Replication is the cornerstone of a cumulative science. However, new tools and …
Replication is the cornerstone of a cumulative science. However, new tools and technologies, massive amounts of data, interdisciplinary approaches, and the complexity of the questions being asked are complicating replication efforts, as are increased pressures on scientists to advance their research. As full replication of studies on independently collected data is often not feasible, there has recently been a call for reproducible research as an attainable minimum standard for assessing the value of scientific claims. This requires that papers in experimental science describe the results and provide a sufficiently clear protocol to allow successful repetition and extension of analyses based on original data. The importance of replication and reproducibility has recently been exemplified through studies showing that scientific papers commonly leave out experimental details essential for reproduction, studies showing difficulties with replicating published experimental results, an increase in retracted papers, and through a high number of failing clinical trials. This has led to discussions on how individual researchers, institutions, funding bodies, and journals can establish routines that increase transparency and reproducibility. In order to foster such aspects, it has been suggested that the scientific community needs to develop a “culture of reproducibility” for computational science, and to require it for published claims. We want to emphasize that reproducibility is not only a moral responsibility with respect to the scientific field, but that a lack of reproducibility can also be a burden for you as an individual researcher. As an example, a good practice of reproducibility is necessary in order to allow previously developed methodology to be effectively applied on new data, or to allow reuse of code and results for new projects. In other words, good habits of reproducibility may actually turn out to be a time-saver in the longer run. We further note that reproducibility is just as much about the habits that ensure reproducible research as the technologies that can make these processes efficient and realistic. Each of the following ten rules captures a specific aspect of reproducibility, and discusses what is needed in terms of information handling and tracking of procedures. If you are taking a bare-bones approach to bioinformatics analysis, i.e., running various custom scripts from the command line, you will probably need to handle each rule explicitly. If you are instead performing your analyses through an integrated framework (such as GenePattern, Galaxy, LONI pipeline, or Taverna), the system may already provide full or partial support for most of the rules. What is needed on your part is then merely the knowledge of how to exploit these existing possibilities.
Career exploration video - These Hands - Austin - Amazon / Technology. …
Career exploration video - These Hands - Austin - Amazon / Technology. The video showcases a deaf software engineer who uses American Sign Language (ASL).
This book is about complexity science, data structures and algorithms, intermediate programming …
This book is about complexity science, data structures and algorithms, intermediate programming in Python, and the philosophy of science. This book focuses on discrete models, which include graphs, cellular automata, and agent-based models. They are often characterized by structure, rules and transitions rather than by equations. They tend to be more abstract than continuous models; in some cases there is no direct correspondence between the model and a physical system.
Use a code to encode and decode secret messages. Colorado Americorp agents …
Use a code to encode and decode secret messages. Colorado Americorp agents in Araphahoe, Denver, Garfield, Larimer, and Weld Counties. Work supported by the Corporation for National and Community Service under Americorps grant number 18AFHCO0010008. Opinions or points of view expressed in this lesson are those of the authors and do not necessarily represent the official position of or a position that is endorsed by the Corporation or the Americorps program. This resource is also available in Spanish in the linked file.
Journal policy on research data and code availability is an important part …
Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38% had a data policy, 22% had a code policy, and 66% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.
This lab explores ontogenetic differences in trilobites, requiring students to measure and …
This lab explores ontogenetic differences in trilobites, requiring students to measure and describe differences in the sizes of different morphological features as trilobites age. Students will also reinforce concepts of allometry, isometry, and morphology of trilobites.
The internet is full of false information and ads. Sometimes it can …
The internet is full of false information and ads. Sometimes it can be challenging to decipher the validity of content. It is important to learn how to critically evaluate online material for several reasons: you want to know what type of information is trustworthy online, you want to be an informed digital citizen, and you want to ensure that the information that you are using for a school assignment is factual. The purpose of “Two Truths and a Lie Online” is to teach you how to critically evaluate online resources so that you can be both an informed consumer and producer of digital content.
Students will be introduced to a few of the different methods used …
Students will be introduced to a few of the different methods used in paleoclimatology, including isotopic ratios as paleotemperature proxies. They will investigate the greenhouse gas connections of two ancient climate episodes, the cold "Snowball Earth" of the Neoproterozoic and the hot "Paleocene-Eocene Thermal Maximum" (PETM) of the Cenozoic. The unit emphasizes the grand challenges of energy resources and climate change by grounding these issues in an understanding of ancient climate from a systems thinking perspective. Students will gain a more robust appreciation for the record of the movement of carbon between atmosphere, geosphere, hydrosphere, and biosphere over geologic time, and how various components of the Earth system respond to those perturbations. The unit practices geoscientific habits of mind, such as comparing modern processes to ancient analogues recorded by geologic processes, as well as the importance of converging lines of evidence, and recognition of Earth as a long-lived, dynamic, and complex system.
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This unit is the module's capstone project: developing a conceptual model of …
This unit is the module's capstone project: developing a conceptual model of the climatic and societal effects of a catastrophic volcanic eruption occurring in modern times. Through independent research and in-class collaboration, students explore the climatic and societal effects of past volcanic eruption events. Students are then introduced to the large Toba eruption event, review concept maps, concept sketches, and system diagrams, and are are given examples and guidelines for conceptual model design. Students complete their written summary outside of class.
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After completing this activity students should be able to: - demonstrate sediment …
After completing this activity students should be able to:
- demonstrate sediment core collection through a field exercise (whether or not you use that core's data). - recognize potential errors and contamination risks and identify ways to minimize them. - distinguish different layers within the cores and use appropriate terminology to describe them. - identify cyclical variations in the core layers, and correlate those with remotely sensed lake temperature data over a regional spatial scale. - estimate lake evaporation rates from lake temperatures. - reconstruct regional lake evaporation based on core layers. - evaluate the effectiveness of point observations to represent regional paleoclimate
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Brain-Computer Interface (BCI) enables direct communication between the brain and an external …
Brain-Computer Interface (BCI) enables direct communication between the brain and an external device. BCI systems have become a popular area of study in recent years. These technologies can be utilized in various ways to assist people with disabilities and healthy individuals. Regarding substantial BCI advancements, we can say that these systems are on the verge of commercialization. This review has considered current trends in BCI research on inclusive education to assist students with disabilities in achieving improved learning outcomes for all students in an inclusive environment.
The use of dendrochronology in determining the geologic history of a location. …
The use of dendrochronology in determining the geologic history of a location. The development of an understanding how tree growth can indicate the relationships between climate, geomorphology, ecology and archeology.
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Introduces the ethical dimension of finding, using, and sharing images in the …
Introduces the ethical dimension of finding, using, and sharing images in the context of the undergraduate research assignment. Students will understand the ethical aspects of finding, using, and sharing images; will engage with copyright issues and concepts of intellectual property; and will find and analyze specific images as examples.
This lab follows the second or third lecture on pollen analysis and …
This lab follows the second or third lecture on pollen analysis and Quaternary paleoecology. It should come after students have been introduced to pollen diagrams and covered such topics as: what is pollen, how are pollen grains dispersed, how are pollen records obtained from lakes and bogs, how are modern pollen data sets used to interpret fossil pollen data, and how are pollen diagrams designed and interpreted. This lab serves as an introduction to the pollen database available from NOAA National Climate Data Center World Data Center for Paleoclimatology (http://www.ncdc.noaa.gov/paleo/pollen.html ( This site may be offline. ) ). The lab allows students to browse the contents of the SiteSeer pollen data base, which contains site information and summary pollen diagrams. SiteSeer allows searching by Site Name or Contact Person. It also allows limited filtering of the data by Age, Range, Location, and Pollen taxon. SiteSeer is a teaching tool to explain how to use and interpret pollen data. With this familiarity, students can obtain up-to-date information on pollen sites and actual pollen data from the NCDC WDC web page, using the Data Search tool and Web Mapper. This lab exercise focuses on sites in the North American Pollen Data Base (NAPD), showing the many ways one might obtain this information. Working through a set of questions helps students understand the impressive pollen database available to study the vegetation history of North America.
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This case study is retrieved from the open book Open Data as …
This case study is retrieved from the open book Open Data as Open Educational Resources. Case studies of emerging practice.
It explores why and how open data can be used as a material with which to produce engaging challenges for students as they are introduced to programming. Through describing the process of producing the assignments, and learner responses to them, we suggest that open data is a powerful material for designing learning activities because of its qualities of ease of access and authenticity.
In two successive years, forms of open data were used to construct coursework assignments for postgraduate students at the University of Nottingham, UK. The rationale for using open data was to shift the focus towards an outward-looking approach to coding with networks, files and data structures, and to engage students in constructing applications that had real-world relevance.
Python was chosen as the programming language.
The assignment in the first year utilised e-book text files from Project Gutenberg1, and required students to build an e-reader application. In the next year, car park status data, which was made available in a regularly updated form by the city council through their open data initiative2 was used as the basis for an assignment in which students developed a city-wide car park monitoring application.
To prepare for this exercise, students do background reading (from journal articles …
To prepare for this exercise, students do background reading (from journal articles selected by instructor) and participate in classroom lectures about various types of qualitative and quantitative paleoclimate data (including rock/sed. type, stable isotopes, and fluid inclusions). Then, they are given the assignment and asked to complete it on their own (or in groups of two). The assignment consists of four paleotemperature curves. One curve is from the Vostok ice core of Antarctica and another represents the GRIP ice core from Greeenland (Jouzel et al., 1987, 1993; Chapellaz et al., 1997). Two halite cores, one from Death Valley and one from Chile, are also represented (Lowenstein et al., 1998, 1999; Hein, 2000). Students answer written questions that ask them to identify coldest and warmest times in the past 150,000 years, that ask them if cores can be correlated, that ask them if they can distinguish local, regional, and global warming and cooling trends. They are also asked how to better resolve paleoclimate data from this time period. The final questions ask students how confident they would feel about using this data to make paleoclimate predictions into the future. After the students have completed in turned in their assignment, we have a class discussion about the exercise, using the questions to guide us. This discussion can be supplemented with predictions from climate models and explanations of different types of paleoclimate data.
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The Data Management and Sharing Plan (DMSP) Tool, or DMPTool, is a …
The Data Management and Sharing Plan (DMSP) Tool, or DMPTool, is a free resource for anyone to use that helps researchers create data management sharing plans as they write their funding proposal.
By the end of this tutorial, you will be able to: - Log in to the DMPTool as an institutional affiliate. - Access and use existing data management plans and templates. - Identify project details for your plan that meet funder and institutional guidelines. - Identify research outputs needed to meet funder and institutional guidelines. - Request expert feedback for your plan.
Recall the steps to save, download, and submit your plan to your Research Administrator and submit updates as your project progresses.
This lesson is part of the Software Carpentry workshops that teach how …
This lesson is part of the Software Carpentry workshops that teach how to use version control with Git. Wolfman and Dracula have been hired by Universal Missions (a space services spinoff from Euphoric State University) to investigate if it is possible to send their next planetary lander to Mars. They want to be able to work on the plans at the same time, but they have run into problems doing this in the past. If they take turns, each one will spend a lot of time waiting for the other to finish, but if they work on their own copies and email changes back and forth things will be lost, overwritten, or duplicated. A colleague suggests using version control to manage their work. Version control is better than mailing files back and forth: Nothing that is committed to version control is ever lost, unless you work really, really hard at it. Since all old versions of files are saved, it’s always possible to go back in time to see exactly who wrote what on a particular day, or what version of a program was used to generate a particular set of results. As we have this record of who made what changes when, we know who to ask if we have questions later on, and, if needed, revert to a previous version, much like the “undo†feature in an editor. When several people collaborate in the same project, it’s possible to accidentally overlook or overwrite someone’s changes. The version control system automatically notifies users whenever there’s a conflict between one person’s work and another’s. Teams are not the only ones to benefit from version control: lone researchers can benefit immensely. Keeping a record of what was changed, when, and why is extremely useful for all researchers if they ever need to come back to the project later on (e.g., a year later, when memory has faded). Version control is the lab notebook of the digital world: it’s what professionals use to keep track of what they’ve done and to collaborate with other people. Every large software development project relies on it, and most programmers use it for their small jobs as well. And it isn’t just for software: books, papers, small data sets, and anything that changes over time or needs to be shared can and should be stored in a version control system.
This webinar will introduce the concept of version control and the version …
This webinar will introduce the concept of version control and the version control features that are built into 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 and Mendeley, to streamline workflows and increase efficiency. This webinar will discuss how keeping track of the different file versions is important for efficient reproducible research practices, how version control works on the OSF, and how researchers can view and download previous versions of files.
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