Register training material
39 materials found

Content provider: Data Carpentry  or ELIXIR Slovenia 


How to get the most out of your microarray experiment. A Webinar

Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017

Scientific topics: Microarray experiment

Keywords: life sciences, microarrays, eLearning, EeLP

Resource type: course materials, Training materials, Slides

How to get the most out of your microarray experiment. A Webinar https://tess.elixir-europe.org/materials/how-to-get-the-most-out-of-your-microarray-experiment-a-webinar Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017 Eva Freyhult Jessica Lindvall Mihaela Martis Microarray experiment life sciences, microarrays, eLearning, EeLP Researchers
ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

ELIXIR eLearning definitions https://tess.elixir-europe.org/materials/elixir-elearning-definitions Materials from the asynchronous learning course "ELIXIR eLearning definitions" Brane Leskosek Jure Dimec Eija Korpelainen Teresa Attwood Sarah Morgan Nicola Mulder Celia van Gelder Patricia Palagi eLearning, training, EeLP Researchers teachers Trainers
RNA-seq data analysis using Chipster

Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017

Scientific topics: Transcriptomics, Genomics

Keywords: transcriptomics, RNA-Seq, eLearning, EeLP

Resource type: course materials, Training materials, Slides, Video

RNA-seq data analysis using Chipster https://tess.elixir-europe.org/materials/rna-seq-data-analysis-using-chipster Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017 Eija Korpelainen Maria Lehtivaara Transcriptomics Genomics transcriptomics, RNA-Seq, eLearning, EeLP Researchers
ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

ELIXIR TtR course: Basic genomics using advanced analysis tools https://tess.elixir-europe.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia Christophe Antoniewski Olivier Inizan Genomics Galaxy, training, Genomics, eLearning, EeLP life scientists beginner bioinformaticians Postgraduate students
Implementation of Data Management Plans & Data Stewardship in practice

Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece.

Scientific topics: Data submission, annotation and curation, Data management

Keywords: data management, data stewardship, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Implementation of Data Management Plans & Data Stewardship in practice https://tess.elixir-europe.org/materials/implementation-of-data-management-plans-data-stewardship-in-practice Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece. Celia van Gelder Roland Krause Mateusz Kuzak Brane Leskosek Marko Vidak Robert Pergl Marek Suchanek Jan Slifka Vojtech Knaisl Data submission, annotation and curation Data management data management, data stewardship, eLearning, EeLP bioinformaticians data stewards
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...

Python for Social Science Data: Instructor Notes https://tess.elixir-europe.org/materials/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 folder. They should be downloaded to the local machine before use.
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...

R for Social Scientists: Instructor Notes https://tess.elixir-europe.org/materials/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 it in their scripts to download the file directly from figshare in their working directory. . If the learners haven’t created the data/ directory and/or are not in the correct working directory, the download.file command will produce an error. Therefore, it is important to use the stickies at this point. Some learners may have previous R installations. On Mac, if a new install is performed, the learner’s system will create a symbolic link, pointing to the new install as ‘Current.’ Sometimes this process does not occur, and, even though a new R is installed and can be accessed via the R console, RStudio does not find it. The net result of this is that the learner’s RStudio will be running an older R install. This will cause package installations to fail. This can be fixed at the terminal. First, check for the appropriate R installation in the library; We are currently using R 3.x.y If it isn’t there, they will need to install it. If it is present, you will need to set the symbolic link to Current to point to the 3.x.y directory: Then restart RStudio.
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...

Data Organization in Spreadsheets for Social Scientists: Instructor Notes https://tess.elixir-europe.org/materials/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 like sorting can help you find outliers in your data. Provide information on setting up your environment for learners to view your live coding (increasing text size, changing text color, etc), as well as general recommendations for working with coding tools to best suit the learning environment. The main challenge with this lesson is that Excel looks very different and how you do things is even different between Mac and PC, and between different versions of Excel. So, the presenter’s environment will only be the same as some of the learners. We need better notes and screenshots of how things work on both Mac and PC. But we likely won’t be able to cover all the different versions of Excel.
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

OpenRefine for Social Science Data: Instructor Notes https://tess.elixir-europe.org/materials/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
Python for Ecologists: Glossary

SciPy ecosystem for Python provides the tools necessary for scientific computing Jupyter Notebook and the Spyder IDE are great tools to code in and interact with Python with its large community it is easy to find help in the internet FIXME FIXME FIXME

Python for Ecologists: Glossary https://tess.elixir-europe.org/materials/python-for-ecologists-glossary SciPy ecosystem for Python provides the tools necessary for scientific computing Jupyter Notebook and the Spyder IDE are great tools to code in and interact with Python with its large community it is easy to find help in the internet FIXME FIXME FIXME
Intro to Geospatial Data with R

A single raster file can contain multiple bands or layers. Spatial objects in sf are similar to standard data frames except for a geometry list-column. It is important to know the projection (if any) of your point data prior to converting to a spatial object. CRAN Spatial Task View Geocomputation...

Intro to Geospatial Data with R https://tess.elixir-europe.org/materials/intro-to-geospatial-data-with-r A single raster file can contain multiple bands or layers. Spatial objects in sf are similar to standard data frames except for a geometry list-column. It is important to know the projection (if any) of your point data prior to converting to a spatial object. CRAN Spatial Task View Geocomputation with R
R for Social Scientists: Glossary

Use install.packages() to install packages (libraries). Access individual values by location using []. Access slices of data using [low:high]. Access arbitrary sets of data using [c(...)]. Use logical operations and logical vectors to access subsets of data.

R for Social Scientists: Glossary https://tess.elixir-europe.org/materials/r-for-social-scientists-glossary Use install.packages() to install packages (libraries). Access individual values by location using []. Access slices of data using [low:high]. Access arbitrary sets of data using [c(...)]. Use logical operations and logical vectors to access subsets of data.
Python for Social Science Data: Glossary

The REPL (Read-Eval-Print loop) allows rapid development and testing of code segments Jupyter notebooks builds on the REPL concepts and allow code results and documentation to be maintained together and shared Jupyter notebooks is a complete IDE (Integrated Development Environment) The Jupyter...

Python for Social Science Data: Glossary https://tess.elixir-europe.org/materials/python-for-social-science-data-glossary The REPL (Read-Eval-Print loop) allows rapid development and testing of code segments Jupyter notebooks builds on the REPL concepts and allow code results and documentation to be maintained together and shared Jupyter notebooks is a complete IDE (Integrated Development Environment) The Jupyter environment can be used to write code segments and display results Datatypes in Python are implicit based on variable values
SQL for Social Science Data: Glossary

SQL (Structured Query Language) is used to extract data from the tables A schema for a table has to be created before data can be added The schema can be used to provide some data validation on input The DB Browser for SQLite application allows you to connect to an existing database or create a...

SQL for Social Science Data: Glossary https://tess.elixir-europe.org/materials/sql-for-social-science-data-glossary SQL (Structured Query Language) is used to extract data from the tables A schema for a table has to be created before data can be added The schema can be used to provide some data validation on input The DB Browser for SQLite application allows you to connect to an existing database or create a new database When connected to a database you can create new tables
OpenRefine for Social Science Data: Glossary

OpenRefine will automatically track any steps allowing you to backtrack as needed and providing a record of all work done OpenRefine can import a variety of file types. OpenRefine can be used to explore data using filters. Clustering in OpenRefine can help to identify different values that might...

OpenRefine for Social Science Data: Glossary https://tess.elixir-europe.org/materials/openrefine-for-social-science-data-glossary OpenRefine will automatically track any steps allowing you to backtrack as needed and providing a record of all work done OpenRefine can import a variety of file types. OpenRefine can be used to explore data using filters. Clustering in OpenRefine can help to identify different values that might mean the same thing. OpenRefine can transform the values of a column.
Data Organization in Spreadsheets for Social Scientists

Never modify your raw data. Always make a copy before making any changes. Keep track of all of the steps you take to clean your data. Organize your data according to tidy data principles. Record metadata in a separate plain text file. Avoid using multiple tables within one spreadsheet.

Data Organization in Spreadsheets for Social Scientists https://tess.elixir-europe.org/materials/lesson-title-glossary Never modify your raw data. Always make a copy before making any changes. Keep track of all of the steps you take to clean your data. Organize your data according to tidy data principles. Record metadata in a separate plain text file. Avoid using multiple tables within one spreadsheet.
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.

Cloud Genomics: Instructor NotesCloud Genomics Pre-WorkshopDuring the workshop https://tess.elixir-europe.org/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.
Wrangling Genomics: Glossary

for loops let you perform the same set of operations on multiple files with a single command. The options you set for the command-line tools you use are important! Data cleaning is an essential step in a genomics workflow. Bioinformatics command line tools are collections of commands that can be...

Wrangling Genomics: Glossary https://tess.elixir-europe.org/materials/wrangling-genomics-glossary for loops let you perform the same set of operations on multiple files with a single command. The options you set for the command-line tools you use are important! Data cleaning is an essential step in a genomics workflow. Bioinformatics command line tools are collections of commands that can be used to carry out bioinformatics analyses. To use most powerful bioinformatics tools, you’ll need to use the command line.
Cloud Genomics: Glossary

You can use one set of log-in credentials for many instances Logging off an instance is not the same as turning off an instance Always check a new instance to verify it started correctly Using a program like tmux can keep your work going even if your internet connection is bad No matter which way...

Cloud Genomics: Glossary https://tess.elixir-europe.org/materials/cloud-genomics-glossary You can use one set of log-in credentials for many instances Logging off an instance is not the same as turning off an instance Always check a new instance to verify it started correctly Using a program like tmux can keep your work going even if your internet connection is bad No matter which way you want to move data, it’s easier to start the transfer from your local machine
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,...

Shell Genomics: Instructor Notes https://tess.elixir-europe.org/materials/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, redirect output and write shell scripts. By the end of the lesson, learners will be prepared to move on to using more advanced bioinformatic command line tools (see the lesson on Data Wrangling and Processing). This lesson is meant to be taught in its entirety. For novice learners, schedule around 4 hours for this lesson. If your learners are already somewhat familiar with the bash shell, the earlier episodes can be condensed. This lesson uses data hosted on an Amazon Machine Instance (AMI). Instructors will be sent information on how to log-in to the AMI by the workshop coordinator a few days before the workshop. If you are running a self-organized workshop, register the workshop with our self-organized workshop form and send us an email at mailto:team@datacarpentry.org with information on how many people you expect to have at the workshop, and we’ll start instances for you to use in the workshop. The day before the workshop, we’ll send you the login information for your learners. Learners will work through an Amazon Web Service (AWS) instance for this lesson. The workshop coordinator will set up AWS instances for your workshop a few days ahead of time. Put the links for all instances on your workshop Etherpad and have learners put their name next to the instance they will use. This prevents learners from accidentally messing up another learner’s filesystem. The workshop coordinator usually sets up more AWS instances than needed for the registered learners. If a learner accidentally deletes or overwrites data files, you can have them change to a different AWS instance.
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 Organization: Instructor Notes https://tess.elixir-europe.org/materials/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 responses in that Etherpad. That etherpad is then a resource for learners after the workshop.
Shell Genomics: Glossary

Useful commands for navigating your file system include: ls, pwd, and cd. Most commands take options (flags) which begin with a -. Tab completion can reduce errors from mistyping and make work more efficient in the shell. The /, ~, and .. characters represent important navigational shortcuts....

Shell Genomics: Glossary https://tess.elixir-europe.org/materials/shell-genomics-glossary Useful commands for navigating your file system include: ls, pwd, and cd. Most commands take options (flags) which begin with a -. Tab completion can reduce errors from mistyping and make work more efficient in the shell. The /, ~, and .. characters represent important navigational shortcuts. Hidden files and directories start with . and can be viewed using ls -a.
Genomics Organization: Glossary

Tabular data needs to be structured to be able to work with it effectively Data being sent to a sequencing center also needs to be structured so you can use it. Raw sequencing data should be kept raw somewhere, so you can always go back to the original files. Public data repositories are a great...

Genomics Organization: Glossary https://tess.elixir-europe.org/materials/genomics-organization-glossary Tabular data needs to be structured to be able to work with it effectively Data being sent to a sequencing center also needs to be structured so you can use it. Raw sequencing data should be kept raw somewhere, so you can always go back to the original files. Public data repositories are a great source of genomic data. FIXME
SQL for Ecology: Glossary

A relational database is made up of tables which are related to each other by shared keys. Different database management systems (DBMS) use slightly different vocabulary, but they are all based on the same ideas. It is useful to apply conventions when writing SQL queries to aid readability. Use...

SQL for Ecology: Glossary https://tess.elixir-europe.org/materials/sql-for-ecology-glossary A relational database is made up of tables which are related to each other by shared keys. Different database management systems (DBMS) use slightly different vocabulary, but they are all based on the same ideas. It is useful to apply conventions when writing SQL queries to aid readability. Use logical connectors such as AND or OR to create more complex queries. Calculations using mathematical symbols can also be performed on SQL queries.
Open Refine for Ecology: Glossary

OpenRefine will automatically track any steps you take in working with your data. Faceting and clustering approaches can identify errors or outliers in data. OpenRefine provides a way to sort and filter data without affecting the raw data. OpenRefine also provides ways to get overviews of...

Open Refine for Ecology: Glossary https://tess.elixir-europe.org/materials/open-refine-for-ecology-glossary OpenRefine will automatically track any steps you take in working with your data. Faceting and clustering approaches can identify errors or outliers in data. OpenRefine provides a way to sort and filter data without affecting the raw data. OpenRefine also provides ways to get overviews of numerical data. All changes are being tracked in OpenRefine, and this information can be used for scripts for future analyses or reproducing an analysis.
Data Organization in Spreadsheets: Glossary

Never modify your raw data. Always make a copy before making any changes. Keep track of all of the steps you take to clean your data. Organize your data according to tidy data principles. Avoid using multiple tables within one spreadsheet. Avoid spreading data across multiple tabs (but do use a...

Data Organization in Spreadsheets: Glossary https://tess.elixir-europe.org/materials/data-organization-in-spreadsheets-glossary Never modify your raw data. Always make a copy before making any changes. Keep track of all of the steps you take to clean your data. Organize your data according to tidy data principles. Avoid using multiple tables within one spreadsheet. Avoid spreading data across multiple tabs (but do use a new tab to record data cleaning or manipulations).
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...

Genomics WorkshopWorkshop OverviewTeaching Platform https://tess.elixir-europe.org/materials/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 and plan to participate actively. To get started, follow the directions in the Setup tab to get access to the required software and data for this workshop. Please note that workshop materials for working with Genomics data in R are under development and will become available in June 2018. This workshop uses data from a long term evolution experiment published in 2012: Genomic analysis of a key innovation in an experimental Escherichia coli population by Blount ZD, Barrick JE, Davidson CJ, and Lenski RE. (doi: 10.1038/nature11514) More information about these data will be presented in the first lesson of the workshop.
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...

Ecology Workshop Overview https://tess.elixir-europe.org/materials/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 Portal Project Database designed for teaching. It is a tabular dataset of observations of small mammals in a desert ecosystem in Arizona, USA, collected over more than 40 years. It provides a real world example of life-history, population, and ecological data, with sufficient complexity to teach many aspects of data analysis and management, but with many complexities removed to allow students to focus on the core ideas and skills being taught. More information on this dataset The workshop can be taught using R or Python as the base language.
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...

Instructor notes https://tess.elixir-europe.org/materials/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 is a decent internet connection in the room where the workshop is being taught. To facilitate the download process, the chunk of code that includes the URL where the csv file lives, and where the file should go and be named is included in the code handout (see next paragraph). Using this approach ensures that the file will be where the lesson expects it to be, and teaches good/reproducible practice of automating the download. If the learners haven’t created the data/ directory and/or are not in the correct working directory, the download.file command will produce an error. Therefore, it is important to use the stickies at this point. The code handout (a link to download it is also available on the top bar of the lesson website) is useful for Data Carpentry workshops. It includes an outline of the lesson content, the text for the challenges, the links for the files that need to be downloaded for the lesson, and pieces of code that may be difficult to type for learners with no programming experience/who are unfamiliar with R’s syntax. We encourage you to distribute it to the learners at the beginning of the lesson. As an instructor, we encourage you to do the live coding directly in this file, so the participants can follow along. Some learners may have previous R installations. On Mac, if a new install is performed, the learner’s system will create a symbolic link, pointing to the new install as ‘Current.’ Sometimes this process does not occur, and, even though a new R is installed and can be accessed via the R console, RStudio does not find it. The net result of this is that the learner’s RStudio will be running an older R install. This will cause package installations to fail. This can be fixed at the terminal. First, check for the appropriate R installation in the library; We are currently using R 3.4.x. If it isn’t there, they will need to install it. If it is present, you will need to set the symbolic link to Current to point to the 3.4.x directory:
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 https://tess.elixir-europe.org/materials/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 basic information about Python syntax, the Jupyter notebook interface, and move through how to import CSV files, using the pandas package to work with data frames, how to calculate summary information from a data frame, and a brief introduction to plotting. The last lesson demonstrates how to work with databases directly from Python. Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow. These lessons assume no prior knowledge of the skills or tools. To get started, follow the directions in the “Setup” tab to download data to your computer and follow any installation instructions. This lesson requires a working copy of Python. To most effectively use these materials, please make sure to install everything before working through this lesson. 2017-10-09