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Automated annotation in UniProt
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CC BY
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UniProt is a high quality, comprehensive protein resource in which the core activity is the expert review and annotation of proteins where the function has been experimentally investigated. At the same time the UniProt database contains large numbers of proteins which are predicted to exist from gene models, but which do not have associated experimental evidence indicating their function. UniProt commits significant resources to developing computational methods for functional annotation of these predicted proteins based on the data in entries that have gone through the expert review process.

We will describe the two main automated annotation systems currently in use. First, UniRule, which is an established UniProt system in which curators manually develop rules for annotation. Second ARBA (Association-Rule-Based Annotator), which has recently been introduced as a significant improvement in fully automated functional annotation. ARBA is a multiclass learning system which uses rule mining techniques to generate concise annotation models. ARBA employs a data exclusion set that censors data not suitable for computational annotation, and generates human-readable rules for each UniProt release.

We will also briefly touch on the mechanism UniProt has set up to enable researchers to run these automated annotation systems on their own protein datasets.

Who is this course for?
This webinar is for scientists and bioinformaticians with an interest in functional annotation of protein sequences.

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

Recall the role of UniProt's two main automated annotation systems
Describe how UniRule and ARBA work
Get started using these automated annotation systems

Subject:
Applied Science
Life Science
Material Type:
Lecture
Provider:
EMBL-EBI
Date Added:
01/14/2021
BA 213 - Principles of Accounting: Managerial
Unrestricted Use
CC BY
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This course demonstrates the use of accounting information to meet organization goals. Methods of extracting accounting information for decision making, management of resources, planning, and product and service costing are covered.

Course Outcomes:
1. Explain the interrelationship of the accounting systems to all areas of business and business decision making.
2. Understand cost behavior and predict break-even points.
3. Recognize the components and processes related to various cost accounting systems.
4. Analyze the performance of the organization and organizational sub-units.
5. Use the budgeting process to prepare budgets and pro forma financial statements.
6. Utilize the time-value-of-money concept to analyze capital investment projects.

Subject:
Accounting
Business and Communication
Material Type:
Full Course
Provider:
Linn-Benton Community College
Author:
Linn Benton Virtual College
Date Added:
07/09/2020
BARTy
Unrestricted Use
CC BY
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Modeling traffic data is important for urban planning, creating transportation systems, and even predicting how much foot traffic a retail store can expect in a given day. This genre of dynamic data science activities could be classified as “finding a needle in a haystack,” giving students a chance to mine big data to make insights about traffic use.

According to the Bay Area Rapid Transit District, about 400,000 people used the BART system daily in 2018. In BARTy, students investigate BART data from 2015 to learn about passenger use and explore traffic patterns. The Teacher Guide includes a game-like investigation to locate a “mystery meeting,” and suggests ways to help students figure out peak passenger use, popular stations, and the impact of events in San Francisco on BART usage.

Subject:
Mathematics
Measurement and Data
Statistics and Probability
Material Type:
Activity/Lab
Simulation
Author:
Concord Consortium
Date Added:
08/20/2020
BARTy
Unrestricted Use
CC BY
Rating
0.0 stars

Modeling traffic data is important for urban planning, creating transportation systems, and even predicting how much foot traffic a retail store can expect in a given day. This genre of dynamic data science activities could be classified as “finding a needle in a haystack,” giving students a chance to mine big data to make insights about traffic use. According to the Bay Area Rapid Transit District, about 400,000 people used the BART system daily in 2018. In BARTy, students investigate BART data from 2015 to learn about passenger use and explore traffic patterns.

Subject:
Applied Science
Mathematics
Material Type:
Activity/Lab
Provider:
Concord Consortium
Provider Set:
Concord Consortium
Author:
Concord Consortium
Date Added:
05/14/2021
The Babylonian mind
Conditional Remix & Share Permitted
CC BY-NC-SA
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Trace the legacy of Babylonian discoveries and ideas, including their mathematical system based on 60 and their desire to predict the future. With British Museum curator Irving Finkel. © Trustees of the British Museum. Created by British Museum.

Subject:
Art History
Arts and Humanities
Material Type:
Lesson
Provider:
Khan Academy
Provider Set:
British Museum
Author:
British Museum
Date Added:
08/04/2021
Backyard Weather Station
Read the Fine Print
Educational Use
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Students use their senses to describe what the weather is doing and predict what it might do next. After gaining a basic understanding of weather patterns, students act as state park engineers and design/build "backyard weather stations" to gather data to make actual weather forecasts.

Subject:
Applied Science
Atmospheric Science
Engineering
Physical Science
Material Type:
Activity/Lab
Provider:
TeachEngineering
Provider Set:
TeachEngineering
Author:
Janet Yowell
Lauren Cooper
Malinda Schaefer Zarske
Date Added:
10/14/2015
Bacterial density is an underreported metric in clinical gut microbiome research
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CC BY
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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:

"In ecology research, population density is an important metric for community analysis studies. Yet even though microbiomes are small ecosystems, microbiome studies rarely report the bacterial density. To evaluate the significance of bacterial density in gut microbiome research, a recent retrospective study examined rectal swabs from hospitalized patients. The authors found that bacterial density had important methodologic significance, as it predicted vulnerability to sequencing contamination. Specifically, low-bacterial-density specimens had higher levels of sequencing contamination. Clinical factors like age, exposure to antibiotics, and comorbidities also varied with bacterial density. Older patients and those with multiple co-morbidities had high bacterial density, while antibiotic exposure correlated with low density. Lastly, bacterial density showed potential as a prognostic indicator, as the density at time of admission correlated with subsequent infection..."

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

Subject:
Biology
Life Science
Material Type:
Diagram/Illustration
Reading
Provider:
Research Square
Provider Set:
Video Bytes
Date Added:
05/17/2022
Bad Date
Read the Fine Print
Some Rights Reserved
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True love has the right ratio. In this humorous animation, the number of words spoken by each partner predicts whether a date goes well or horribly. What do you do when someone asks if you listen to country music backwards, but won't let you get a word in edgewise?

Subject:
Mathematics
Material Type:
Lecture
Provider:
Learning Games Lab
Author:
NMSU Learning Games Lab
Date Added:
07/15/2015
The Beat Goes On
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Educational Use
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In this activity, students learn about their heart rate and different ways it can be measured. Students construct a simple measurement device using clay and a toothpick, and then use this device to measure their heart rate under different circumstances (i.e., sitting, standing and jumping). Students make predictions and record data on a worksheet.

Subject:
Applied Science
Engineering
Health, Medicine and Nursing
Material Type:
Activity/Lab
Provider:
TeachEngineering
Provider Set:
TeachEngineering
Author:
Denali Lander
Janet Yowell
Jessica Todd
Malinda Schaefer Zarske
Sara Born
Date Added:
09/18/2014
The Beauty of Data Visualization
Only Sharing Permitted
CC BY-NC-ND
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David McCandless turns complex data sets (like worldwide military spending, media buzz, Facebook status updates) into beautiful, simple diagrams that tease out unseen patterns and connections. Good design, he suggests, is the best way to navigate information glut -- and it may just change the way we see the world. A quiz, thought provoking question, and links for further study are provided to create a lesson around the 18-minute video. Educators may use the platform to easily "Flip" or create their own lesson for use with their students of any age or level.

Subject:
Business and Communication
Journalism
Material Type:
Lecture
Provider:
TED
Provider Set:
TED-Ed
Author:
David McCandless
Date Added:
08/23/2010
Bedform mapping in a coastal environment
Conditional Remix & Share Permitted
CC BY-NC-SA
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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.

(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.)

Subject:
Biology
Life Science
Material Type:
Activity/Lab
Module
Provider:
Science Education Resource Center (SERC) at Carleton College
Provider Set:
Teach the Earth
Author:
Peter Lea
Date Added:
09/23/2022
Bedforms to Facies to Prediction: Walther's Law and Sequence Stratigraphic Analysis, Blackhawk Formation, Utah
Conditional Remix & Share Permitted
CC BY-NC-SA
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Students are given the task of predicting where parasequence boundaries would exist within a vertical section of the Blackhawk Formation, Utah. This activity challenges students to apply their knowledge of bedforms in order to interpret the facies they observe. The students work in groups of two as they make their observations. The vertical section consists of four main outcrops to be observed by the students. After making their observations and interpretations of these four outcrops, the students then make predictions of what should be found up section. Students begin down section by observing the lowest section of the four outcrops. The students make observations about lithology, grain size, sedimentary structures and trace fossils. After recording their observations in their field notebook the class gathers for a discussion. Students are called on randomly to discuss what they observed. The class creates a group stratigraphic column on a white board and includes their observations to the right of the drawn profile. They are then asked to interpret what facies these observations represent. The students defend their interpretations and, as a group, agree upon an interpretation. The facies interpretation is then added to the white board and the group moves to the next outcrop up section. After observing, describing and interpreting each of the four outcrops the students are challenged to use all of the information gathered thus far to predict what facies should be observed further up section. This exercise provides an opportunity for the students to make and defend observations and interpretations. They also get a sense for the importance of Walther's Law and how it relates to sequence stratigraphy.

(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.)

Subject:
Biology
Life Science
Mathematics
Measurement and Data
Statistics and Probability
Material Type:
Activity/Lab
Provider:
Science Education Resource Center (SERC) at Carleton College
Provider Set:
Teach the Earth
Author:
Tom Morris
Date Added:
08/20/2020
Beetle Outbreaks and Climate Change
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This interactive shows the extent of the killing of lodgepole pine trees in western Canada. The spread of pine beetle throughout British Columbia has devastated the lodgepole pine forests there. This animation shows the spread of the beetle and the increasing numbers of trees affected from 1999-2008 and predicts the spread up until 2015.

Subject:
Life Science
Provider:
CLEAN: Climate Literacy and Energy Awareness Network
Provider Set:
CLEAN: Climate Literacy and Energy Awareness Network
Author:
American Museum of Natural History
Date Added:
10/27/2014
Big Data, What Are You Saying?
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Educational Use
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Students act as R&D entrepreneurs, learning ways to research variables affecting the market of their proposed (hypothetical) products. They learn how to obtain numeric data using a variety of Internet tools and resources, sort and analyze the data using Excel and other software, and discover patterns and relationships that influence and guide decisions related to launching their products. First, student pairs research and collect pertinent consumer data, importing the data into spreadsheets. Then they clean, organize, chart and analyze the data to inform their product production and marketing plans. They calculate related statistics and gain proficiency in obtaining and finding relationships between variables, which is important in the work of engineers as well as for general technical literacy and decision-making. They summarize their work by suggesting product launch strategies and reporting their findings and conclusions in class presentations. A finding data tips handout, project/presentation grading rubric and alternative self-guided activity worksheet are provided. This activity is ideal for a high school statistics class.

Subject:
Mathematics
Statistics and Probability
Material Type:
Activity/Lab
Provider:
TeachEngineering
Provider Set:
Activities
Author:
Tom Falcone
Date Added:
05/03/2017
Billion-Dollar Weather and Climate Disasters
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This set of interactive data visualizations show the weather and climate events that have had the greatest economic impact on the US from 1980 to 2016.

Subject:
Applied Science
Atmospheric Science
Career and Technical Education
Economics
Environmental Science
Environmental Studies
Physical Science
Social Science
Provider:
CLEAN: Climate Literacy and Energy Awareness Network
Provider Set:
CLEAN: Climate Literacy and Energy Awareness Network
Author:
NOAA
National Center for Environmental Education
Date Added:
09/24/2018
Bioinformatics II Lab
Conditional Remix & Share Permitted
CC BY-NC-SA
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This course is a continuation of Bioinformatics I. Topics include gene expression, microarrays, next- generation sequencing methods, RNA-seq, large genomic projects, protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; and protein-nucleic acid interactions. The lab component includes R-based statistical data analysis on large datasets, introduction to big data analysis tools, protein visualization software, internet-based tools and high-level programming languages.

Subject:
Biology
Life Science
Material Type:
Activity/Lab
Full Course
Provider:
CUNY
Provider Set:
New York City College of Technology
Author:
Eugenia Giannopoulou
Date Added:
06/16/2022
Biology
Unrestricted Use
CC BY
Rating
0.0 stars

Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

Subject:
Biology
Life Science
Material Type:
Full Course
Provider:
Rice University
Provider Set:
OpenStax College
Date Added:
08/22/2012
Biology, Ecology, Conservation Biology and Biodiversity, Threats to Biodiversity
Conditional Remix & Share Permitted
CC BY-NC
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By the end of this section, you will be able to:Identify significant threats to biodiversityExplain the effects of habitat loss, exotic species, and hunting on biodiversityIdentify the early and predicted effects of climate change on biodiversity

Subject:
Applied Science
Biology
Life Science
Material Type:
Module
Date Added:
07/10/2017