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Content provider: Coursera  or Data Carpentry 


Access Bioinformatics Databases with Biopython

In this 1-hour long project-based course, you will learn how to access, parse, and visualize data from various bioinformatics sequence and structural online databases such as ENTREZ, PDB, KEGG and NCBI using Biopython.
You will also interact with various bioinformatics file formats such as FASTA,...

Keywords: data-science, life-sciences, data-analysis, health-informatics

Bacterial Bioinformatics

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center,...

Keywords: life-sciences, health-informatics, research

Plant Bioinformatics Capstone

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply...

Keywords: physical-science-and-engineering, life-sciences, research-methods, basic-science

Research Data Management and Sharing

This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management...

Scientific topics: Data management

Resource type: e-learning

Plant Bioinformatics

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply...

Keywords: life-sciences, physical-science-and-engineering, health-informatics, research-methods

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

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...

Big Data, Genes, and Medicine

This course distills for you expert knowledge and skills mastered by professionals in Health Big Data Science and Bioinformatics. You will learn exciting facts about the human body biology and chemistry, genetics, and medicine that will be intertwined with the science of Big Data and skills to...

Keywords: life-sciences, computer-science, bioinformatics, algorithms

Bioinformatics: Life Sciences on Your Computer

What makes bioinformatics education exciting is that people of a variety of education levels can get started quickly, with just a computer and internet access.

Keywords: life-sciences, bioinformatics

Bioinformatic Methods II

Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful...

Keywords: life-sciences, bioinformatics

Bioinformatics Capstone: Big Data in Biology

In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.

In particular, in a series of Application Challenges will see how genome assembly can be used...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Bioinformatics: Introduction and Methods 生物信息学: 导论与方法

A big welcome to “Bioinformatics: Introduction and Methods” from Peking University! In this MOOC you will become familiar with the concepts and computational methods in the exciting interdisciplinary field of bioinformatics and their applications in biology, the knowledge and skills in...

Keywords: life-sciences, health-informatics

Finding Hidden Messages in DNA (Bioinformatics I)

Named a top 50 MOOC of all time by Class Central!

This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat.

In the first half of the...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Finding Mutations in DNA and Proteins (Bioinformatics VI)

In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins.

In the first half of the course, we would like to ask how an individual's genome differs from the...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Genome Sequencing (Bioinformatics II)

You may have heard a lot about genome sequencing and its potential to usher in an era of personalized medicine, but what does it mean to sequence a genome?

Biologists still cannot read the nucleotides of an entire genome as you would read a book from beginning to end. However, they can read...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Bioinformatic Methods I

Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful...

Keywords: life-sciences, bioinformatics

Biology Meets Programming: Bioinformatics for Beginners

Are you interested in learning how to program (in Python) within a scientific setting?

This course will cover algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms in Python. It offers a gently-paced introduction...

Keywords: life-sciences, computer-science, health-informatics, software-development