Register training material
11 materials found

Authors: Jan Slifka  or Daniel Blankenberg 


Hands-on for 'From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis' tutorial

The questions this addresses are:
- Learn how to get and use data from the Sequence Read Archive in Galaxy.

The objectives are:
- Understand how Galaxy and the Sequence Read Archive interact.
- Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send...

Scientific topics: Genetic variation

Keywords: variant-analysis, covid19

Resource type: hands-on tutorial

Hands-on for 'Pre-processing of 10X Single-Cell RNA Datasets' tutorial

The questions this addresses are:
- What is 10X?
- What is STARsolo and what is Cell Ranger?
- What are BCL and MTX files?
- What is an HDF5 file, and why is it important?

The objectives are:
- Demultiplex single-cell FASTQ data from 10X Genomics
- Learn about transparent matrix formats
...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, 10x

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?

The 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 '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?

The 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 'Peptide Library Data Analysis' tutorial

The questions this addresses are:
- How to utilize quantitative properties of amino acids and peptide sequence to analyse peptide data?

The objectives are:
- Calculate descriptors
- Quantitative analysis of peptide sequence properties

Scientific topics: Proteomics

Keywords: proteomics

Resource type: hands-on tutorial

Hands-on for 'Machine Learning Modeling of Anticancer Peptides' tutorial

The questions this addresses are:
- Which machine learning (ML) algorithm is superior in classifying anticancer peptides (ACPs) and non-anticancer peptides (non-ACPs)?

The objectives are:
- Learn, how to calculate peptide descriptor
- Learn, how to create training data set from features?
-...

Scientific topics: Proteomics

Keywords: proteomics, ML, cancer

Resource type: hands-on tutorial

Hands-on for 'NGS data logistics' tutorial

The questions this addresses are:
- How to manipulate and process NGS data

The objectives are:
- Understand most common types of NGS-related datatypes
- Learn about how Galaxy handles NGS data using Illumina data derived from patients infected with SARS-CoV-2

Keywords: introduction

Resource type: hands-on tutorial

Slides for 'Reference Data with CVMFS' tutorial

The objectives are:
- Have an understanding of what CVMFS is and how it works
- Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
- Configure your Galaxy to use these reference genomes and indices
- Use an ansible playbook for all of the...

Keywords: admin

Resource type: slides

DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind Data Stewardship Wizard, and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

A Gentle Introduction to DSW for Convergers

Data Stewardship Wizard brings together data stewards and researchers to efficiently compose data management plans (DMPs) for their research projects. Data stewards capture their knowledge and expertise in so-called knowledge models that are turned into smart...

Scientific topics: Data management, Data governance

Keywords: Data managment plan, data stewardship, data management, software tools

Resource type: Video, Slides, Webinar

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides