This is a recording of a 45 minute introductory webinar on preprints. With our guest speaker Philip Cohen, we’ll cover what preprints/postprints are, the benefits of preprints, and address some common concerns researcher may have. We’ll show how to determine whether you can post preprints/postprints, and also demonstrate how to use OSF preprints (https://osf.io/preprints/) to share preprints. The OSF is the flagship product of the Center for Open Science, a non-profit technology start-up dedicated to improving the alignment between scientific values and scientific practices. Learn more at cos.io and osf.io, or email contact@cos.io.

In this webinar, Doctors David Mellor (Center for Open Science) and Stavroula Kousta (Nature Human Behavior) discuss the Registered Reports publishing workflow and the benefits it may bring to funders of research. Dr. Mellor details the workflow and what it is intended to do, and Dr. Kousta discusses the lessons learned at Nature Human Behavior from their efforts to implement Registered Reports as a journal.

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.

This video is an introduction to power analyses to improve the reproducibility of your research.

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.

This video will introduce how to calculate confidence intervals around effect sizes using the MBESS package in R. All materials shown in the video, as well as content from our other videos, can be found here: https://osf.io/7gqsi/

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.

The book is associated with the lsr package on CRAN and GitHub. The package is probably okay for many introductory teaching purposes, but some care is required. The package does have some limitations (e.g., the etaSquared function does strange things for unbalanced ANOVA designs), and it has not been updated in a while.

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.

Join us for a 30 minute guest webinar by Brandon Butler, Director of Information Policy at the University of Virginia. This webinar will introduce questions to think about when picking a license for your research. You can signal which license you pick using the License Picker on the Open Science Framework (OSF; https://osf.io). The OSF is a free, open source web application built to help researchers manage their workflows. The OSF is part collaboration tool, part version control software, and part data archive. The OSF connects to popular tools researchers already use, like Dropbox, Box, Github, Mendeley, and now is integrated with JASP, to streamline workflows and increase efficiency.

A class on setting up and managing research materials; caring for digital files to enable collaboration, sharing, and re-use; and helpful software/digital tools for organizing personal research files.

Expectations by funders for transparent and reproducible methods are on the rise. This session covers expectations for preregistration, data sharing, and open access results of three key funders of education research including the Institute of Education Sciences, the National Science Foundation, and Arnold Ventures. Presenters cover practical resources for meeting these requirements such as the Registry for Efficacy and Effectiveness Studies (REES), the Open Science Framework (OSF), and EdArXiv. Presenters: Jessaca Spybrook, Western Michigan University Bryan Cook, University of Virginia David Mellor, Center for Open Science

Non-significant results are less likely to be reported by authors and, when submitted for peer review, are less likely to be published by journal editors. This phenomenon, known collectively as publication bias, is seen in a variety of scientific disciplines and can erode public trust in the scientific method and the validity of scientific theories. Public trust in science is especially important for fields like climate change science, where scientific consensus can influence state policies on a global scale, including strategies for industrial and agricultural management and development. Here, we used meta-analysis to test for biases in the statistical results of climate change articles, including 1154 experimental results from a sample of 120 articles. Funnel plots revealed no evidence of publication bias given no pattern of non-significant results being under-reported, even at low sample sizes. However, we discovered three other types of systematic bias relating to writing style, the relative prestige of journals, and the apparent rise in popularity of this field: First, the magnitude of statistical effects was significantly larger in the abstract than the main body of articles. Second, the difference in effect sizes in abstracts versus main body of articles was especially pronounced in journals with high impact factors. Finally, the number of published articles about climate change and the magnitude of effect sizes therein both increased within 2 years of the seminal report by the Intergovernmental Panel on Climate Change 2007.

This webinar walks you through the basics of creating an OSF project, structuring it to fit your research needs, adding collaborators, and tying your favorite online tools into your project structure. OSF is a free, open source web application built by the Center for Open Science, a non-profit dedicated to improving the alignment between scientific values and scientific practices. OSF is part collaboration tool, part version control software, and part data archive. It is designed to connect to popular tools researchers already use, like Dropbox, Box, Github, and Mendeley, to streamline workflows and increase efficiency.