To prepare for this activity, students receive background on bedforms and flow regimes in class and practice identifying and classifying bedforms from field photographs. Students are then given a map of a barrier beach/inlet/tidal delta complex in mid-coast Maine and asked to predict what bedforms they expect to find in specific sub-environments. During a subsequent field trip to the area, students observe, classify and map bedforms and relate them qualitatively to formative flows. Qualitative description and classification are supplemented by quantitative measurements of bedform morphology and orientation, and by GPS-located digital photographs. After the trip, students compare their predictions and observations of bedforms in the sub-environments, reflecting on the reasons for the differences and the evolution of their thinking. The exercise also serves to set the stage for subsequent quantitative studies of bedforms and bedload transport, as well as interpretation of sedimentary structures and clastic depositional environments in the geological record.

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In this exercise, students will use the Neotoma database and ArcGIS Online to create a distribution map of modern collection localities of beetle taxa associated with an assemblage of fossil beetles from the Conklin Quarry site in eastern Iowa.

a data rich exercise to help students discover how organisms move in response to climate change

(Note: this resource was added to OER Commons as part of a batch upload of over 2,200 records. If you notice an issue with the quality of the metadata, please let us know by using the 'report' button and we will flag it for consideration.)

Begin Research“Where Do I Start?”Do you have an assignment to write a research paper but you’re not sure where to start? Take a deep breath and begin by carefully reading the assignment requirements. This will help you understand the work you need to do.First, let’s think about what we mean when we say “research.”HOW MUCH DO YOU ALREADY KNOW?What makes a good topic?It is broad enough that you can find enough information on the subject.It is focused enough that you are not overwhelmed with too much information.The topic is interesting to you.All of the above.If you don’t know much about your topic, what resources would be most helpful when you being your research?Encyclopedias and websitesScholarly articlesNewspapers and magazinesStatistical informationIt is always a good idea to brainstorm different words for similar ideas when you first begin to research your topic.TrueFalseWhat statement below is generally true about beginning research?It is pretty easy to find information on any topic.As long as you have a good topic, researching for it will not take a long time.No matter t he assignment, good research takes time and effort.None of the above.ANSWERSAll of the above.2.1True4.3Read Your Assignment CarefullyBefore you can even begin your research, though, you need to read the assignment instructions carefully—more than once! This will help you understand the work you need to do.Highlight topic guidelines, required length, and the types of information sources allowed.Let’s take a look at a sample assignment.UNDERSTAND YOUR ASSIGNMENTLily is taking a University Studies class and must complete this assignment:In this paper, you will analyze the scientific aspects of a known environmental problem and identify and discuss at least two proposed solutions.Now, analyze this assignment step by step.Find the words that tell you what to do (think verbs!): analyze, identify, and discuss.Find the limits of the assignment: scientific aspects and two proposed solutions.Find the key theme: a known environmental problemBy reading the assignment carefully, we know that Lily has to analyze an environmental problem and identify and discuss at least two proposed solutions.Pick a Good TopicLily’s assignment is broad enough to give her some choices when picking a topic. So, what makes a good topic?It interests you! You’ll enjoy it and do a better job.It meets the requirements of your assignment.It’s broad enough to give you several search options.It’s focused enough that you’re not overwhelmed with information.HOT TIP!Explore the library’s databases to get you started.Browse newspapers and news sources.Talk to your instructors and fellow students.Consult with a librarian.TOO BROAD, TOO NARROW, OR JUST RIGHT?Air pollution in urban areasToo broadToo narrowJust rightRespiratory diseases in children in high-density urban areasToo broadToo narrowJust rightEnvironmental consequences of California’s October 2007 forest firesToo broadToo narrowJust rightPolar bear adaptation to global warming in the ArcticToo broadToo narrowJust rightRenewable energy in the United StatesToo broadToo narrowJust rightThe design and implementation of Cal-Cars—the California Cars InitiativeToo broadToo narrowJust rightANSWERSToo broad. You’d need to identify an aspect of air pollution to narrow down the scopeJust right! This is a good topic. You’ll continue to refine your ideas as you learn more about the topic.A bit narrow. It will be hard to find information on just one event. Look more broadly for information on forest fires in California or the West.Just right. There should be just enough information to get you started. You will continue to refine your ideas as you learn more about the topic.Too broad. This is a good starting place, but you’d want to focus the topic by selecting a specific renewable energy like solar power or wind.Too narrow. It’s going to be difficult to find information on such a narrow topic. Broaden the focus to look at initiatives like this one that are less regional.Identify Potential IdeasNow it’s time to really focus your topic. Browse a few resources for ideas and identify different aspects of the topic.Remember, if you pick a subject that interests you, you’ll enjoy the research process much more!Customize Your TopicLet’s say your assignment is to research an environmental issue. This is a broad starting point, which is a normal first step.One way to customize your topic is to consider how different disciplines approach the same topic in different ways. For example, here’s how your broad topic of “environmental issues” might be approached from different perspectives.Social Sciences: Economics of Using Wind to Produce Energy in the United StatesSciences: Impact of Climate Change on the Habitat of Desert Animals in ArizonaArts and Humanities: Analysis of the Rhetoric of Environmental Protest LiteratureTurn Your Topic into a QuestionWhen you’ve chosen a topic, it’s time to ask some questions. Using “environmental issues” as our general research interest, let’s ask some questions about environmental issues and agriculture.How: How do government agricultural subsidies impact the price of food?  How does the use of pesticides affect food safety?Who: Consumers, farmers, farm workersWhat: Food safety, pesticides, food prices, genetically modified food, organic farmingWhere: United States, developing nations, European UnionWhy: Why does the European Union ban the sale and distribution of genetically modified food?What’s Your Angle?Let’s say that the most interesting question that emerged from the last exercise was: “How does repeated pesticide use in agriculture impact soil and groundwater pollution?”Find Your KeywordsNow that we have our sample research question, we need to identify the key concepts and their related keywords.Using our research question, “How does repeated pesticide use in agriculture impact soil and groundwater pollution?” we might consider these keywords:A SYMPHONY OF SYNONYMSLet’s examine our research question again:How does repeated pesticide use in agriculture impact soil and groundwater pollution?Now analyze this assignment step by step:Find important words and phrases that describe this topic (you can ignore common words that don’t have a lot of meaning, such as prepositions, articles, and adjectives): pesticide, agriculture, soil, and pollution.Now, think of some synonyms for the keywords you found:pesticideagrochemicals, pest management, weed management,diazinan, malathionagriculturefarming, food crops, specific types of cropssoilclay, organic componentsgroundwater watershed, water resources, water table, aquaticspollutionenvironmental impact, degradation, exposure, acid rainWhy are synonyms necessary? You’ll often need to search for different words relating to the same concept.Dive Into a Sea of Resources!Browse through general sources to get familiar with your topic. You will find many sources for locating background information. Remember our point from earlier in this tutorial: the source you select will determine what you find. Make sure you spend your time looking in the right places.HOT TIP!Is there enough info on your topic? If not, review the earlier steps for starting your research. It’s normal to refine and revise your topic multiple times.What Do You Know?Once you’ve established your focused topic, you need to get familiar with it by doing some reading. Start with more general sources and then work up to more specific and detailed sources. Where you go next depends on how much you know.So, just how much do you know about your topic?Not All That MuchI’ve Got the BasicsI’m Ready for DetailsSounds like you need the type of information typically found in encyclopedias and websites.Sounds like you’ve got a basic understanding of your topic and just need to learn more. Check out books, magazines, and newspapers.Specific information is what you need. You’ll want to find relevant scholarly articles, statistical sources, and government publications.Matching Resources to Your Information NeedNewspaper: Current regional or local informationScholarly journal article: Detailed analysis of a complex problem.Book or book chapter: Summary of what is known about a topic.Encyclopedia or website: Factual information like names, dates, and definitions.TEST YOURSELF: WHAT HAVE YOU LEARNED?What are the characteristics of a good topic?(Select all that apply) It interests you.It meets the requirements of your assignment.It’s broad enough to give you several search options.It’s focused enough that you’re not overwhelmed with information.Rank the following questions in order from most general to most specific (1 being the most general):Are pesticides bad?Do video games cause violent behavior in adolescent males?Are agricultural workers in Mexico at a higher risk of health problems due to pesticide exposure because of lax government safety standards?Is there a relationship between fast food consumption and obesity?What is the best way to focus  your topic?Think about the discipline that you are researching for.Tailor your topic to the requirements of your assignment.Talk to a librarian about the resources that are available for your topic.All of the above.Pick the best set of keywords to begin searching for information on global warming.Rising ocean levels, air pollution, greenhouse gasesBiodiversity, atmospheric temperature, ozone layerGlobal climate change, greenhouse effect, atmospheric carbon dioxideEnvironment sustainability, alternative energy, biofuelsWhy is it a good idea to use different words to describe similar ideas when you are beginning research?(Select all that apply) Because there is only one right answer and you can find it by trial and error.Because  using different words will help you cast a broader net than just using the same term over and over.Different researchers might use different terms to describe the same idea.You might spell some of the words wrong and not get any results.What is the most difficult aspect of beginning to research a topic that you don’t know very much about?You don’t know enough about the topic to know what is important and what is not.You don’t understand the technical aspects of the topic.It takes a lot of time to do research.All of the above.For you, what the most difficult part about beginning your research?ANSWERSA good topic will incorporate all these characteristics.1 = Are pesticides bad?2 = Is there a relationship between fast food consumption and obesity?3 = Do video games cause violent behavior in adolescent males?4 = Are agricultural workers in Mexico at a higher risk of health problems due to pesticide exposure because of lax government safety standards?The more a research question incorporates the concepts of Who, What, When, Where, Why, and  How the more specific it will be.All of the above.4.3; think carefully about which terms are closely related to global warming.5.2 and 5.3; there may be many ways to describe a single topic. Using as many related words as possible will help you find the most information!All of the above; remember that research takes time and energy and isn’t an easy thing to do!No matter what, coming to the library and talking to a librarian will help you get started. Finding information effectively and efficientlyLevel 2 teaches you how to structure a search for the information you need to write a paper, for example. You will learn the following:how to construct a search strategy using the aspects defined in level 1how to perform a smart search using the information sources available at TU Delft LibraryDetermining search termsNow it is time to do an actual search! In level 1 you divided the search topic into its different aspects. What’s next? Are you going to use Google and type in all the aspects, like you probably do every day? What will you do with all the search results? Are you going to study them all? No, there is a smarter way!Exercise 1Plug in your earphones or turn down the volume and watch the clip ‘Web Search Strategies Explained in Plain English‘ by Commoncraft about smart searching on the web.Searching the web is very similar to searching other information sources such as Worldcat Discovery. Doing the following exercise will teach you how to apply the aspects of your search topic in a smart search. Complete the exercise on how to find suitable search terms matching the aspects of the search topic. Determining search strategyNow you are going to convert the synonyms you have found into a smart search strategy. You have to use search operators to use all the synonyms properly.Exercise 2Study the TUlib module Search operators.If you want to perform a smart search, you must combine your search terms. Complete thisexercise on combining search terms with Boolean operators.Towards information sourcesNow you have formulated a search strategy, which you will use to search the various information sources. But where to start? How do you choose which information source you want to use? This table gives an overview of the differences between Worldcat Discovery, Scopus and Google Scholar and helps you determine when to use each one.Exercise 3Watch the first two sections (“Basic searching” and “Retrieving documents”) of this video about searching in WorldCat Discovery (which includes the TU Delft Library catalogue).Watch this video with an example of a search strategy carried out in article database Scopus.Complete the exercise on carrying out your search strategy in various information sources.Now you have learned how to convert the aspects of your search topic into a search strategy and how to apply this strategy in a number of information sources.You can find other relevant information sources for your subject area in the “Useful links” overview in the section “What’s next”.

This is an activity that involves students modeling the behavior and competition that Charles Darwin's finches would have gone through as they competed for food and space on the Galapagos Islands. Some will survive. Some won't.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Plants lack the nervous system of animals and are usually firmly rooted in the ground, making it easy to think of them as being unaware of the world around them. But evidence suggests that plants can indeed sense and actively respond to their environment. When under attack by microbial pathogens, some plants have been shown to recruit beneficial microbes to aid in their defense. A recent study uncovered this phenomenon in tangerine trees infected with the fungus that causes melanose, one of the most destructive diseases of citrus plants worldwide. Researchers identified the microorganisms living on infected and uninfected leaves with both culture-based and DNA sequencing techniques. They found that the infected and uninfected leaves hosted distinct microbial communities, with the microbes occupying infected leaves having beneficial and antifungal characteristics..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Students toss coins to determine what traits a set of mouse parents possess, such as fur color, body size, heat tolerance, and running speed. Then they use coin tossing to determine the traits a mouse pup born to these parents possesses. Then they compare these physical features to features that would be most adaptive in several different environmental conditions. Finally, students consider what would happen to the mouse offspring if those environmental conditions were to change: which mice would be most likely to survive and produce the next generation?

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Next-generation sequencing (NGS) studies have led to dramatic improvements in our understanding of human microbiomes. However, this method is based on the presence of DNA and cannot distinguish between living and dead microbes on its own. Environments like our skin are hostile and have high microbe turnover, which leads to significant amounts of DNA from dead microbes, which can lead to inaccurate community estimations in NGS studies. To overcome this, researchers tested the feasibility of pre-treatment with Benzonase to digest unprotected DNA. They used both mock bacterial communities and skin microbiome samples with inactivated bacteria or bacteria-free DNA spiked-in. Benzonase (BDA) pre-treatment reduced the levels of DNA from dead bacteria in both mock and natural communities. It also reduced the amount of host DNA in samples with high human-to-microbial DNA ratios without obvious impact on the microbial profile..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Metagenomic analysis frequently plays an important role in development pipelines for human fecal microbiome-related products, but validation and standardization of the methods used to extract DNA and assemble sequence libraries for these studies is currently lacking. To close this gap, researchers recently characterized existing protocols for accuracy and precision. First, they tested the quantification accuracy by using a defined mock community of bacteria. Then, the protocols that performed as expected were evaluated for both within- and inter-laboratory precision metrics. The protocols were also tested against the MOSAIC Standards Challenge samples. Lastly, they defined performance metrics for the recommended protocols to provide best-practice guidance. The uptake of the recommendations generated here should improve reproducibility in human metagenomic research and therefore facilitate development and commercialization of human microbiome-related products..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"HIV infection remains unacceptably common among women in sub-Saharan Africa. One possible contributing factor is the composition of the vaginal microbiota, as African, Caribbean and other Black (ACB) women have an increased rate of bacterial vaginosis (BV), which is associated with increased HIV risk. Targeting the vaginal microbiota and treating BV could help prevent HIV among women. In the absence of BV, the vaginal microbiota is predominated by one of several _Lactobacillus_ species that provide different levels of BV and HIV protection. _L. crispatus_ is associated with exclusion of BV-associated bacteria and reduced HIV risk while _L. iners_, the most common species among ACB women, seems less protective. The reduced protection provided by _L. iners_ is supported by genomic differences, such as the absence of a gene encoding an HIV-trapping D-lactate isomer and the presence of genes encoding pro-inflammatory cytotoxins..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Students act as if they are biological engineers following the steps of the engineering design process to design and create protein models to replace the defective proteins in a child’s body. Jumping off from a basic understanding of DNA and its transcription and translation processes, students learn about the many different proteins types and what happens if protein mutations occur. Then they focus on structural, transport and defense proteins during three challenges posed by the R&D; bio-engineering hypothetical scenario. Using common classroom supplies such as paper, tape and craft sticks, student pairs design, sketch, build, test and improve their own protein models to meet specific functional requirements: to strengthen bones (collagen), to capture oxygen molecules (hemoglobin) and to capture bacteria (antibody). By designing and testing physical models to accomplish certain functional requirements, students come to understand the relationship between protein structure and function. They graph and analyze the class data, then share and compare results across all teams to determine which models were the most successful. Includes a quiz, three worksheets and a reference sheet.

Bioethics is the study of the moral implications of new and emerging medical technologies and looks to answer questions such as selling organs, euthanasia and whether should we clone people. The series consists of a series of interviews by leading bioethics academics and is aimed at individuals looking to explore often difficult and confusing questions surrounding medical ethics. The series lays out the issue in a clear and precise way and looks to show all sides of the debate.

The course Bio-Inspired Design gives an overview of non-conventional mechanical approaches in nature and shows how this knowledge can lead to more creativity in mechanical design and to better (simpler, smaller, more robust) solutions than with conventional technology. The course discusses a large number of biological organisms with smart constructions, unusual mechanisms or clever sensing and processing methods and presents a number of technical examples and designs of bio-inspired instruments and machines.

This quick tour provides a brief introduction to EMBL-EBI’s resource of mathematical models of biological/biomedical systems.

By the end of the course you will be able to:
Identify how mathematical models are used in investigating the mechanism underlying biological systems and why do we need them.
Explore the content, features, functionality and use of BioModels
Determine where to find out more about BioModels Database

This quick tour provides a brief introduction to BioSamples data resource, the EMBL-EBI resource that stores and supplies descriptions and metadata about biological samples.

By the end of the course you will be able to:
Describe the role of BioSamples
Navigate the BioSamples website
Describe where to find out more about BioSamples

BioSamples is the EMBL-EBI archive which records and supplies metadata about biological samples and connects sample records across EBI databases to the corresponding experimental data. BioSamples aims to improve metadata quality through ontology annotation, metadata curation, data validation and certification.

In this webinar, we will briefly introduce BioSamples and highlight specific use cases from current collaborations and features deployed to increase FAIRness (Findability, Accessibility, Interoperability, Reusability) of the data.

Ongoing collaboration with major consortia rely on and drive addition of new features to BioSamples:

Ability to walk an ontology hierarchy such as disease for the Global Alliance for Genomics and Health (GA4GH)
Synthetic dataset and linking to human controlled access data for the Common Infrastructure for National Cohorts in Europe, Canada, and Africa (CINECA)
Metrics and automated processes for FAIRplus
Who is this course for?
Biologists and bioinformaticians who are interested in sample metadata and FAIR practices.

Outcomes
By the end of the webinar you will be able to:

Describe the role of BioSamples
Recall use cases that increase FAIRness of data

Patterns of diversity, ecology, and evolutionary biology. Emphasis is on the Tree of Life and how its members are distributed and interact. Partial Course.

The goal of the BioStudies database is to facilitate transparency and reproducibility of research by aggregating all the outputs of a study (a ‘data package’) in a single place. A data package consists of the overall biological study description (metadata), links to data generated in this study in key community databases at EMBL-EBI and elsewhere, as well as “orphan data” such as supplemental data. The database can accept a wide range of types of studies described via a simple format and does not impose minimum requirements outside those agreed by the respective community.

In this webinar we will introduce the basic principles of BioStudies, explore data access and data deposition interfaces, as well as briefly consider some more advanced topics such as use of BioStudies for data sharing in an ongoing project.

Who is this course for?
No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.

Although we've spent a lot of time in this series looking at human-made organic chemicals, the term "organic chemistry" was originally used to describe molecules isolated from living things. In this episode of Crash Course Organic Chemistry, we're going back to our roots to learn more about the best synthetic chemists: living things. We'll look at the biochemical building blocks of life from the nitrogenous bases, sugars, and phosphate groups that make up DNA and RNA, to amino acids and lipids, and we'll learn how to convert between Fischer and Haworth projections of carbohydrates.

We are happy to welcome you to our second Open Educational Resource (OER) textbook, Biochemistry Free For All. Biochemistry is a relatively young science, but its rate of growth has been truly impressive. The rapid pace of discoveries, which shows no sign of slowing, is reflected in the steady increase in the size of biochemistry textbooks. Growing faster than the size of biochemistry books have been the skyrocketing costs of higher education and the even faster rising costs of college textbooks. These unfortunate realities have created a situation where the costs of going to college are beyond the means of increasing numbers of students.

The course, which spans two thirds of a semester, provides students with a research-inspired laboratory experience that introduces standard biochemical techniques in the context of investigating a current and exciting research topic, acquired resistance to the cancer drug Gleevec. Techniques include protein expression, purification, and gel analysis, PCR, site-directed mutagenesis, kinase activity assays, and protein structure viewing.
This class is part of the new laboratory curriculum in the MIT Department of Chemistry. Undergraduate Research-Inspired Experimental Chemistry Alternatives (URIECA) introduces students to cutting edge research topics in a modular format.
Acknowledgments
Development of this course was funded through an HHMI Professors grant to Professor Catherine L. Drennan.