This lesson shows how to use Python and skimage to do basic image processing. With support from an NSF iUSE grant, Dr. Tessa Durham Brooks and Dr. Mark Meysenburg at Doane College, Nebraska, USA have developed a curriculum for teaching image processing in Python. This lesson is currently being piloted at different institutions. This pilot phase will be followed by a clean-up phase to incorporate suggestions and feedback from the pilots into the lessons and to make the lessons teachable by the broader community. Development for these lessons has been supported by a grant from the Sloan Foundation.

Data Carpentry lesson to learn how to work with Amazon AWS cloud computing and how to transfer data between your local computer and cloud resources. The cloud is a fancy name for the huge network of computers that host your favorite websites, stream movies, and shop online, but you can also harness all of that computing power for running analyses that would take days, weeks or even years on your local computer. In this lesson, you’ll learn about renting cloud services that fit your analytic needs, and how to interact with one of those services (AWS) via the command line.

Data Carpentry lesson to understand data structures and common storage and transfer formats for spatial data. The goal of this lesson is to provide an introduction to core geospatial data concepts. It is intended for learners who have no prior experience working with geospatial data, and as a pre-requisite for the R for Raster and Vector Data lesson . This lesson can be taught in approximately 75 minutes and covers the following topics: Introduction to raster and vector data format and attributes Examples of data types commonly stored in raster vs vector format Introduction to categorical vs continuous raster data and multi-layer rasters Introduction to the file types and R packages used in the remainder of this workshop Introduction to coordinate reference systems and the PROJ4 format Overview of commonly used programs and applications for working with geospatial data The Introduction to R for Geospatial Data lesson provides an introduction to the R programming language while the R for Raster and Vector Data lesson provides a more in-depth introduction to visualization (focusing on geospatial data), and working with data structures unique to geospatial data. The R for Raster and Vector Data lesson assumes that learners are already familiar with both geospatial data concepts and the core concepts of the R language.

Data Carpentry lesson to open, work with, and plot vector and raster-format spatial data in R. The episodes in this lesson cover how to open, work with, and plot vector and raster-format spatial data in R. Additional topics include working with spatial metadata (extent and coordinate reference systems), reprojecting spatial data, and working with raster time series data.

The goal of this lesson is to provide an introduction to R for learners working with geospatial data. It is intended as a pre-requisite for the R for Raster and Vector Data lesson for learners who have no prior experience using R. This lesson can be taught in approximately 4 hours and covers the following topics: Working with R in the RStudio GUI Project management and file organization Importing data into R Introduction to R’s core data types and data structures Manipulation of data frames (tabular data) in R Introduction to visualization Writing data to a file The the R for Raster and Vector Data lesson provides a more in-depth introduction to visualization (focusing on geospatial data), and working with data structures unique to geospatial data.

Command line interface (OS shell) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. The shell is a program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination. There are quite a few reasons to start learning about the shell: The shell gives you power. The command line gives you the power to do your work more efficiently and more quickly. When you need to do things tens to hundreds of times, knowing how to use the shell is transformative. To use remote computers or cloud computing, you need to use the shell.

Data Carpentry lesson to learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards with genomics data. Command line interface (OS shell) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. The shell is a program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination. There are quite a few reasons to start learning about the shell: For most bioinformatics tools, you have to use the shell. There is no graphical interface. If you want to work in metagenomics or genomics you’re going to need to use the shell. The shell gives you power. The command line gives you the power to do your work more efficiently and more quickly. When you need to do things tens to hundreds of times, knowing how to use the shell is transformative. To use remote computers or cloud computing, you need to use the shell.

Welcome to R! Working with a programming language (especially if it’s your first time) often feels intimidating, but the rewards outweigh any frustrations. An important secret of coding is that even experienced programmers find it difficult and frustrating at times – so if even the best feel that way, why let intimidation stop you? Given time and practice* you will soon find it easier and easier to accomplish what you want. Why learn to code? Bioinformatics – like biology – is messy. Different organisms, different systems, different conditions, all behave differently. Experiments at the bench require a variety of approaches – from tested protocols to trial-and-error. Bioinformatics is also an experimental science, otherwise we could use the same software and same parameters for every genome assembly. Learning to code opens up the full possibilities of computing, especially given that most bioinformatics tools exist only at the command line. Think of it this way: if you could only do molecular biology using a kit, you could probably accomplish a fair amount. However, if you don’t understand the biochemistry of the kit, how would you troubleshoot? How would you do experiments for which there are no kits? R is one of the most widely-used and powerful programming languages in bioinformatics. R especially shines where a variety of statistical tools are required (e.g. RNA-Seq, population genomics, etc.) and in the generation of publication-quality graphs and figures. Rather than get into an R vs. Python debate (both are useful), keep in mind that many of the concepts you will learn apply to Python and other programming languages. Finally, we won’t lie; R is not the easiest-to-learn programming language ever created. So, don’t get discouraged! The truth is that even with the modest amount of R we will cover today, you can start using some sophisticated R software packages, and have a general sense of how to interpret an R script. Get through these lessons, and you are on your way to being an accomplished R user! * We very intentionally used the word practice. One of the other “secrets” of programming is that you can only learn so much by reading about it. Do the exercises in class, re-do them on your own, and then work on your own problems.

Software Carpentry lección para la terminal de Unix La terminal de Unix ha existido por más tiempo que la mayoría de sus usuarios. Ha sobrevivido tanto tiempo porque es una herramienta poderosa que permite a las personas hacer cosas complejas con sólo unas pocas teclas. Lo más importante es que ayuda a combinar programas existentes de nuevas maneras y automatizar tareas repetitivas, en vez de estar escribiendo las mismas cosas una y otra vez. El uso del terminal o shell es fundamental para usar muchas otras herramientas poderosas y recursos informáticos (incluidos los supercomputadores o “computación de alto rendimiento”). Esta lección te guiará en el camino hacia el uso eficaz de estos recursos.

Library Carpentry lesson: An introduction to Git. What We Will Try to Do Begin to understand and use Git/GitHub. You will not be an expert by the end of the class. You will probably not even feel very comfortable using Git. This is okay. We want to make a start but, as with any skill, using Git takes practice. Be Excellent to Each Other If you spot someone in the class who is struggling with something and you think you know how to help, please give them a hand. Try not to do the task for them: instead explain the steps they need to take and what these steps will achieve. Be Patient With The Instructor and Yourself This is a big group, with different levels of knowledge, different computer systems. This isn’t your instructor’s full-time job (though if someone wants to pay them to play with computers all day they’d probably accept). They will do their best to make this session useful. This is your session. If you feel we are going too fast, then please put up a pink sticky. We can decide as a group what to cover.

This Library Carpentry lesson introduces librarians and others to working with data. This Library Carpentry lesson introduces people with library- and information-related roles to working with data using regular expressions. The lesson provides background on the regular expression language and how it can be used to match and extract text and to clean data.

Library Carpentry lesson: an introduction to OpenRefine for Librarians This Library Carpentry lesson introduces people working in library- and information-related roles to working with data in OpenRefine. At the conclusion of the lesson you will understand what the OpenRefine software does and how to use the OpenRefine software to work with data files.

Library Carpentry, an introduction to SQL for Librarians This Library Carpentry lesson introduces librarians to relational database management system using SQLite. At the conclusion of the lesson you will: understand what SQLite does; use SQLite to summarise and link data.

Library Carpentry lesson to learn how to use the Shell. This Library Carpentry lesson introduces librarians to the Unix Shell. At the conclusion of the lesson you will: understand the basics of the Unix shell; understand why and how to use the command line; use shell commands to work with directories and files; use shell commands to find and manipulate data.

Lesson on OpenRefine for social scientists. A part of the data workflow is preparing the data for analysis. Some of this involves data cleaning, where errors in the data are identifed and corrected or formatting made consistent. This step must be taken with the same care and attention to reproducibility as the analysis. 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 make. Many people comment that this tool saves them literally months of work trying to make these edits by hand.

This lesson is part of Software Carpentry workshops and teach an introduction to plotting and programming using python. This lesson is an introduction to programming in Python for people with little or no previous programming experience. It uses plotting as its motivating example, and is designed to be used in both Data Carpentry and Software Carpentry workshops. This lesson references JupyterLab, but can be taught using a regular Python interpreter as well. Please note that this lesson uses Python 3 rather than Python 2.

The best way to learn how to program is to do something useful, so this introduction to MATLAB is built around a common scientific task: data analysis. Our real goal isn’t to teach you MATLAB, but to teach you the basic concepts that all programming depends on. We use MATLAB in our lessons because: we have to use something for examples; it’s well-documented; it has a large (and growing) user base among scientists in academia and industry; and it has a large library of packages available for performing diverse tasks. But the two most important things are to use whatever language your colleagues are using, so that you can share your work with them easily, and to use that language well.

The best way to learn how to program is to do something useful, so this introduction to Python is built around a common scientific task: data analysis. Arthritis Inflammation We are studying inflammation in patients who have been given a new treatment for arthritis, and need to analyze the first dozen data sets of their daily inflammation. The data sets are stored in comma-separated values (CSV) format: each row holds information for a single patient, columns represent successive days. The first three rows of our first file look like this: 0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0 0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1 0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1 Each number represents the number of inflammation bouts that a particular patient experienced on a given day. For example, value “6” at row 3 column 7 of the data set above means that the third patient was experiencing inflammation six times on the seventh day of the clinical study. So, we want to: Calculate the average inflammation per day across all patients. Plot the result to discuss and share with colleagues. To do all that, we’ll have to learn a little bit about programming.

The best way to learn how to program is to do something useful, so this introduction to R is built around a common scientific task: data analysis. Our real goal isn’t to teach you R, but to teach you the basic concepts that all programming depends on. We use R in our lessons because: we have to use something for examples; it’s free, well-documented, and runs almost everywhere; it has a large (and growing) user base among scientists; and it has a large library of external packages available for performing diverse tasks. But the two most important things are to use whatever language your colleagues are using, so you can share your work with them easily, and to use that language well. We are studying inflammation in patients who have been given a new treatment for arthritis, and need to analyze the first dozen data sets of their daily inflammation. The data sets are stored in CSV format (comma-separated values): each row holds information for a single patient, and the columns represent successive days. The first few rows of our first file look like this: 0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0 0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1 0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1 0,0,2,0,4,2,2,1,6,7,10,7,9,13,8,8,15,10,10,7,17,4,4,7,6,15,6,4,9,11,3,5,6,3,3,4,2,3,2,1 0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1 We want to: load that data into memory, calculate the average inflammation per day across all patients, and plot the result. To do all that, we’ll have to learn a little bit about programming.

Data Carpentry Genomics workshop lesson to learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database. Good data organization is the foundation of any research project. It not only sets you up well for an analysis, but it also makes it easier to come back to the project later and share with collaborators, including your most important collaborator - future you. Organizing a project that includes sequencing involves many components. There’s the experimental setup and conditions metadata, measurements of experimental parameters, sequencing preparation and sample information, the sequences themselves and the files and workflow of any bioinformatics analysis. So much of the information of a sequencing project is digital, and we need to keep track of our digital records in the same way we have a lab notebook and sample freezer. In this lesson, we’ll go through the project organization and documentation that will make an efficient bioinformatics workflow possible. Not only will this make you a more effective bioinformatics researcher, it also prepares your data and project for publication, as grant agencies and publishers increasingly require this information. In this lesson, we’ll be using data from a study of experimental evolution using E. coli. More information about this dataset is available here. In this study there are several types of files: Spreadsheet data from the experiment that tracks the strains and their phenotype over time Spreadsheet data with information on the samples that were sequenced - the names of the samples, how they were prepared and the sequencing conditions The sequence data Throughout the analysis, we’ll also generate files from the steps in the bioinformatics pipeline and documentation on the tools and parameters that we used. In this lesson you will learn: How to structure your metadata, tabular data and information about the experiment. The metadata is the information about the experiment and the samples you’re sequencing. How to prepare for, understand, organize and store the sequencing data that comes back from the sequencing center How to access and download publicly available data that may need to be used in your bioinformatics analysis The concepts of organizing the files and documenting the workflow of your bioinformatics analysis