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InterMine user tutorial

A tutorial for end users of InterMine

Keywords: Data querying, Data analysis, Data download, FAIR

Resource type: Tutorial

InterMine user tutorial https://tess.elixir-europe.org/materials/intermine-user-tutorial A tutorial for end users of InterMine Data querying, Data analysis, Data download, FAIR Life Science Researchers Bioinformaticians
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...

SQL for Ecology: Instructor Notes https://tess.elixir-europe.org/materials/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 -> import and analyze -> results -> visualization), it can be helpful to identify that you’re now somewhere between clean data and analysis. Tips 2017-10-09
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.
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 Python for Ecologists https://tess.elixir-europe.org/materials/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 Portal Project Teaching Database - available on FigShare. The data files used in this lesson are surveys.csv download link - https://ndownloader.figshare.com/files/2292172 and species.csv download link - https://ndownloader.figshare.com/files/3299483. Requirements: Data Carpentry's teaching is hands-on, so participants are encouraged to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. (We will provide instructions on setting up the required software several days in advance, and the classroom will have computers with the software installed). There are no pre-requisites, and we will assume no prior knowledge about the tools. Participants are required to abide by Software Carpentry's Code of Conduct. Twitter: #datacarpentry 2016-03-07
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.