

Resource type: hands-on tutorial

Hands-on for 'PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis' tutorial

The questions this addresses are:
- How to predict aberrant pathway activity in The Cancer Genome Atlas (TCGA) using Machine learning approaches?

\nThe objectives are:
- Learn to predict aberrant pathway activity using RNA-Seq data, mutational status and copy number variation data from TCGA.
...

Scientific topics: Statistics and probability

Keywords: statistics, Machine learning, Pan-cancer, cancer biomarkers, oncogenes and tumor suppressor genes

Resource type: hands-on tutorial

Hands-on for 'Classification in Machine Learning' tutorial

The questions this addresses are:
- What is classification and how we can use classification techniques?

\nThe objectives are:
- Learn classification background
- Learn what a quantitative structure-analysis relationship (QSAR) model is and how it can be constructed in Galaxy
- Learn to...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Regression in Machine Learning' tutorial

The questions this addresses are:
- How to use regression techniques to create predictive models from biological datasets?

\nThe objectives are:
- Learn regression background
- Apply regression based machine learning algorithms
- Learn ageing biomarkers and predict age from DNA methylation...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Text-mining with the SimText toolset' tutorial

The questions this addresses are:
- How can I automatically collect PubMed data for a set of biomedical entities such as genes?
- How can I analyze similarities among biomedical entities based on PubMed data on large-scale?

\nThe objectives are:
- Learn how to use the SimText toolset
-...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Machine learning: classification and regression' tutorial

The questions this addresses are:
- what are classification and regression techniques?
- How they can be used for prediction?
- How visualizations can be used to analyze predictions?

\nThe objectives are:
- Explain the types of supervised machine learning - classification and regression.
-...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Interval-Wise Testing for omics data' tutorial

The questions this addresses are:
- How to visualize high-resolution omics data in different groups of genomic regions?
- How to evaluate differences in high-resolution omics data between groups of genomic regions?
- How to detect locations and scales at which the significant effects...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Age prediction using machine learning' tutorial

The questions this addresses are:
- How to use machine learning to create predictive models from biological datasets (RNA-seq and DNA methylation)?

\nThe objectives are:
- Learn ageing biomarkers from RNA-seq and DNA methylation datasets
- Apply regression based machine learning algorithms
...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Introduction to Machine Learning using R' tutorial

The questions this addresses are:
- What are the main categories in Machine Learning algorithms?
- How can I perform exploratory data analysis?
- What are the main part of a clustering process?
- How can a create a decision tree?
- How can I assess a linear regression model?

\nThe...

Scientific topics: Statistics and probability

Keywords: statistics, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Image classification in Galaxy with fruit 360 dataset' tutorial

The questions this addresses are:
- How to solve an image classification problem using convolutional neural network (CNN)?

\nThe objectives are:
- Learn how to create a CNN using Galaxy's deep learning tools
- Solve an image classification problem on fruit 360 dataset using CNN in Galaxy

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Basics of machine learning' tutorial

The questions this addresses are:
- What is machine learning?
- Why is it useful?
- What are its different approaches?

\nThe objectives are:
- Provide the basics of machine learning and its variants.
- Learn how to do classification using the training and test data.
- Learn how to use...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Clustering in Machine Learning' tutorial

The questions this addresses are:
- How to use clustering algorithms to categorize data in different clusters

\nThe objectives are:
- Learn clustering background
- Learn hierarchical clustering algorithm
- Learn k-means clustering algorithm
- Learn DBSCAN clustering algorithm
- Apply...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Deep Learning (Part 2) - Recurrent neural networks (RNN)' tutorial

The questions this addresses are:
- What is a recurrent neural network (RNN)?
- What are some applications of RNN?

\nThe objectives are:
- Understand the difference between feedforward neural networks (FNN) and RNN
- Learn various RNN types and architectures
- Learn how to create a neural...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Slides for 'Recurrent neural networks (RNN) Deep Learning - Part 2' tutorial

The questions this addresses are:
- What is a recurrent neural network (RNN)?
- What are some applications of RNN?

\nThe objectives are:
- Understand the difference between feedforward neural networks (FNN) and RNN
- Learn various RNN types and architectures
- Learn how to create a neural...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Hands-on for 'Deep Learning (Part 1) - Feedforward neural networks (FNN)' tutorial

The questions this addresses are:
- What is a feedforward neural network (FNN)?
- What are some applications of FNN?

\nThe objectives are:
- Understand the inspiration for neural networks
- Learn various activation functions, and classification/regression problems solved by neural networks
...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Hands-on for 'Deep Learning (Part 3) - Convolutional neural networks (CNN)' tutorial

The questions this addresses are:
- What is a convolutional neural network (CNN)?
- What are some applications of CNN?

\nThe objectives are:
- Understand the inspiration behind CNN and learn the CNN architecture
- Learn the convolution operation and its parameters
- Learn how to create a...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Slides for 'Convolutional neural networks (CNN) Deep Learning - Part 3' tutorial

The questions this addresses are:
- What is a convolutional neural network (CNN)?
- What are some applications of CNN?

\nThe objectives are:
- Understand the inspiration behind CNN and learn the CNN architecture
- Learn the convolution operation and its parameters
- Learn how to create a...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Slides for 'Image classification in Galaxy with fruit 360 dataset' tutorial

The questions this addresses are:
- How to solve an image classification problem using convolutional neural network (CNN)?

\nThe objectives are:
- Learn how to create a CNN using Galaxy's deep learning tools
- Solve an image classification problem on fruit 360 dataset using CNN in Galaxy

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Hands-on for 'Introduction to deep learning' tutorial

The questions this addresses are:
- What are deep learning and neural networks?
- Why is it useful?
- How to create a neural network architecture for classification?

\nThe objectives are:
- Learn basic principles of deep learning
- Learn about how to create an end-to-end neural network...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: hands-on tutorial

Slides for 'Feedforward neural networks (FNN) Deep Learning - Part 1' tutorial

The questions this addresses are:
- What is a feedforward neural network (FNN)?
- What are some applications of FNN?

\nThe objectives are:
- Understand the inspiration for neural networks
- Learn activation functions & various problems solved by neural networks
- Discuss various...

Scientific topics: Statistics and probability

Keywords: statistics

Resource type: slides

Machine Learning & BioStatistics Hackathon 2020

Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020.

Scientific topics: Computer science, Statistics and probability, Machine learning

Keywords: machine learning, biostatistics, eLearning, EeLP

Resource type: Training materials

Introduction to qualitative modelling with MaBoSS

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...

Scientific topics: Statistics and probability, Molecular interactions, pathways and networks, Personalised medicine, Simulation experiment

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, cell simulations, Boolean

Resource type: Webinar

OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

Bioinformatics Summer School 2019

This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are...

Scientific topics: Statistics and probability, Omics, RNA-Seq, Proteomics

Operations: Data handling

Multiple testing

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
Bioconductor uses the R statistical programming language, and is open source and open development.
It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Adding nanomaterial data

This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.

Scientific topics: Database management, Toxicology

Keywords: nanotoxicology, enanomapper, resource description framework, ontology

Resource type: Tutorial

Statistical Analysis using SPSS

Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.

Course Content

*...

Scientific topics: Statistics and probability

Keywords: Babraham Institute

Introduction to R: A software environment for statistical computing

Overview

R is a programming language and associated environment developed for statistical computing and data analysis. It provides many powerful tools for statistics, data visualisation and bioinformatics.

Learning outcomes

  • What R is suitable for.
  • How to use R...

Scientific topics: Software engineering, Statistics and probability

Keywords: John Innes Centre, JIC

Statistics with R

The aim of this course is to teach you how to perform basic statistical analysis using R. First we review the foundations (sampling theory, discrete and continuous distributions), then we focus on classical hypothesis testing. This course will improve your generic statistics knowledge....

Scientific topics: Statistics and probability

Keywords: Biostatistics, R