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31 materials found

Content provider: CSC - IT Center for Science  or Data Carpentry 


Introduction to using containers - OpenShift, Kubernetes and Docker oriented view

This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez

Keywords: Containers, Kubernetes, Cloud computing

Introduction to research data management, data management planning and services provided by CSC – IT Center for Science

This training video series includes four short videos on research data management. The titles of the videos are the following:

  1. Introduction to data management for life science researchers
  2. Introduction to data management planning
  3. Introduction to sections of a generic ​data management...

Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE

Resource type: Series of videos, Video, youtube video

Detecting differentially expressed genes with RNA-seq 11.9.2019

This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. While this course focuses on differential gene expression analysis...

Scientific topics: RNA-Seq

Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Introduction to using cloud and containers for training - OpenStack and Docker oriented view

This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object...

Keywords: Cloud computing, Containers

Resource type: Slides, course materials

Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Python for Social Science Data: Instructor Notes

PIP is referred to in the text but it shouldn’t need to be used. It is assumed that Jupyter notebooks will be used for all of the coding. (The shell is used in explaining REPL) How to start Jupyter is included in the setup instructions. All of the datasets used have been placed in the data...

R for Social Scientists: Instructor Notes

This lesson uses SAFI_clean.csv. The direct download link for this file is:
https://ndownloader.figshare.com/files/11492171. When time comes in the lesson to use this file, we recommend that the
instructors, place the download.file() command in the Etherpad, and that the
learners copy and paste...

Data Organization in Spreadsheets for Social Scientists: Instructor Notes

The challenge with this lesson is that the instructor’s version of the spreadsheet software is going to look different than about half the room’s. It makes
it challenging to show where you can find menu options and navigate through. Instead discuss the concepts of quality control, and how things...

OpenRefine for Social Science Data: Instructor Notes

There is a separate file for the setup instructions for installing OpenRefine
(setup). Introduction Working with OpenRefine Filtering and Sorting Examining Numbers in OpenRefine

Community analysis of amplicon sequencing data (16S rRNA)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...

Resource type: course materials, Video

Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

Scientific topics: RNA-Seq

Resource type: course materials, Video

RNA-seq data analysis

This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...

Scientific topics: RNA-Seq

Resource type: course materials, Video

Metagenomics data analysis

Metagenomics investigates the composition and function of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances in high-throughput sequencing technologies, and the increasing data sizes require efficient analysis...

Scientific topics: Metagenomics

Resource type: Video, course materials

Cloud Genomics: Instructor NotesCloud Genomics Pre-WorkshopDuring the workshop

VM Image Directories
A high-level listing of the directory tree from the dcuser account is shown below. Please note that is may be subject to change over time, but we’ll try to remember to update this doc. We had a couple instances die as we were going through our workshop.

Shell Genomics: Instructor Notes

This lesson will introduce learners to fundamental skills needed for working with their computers through a command-line interface (using
the bash shell). They will learn how to navigate their file system, computationally manipulate their files (e.g. copying, moving, renaming), search files,...

Genomics Organization: Instructor Notes

Discussions can happen between neighbors in a workshop. Then after paired discussion there can be a short general discussion of the types of things that came up in the discussion. You could also have people enter responses to the discussion in the workshop etherpad. Or capture the general...

Genomics WorkshopWorkshop OverviewTeaching Platform

This lesson assumes no prior experience with the tools covered in the workshop.
However, learners are expected to have some familiarity with biological concepts,
including nucleotide abbreviations and the
concept of genomic variation within a population. Participants should bring their laptops...

Ecology Workshop Overview

There are no pre-requisites, and the materials assume no prior knowledge about the tools. The data for this workshop are is the Portal Project Teaching Database available on FigShare, with a CC-BY license available for reuse. The Portal Project Teaching Database is a simplified version of the...

Instructor notes

This lesson uses mostly combined.csv. The 3 other csv files: plots.csv, species.csv and surveys.csv are only needed for the lesson on databases. combined.csv is downloaded directly in the chapter “Starting with Data” and does not need to be downloaded before hand. It however requires that there...

Python for Ecologists

Python is a general purpose programming language that is useful for writing scripts to work effectively and reproducibly with data. This is an introduction to Python designed for participants with no programming experience. These lessons can be taught in a day (~ 6 hours). They start with some...

Python for Ecologists: Instructor NotesChallenge solutions

To install Homebrew, you need have xcode command line tools installed, from the terminal, type: then Run the following command to ensure Homebrew is installed properly: install Python 3:

SQL for Ecology: Instructor Notes

Note that the figshare download is an archive (.zip) file that rudely explodes all of the files into your current directory. See this slide deck as a sample intro for the lesson:
SQL Intro Deck Key points: If you’ve written up a diagram of the data analysis pipeline (raw data ->
clean data...

Open Refine for Ecology: Instructor Notes

Note the file types OpenRefine handles: TSV, CSF, *SV, Excel (.xls .xlsx), JSON, XML, RDF as XML, Google Data documents. Support for other formats can be added with OpenRefine extensions. In this first step, we’ll browse our computer to the sample data file for this lesson (If you haven’t...

Data Organization in Spreadsheets: Instructor Notes

This lesson is optional The challenge with this lesson is that the instructor’s version of the spreadsheet software is going to look different than about half the room’s. It makes
it challenging to show where you can find menu options and navigate through. Instead discuss the concepts of quality...

Data Carpentry Python for Ecologists

Data Carpentry's aim is to teach researchers basic concepts, skills,
and tools for working with data so that they can get more done in less
time, and with less pain. The lessons below were designed for those interested in
working with ecological data in Python. Data for this lesson is from the...

Data Carpentry: R for data analysis and visualization of Ecological Data

Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. The lessons below were designed for those interested in working with ecology data in R. This is an introduction to R designed for...

SQL for Ecology

This lesson will teach you what relational databases are, how you can load data
into them and how you can query databases to extract just the information that you need. Data Carpentry’s teaching is hands-on, so participants are encouraged to use
their own computers to insure the proper setup of...

Open Refine for Ecology

OpenRefine (formerly Google Refine) is a powerful free and open source tool
for working with messy
data: cleaning it and transforming it from one format into another. This lesson will teach you to use OpenRefine to effectively clean and format
data and automatically track any changes that you...