The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects in much the same sense as fossil bones or dried specimens: they can be archived, studied, and displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate designation for the collection of displays that we are assembling. The OMM's exhibits are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand.

Why devote a site to detailed visualizations of different macromolecules? In learning about the intricacies of life processes at the molecular level, it is important to understand how natural selection has fashioned the structure and chemistry of macromolecular machines to suit them for particular functions. This understanding is greatly facilitated by the visualization of 3-dimensional structure, when known. So, if static views of molecules (even in stereo) are worth a thousand words, then interactive animations of molecules should be worth much more. Indeed, we have found the types of displays represented here invaluable in gaining an appreciation for the details of key biochemical processes.

As Carl Brandon and John Tooze stated in their classic text, Introduction to Protein Structure:
"Molecular biology began some 40 years ago with the realization that structure was crucial for a proper understanding of function. Paradoxically, the dazzling achievements of molecular genetics and biochemistry led to the eclipse of structural studies. We believe the wheel has now come full circle, and those very achievements have increased the need for structural analysis at the same time that they have provided the means for it."

It is our opinion that structural analysis should extend into the classroom: as students learn about cellular mechanisms it is important that they study the chemistry of the molecular machines involved. These considerations have motivated the construction of the OMM.

The OMM is part of a collaborative effort by faculty and students interested in macromolecular structure-function relationships. The primary authors of some tutorials are students of David Marcey and he serves as author, co-author and site editor, and assumes all responsibility for content. Any criticisms, suggestions, comments, or questions should be sent to him at: marcey@callutheran.edu. All tutorials are copyrighted.

The OMM was started in 1996 for a Molecular Biology class at Kenyon College, where DM was a professor in the Biology Department (1990-1999). The OMM is now developed and housed at California Lutheran University, where DM has been a professor since 1999.

Like in Output Data as HTML File, this lesson takes the frequency pairs collected in Counting Frequencies and outputs them in HTML. This time the focus is on keywords in context (KWIC) which creates n-grams from the original document content – in this case a trial transcript from the Old Bailey Online. You can use your program to select a keyword and the computer will output all instances of that keyword, along with the words to the left and right of it, making it easy to see at a glance how the keyword is used.

Once the KWICs have been created, they are then wrapped in HTML and sent to the browser where they can be viewed. This reinforces what was learned in Output Data as HTML File, opting for a slightly different output.

At the end of this lesson, you will be able to extract all possible n-grams from the text. In the next lesson, you will be learn how to output all of the n-grams of a given keyword in a document downloaded from the Internet, and display them clearly in your browser window.

RStudio Cheatsheets

The cheatsheets below make it easy to use some of our favorite packages. Cheatsheets include the following topics:

Python with R and Reticulate Cheatsheet
The reticulate package provides a comprehensive set of tools for interoperability between Python and R. With reticulate, you can call Python from R in a variety of ways including importing Python modules into R scripts, writing R Markdown Python chunks, sourcing Python scripts, and using Python interactively within the RStudio IDE. This cheatsheet will remind you how.

Factors with forcats Cheatsheet
Factors are R’s data structure for categorical data. The forcats package makes it easy to work with factors. This cheatsheet reminds you how to make factors, reorder their levels, recode their values, and more.

Tidy Evaluation with rlang Cheatsheet
Tidy Evaluation (Tidy Eval) is a framework for doing non-standard evaluation in R that makes it easier to program with tidyverse functions. Non-standard evaluation, better thought of as “delayed evaluation,” lets you capture a user’s R code to run later in a new environment or against a new data frame. The tidy evaluation framework is implemented by the rlang package and used by functions throughout the tidyverse.

Deep Learning with Keras Cheatsheet
Keras is a high-level neural networks API developed with a focus on enabling fast experimentation. Keras supports both convolution based networks and recurrent networks (as well as combinations of the two), runs seamlessly on both CPU and GPU devices, and is capable of running on top of multiple back-ends including TensorFlow, CNTK, and Theano.

Dates and Times Cheatsheet
Lubridate makes it easier to work with dates and times in R. This lubridate cheatsheet covers how to round dates, work with time zones, extract elements of a date or time, parse dates into R and more. The back of the cheatsheet describes lubridate’s three timespan classes: periods, durations, and intervals; and explains how to do math with date-times.

Work with Strings Cheatsheet
The stringr package provides an easy to use toolkit for working with strings, i.e. character data, in R. This cheatsheet guides you through stringr’s functions for manipulating strings. The back page provides a concise reference to regular expresssions, a mini-language for describing, finding, and matching patterns in strings.

Apply Functions Cheatsheet
The purrr package makes it easy to work with lists and functions. This cheatsheet will remind you how to manipulate lists with purrr as well as how to apply functions iteratively to each element of a list or vector. The back of the cheatsheet explains how to work with list-columns. With list columns, you can use a simple data frame to organize any collection of objects in R.

Data Import Cheatsheet
The Data Import cheatsheet reminds you how to read in flat files with http://readr.tidyverse.org/, work with the results as tibbles, and reshape messy data with tidyr. Use tidyr to reshape your tables into tidy data, the data format that works the most seamlessly with R and the tidyverse.

Data Transformation Cheatsheet
dplyr provides a grammar for manipulating tables in R. This cheatsheet will guide you through the grammar, reminding you how to select, filter, arrange, mutate, summarise, group, and join data frames and tibbles.

Sparklyr Cheatsheet
Sparklyr provides an R interface to Apache Spark, a fast and general engine for processing Big Data. With sparklyr, you can connect to a local or remote Spark session, use dplyr to manipulate data in Spark, and run Spark’s built in machine learning algorithms.

R Markdown Cheatsheet
R Markdown is an authoring format that makes it easy to write reusable reports with R. You combine your R code with narration written in markdown (an easy-to-write plain text format) and then export the results as an html, pdf, or Word file. You can even use R Markdown to build interactive documents and slideshows.

RStudio IDE Cheatsheet
The RStudio IDE is the most popular integrated development environment for R. Do you want to write, run, and debug your own R code? Work collaboratively on R projects with version control? Build packages or create documents and apps? No matter what you do with R, the RStudio IDE can help you do it faster. This cheatsheet will guide you through the most useful features of the IDE, as well as the long list of keyboard shortcuts built into the RStudio IDE.

Shiny Cheatsheet
If you’re ready to build interactive web apps with R, say hello to Shiny. This cheatsheet provides a tour of the Shiny package and explains how to build and customize an interactive app. Be sure to follow the links on the sheet for even more information.

Data Visualization Cheatsheet
The ggplot2 package lets you make beautiful and customizable plots of your data. It implements the grammar of graphics, an easy to use system for building plots. See docs.ggplot2.org for detailed examples.

Package Development Cheatsheet
The devtools package makes it easy to build your own R packages, and packages make it easy to share your R code. Supplement this cheatsheet with r-pkgs.had.co.nz, Hadley’s book on package development.

This reading anthology is a curated collection of openly licensed full-text essays and stories on a variety of subjects, designed to be used for discussions and writing assignments. The anthology is organized according to three levels of reading difficulty, but instructors can easily mix and match reading selections.

Utilize the online GIS of the USGS real-time stream gage network to introduce basic concepts of data-driven maps and GIS. This exercise can be used independently or with other hydrology exercises.

(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.)

Abstract: Authoring America: A Survey of American Literature from Its Beginnings to 2020 is a five-volume, completely-open anthology that features full text by over 100 authors. From Native American tales of origins to the latest poem read at a presidential inauguration, the selections represent the diverse voices in American literature. This anthology charts the development of the literary production in the United States, highlighting the writers who influenced and authored American letters.

Volume 1 was developed as an adaptation of the textbook "Becoming America: An Exploration of American Literature from Precolonial to Post-Revolution" by Wendy Kurant, developed at the University of Georgia and the Galileo Open Learning Materials program.

Volumes 2-5 were developed as an adaptation of the textbook Writing the Nation a Concise Introduction… by Amy Berke, Robert Bleil, Jordan Cofer and Doug Davis, developed at the University of Georgia and the Galileo Open Learning Materials program. In volumes 4-5, copyrighted materials are linked to the University of Delaware Library's collections. Others using these volumes should check with their librarians to see if these materials are available and can be linked.

Description: Features: Contextualizing introductions to the major literary periods, over 100 historical images, and In-depth biographies of each author.

This collection of Victorian Poetry and Fiction on the Great Writers Inspire site includes a selection of writers we feel to be particularly inspiring in an age dominated by authors and literature. It includes audio and video lectures and short talks, downloadable electronic texts and eBooks, and background contextual resources curated by specialists at the University of Oxford. This landing page allows users to explore topics such as The Victorian Gothic, Victorian Publishing History, Literature and Religion as well as majors authors.

In this engaging unit, students will design and plant a square-foot garden that will be their central tool. Through the growing season, they will explore nutrition content in their everyday lives and see how it relates to what they are growing.

This paper addresses the implications, for ELLs, of the new standard's requirement that students be able to read and understand complex, informationally dense texts. The authors discuss the types of supports that learners need in order to work with complex texts. They also provide a sample of what academic discourse involves, using an excerpt from Martin Luther King, Jr.'s Letter from Birmingham Jail. They demonstrate how English learners can be provided with strategies for accessing complex texts, such as closely examining one sentence at a time. The authors argue that instruction must go beyond vocabulary and should begin with an examination of our beliefs about language, literacy and learning.

This grammar provides a grammatical description of Palula, an Indo-Aryan language of the Shina group. The language is spoken by about 10,000 people in the Chitral district in Pakistan’s Khyber Pakhtunkhwa Province. This is the first extensive description of the formerly little-documented Palula language, and is one of only a few in-depth studies available for languages in the extremely multilingual Hindukush-Karakoram region. The grammar is based on original fieldwork data, collected over the course of about ten years, commencing in 1998. It is primarily in the form of recorded, mainly narrative, texts, but supplemented by targeted elicitation as well as notes of observed language use. All fieldwork was conducted in close collaboration with the Palula-speaking community, and a number of native speakers took active part in the process of data gathering, annotation and data management. The main areas covered are phonology, morphology and syntax, illustrated with a large number of example items and utterances, but also a few selected lexical topics of some prominence have received a more detailed treatment as part of the morphosyntactic structure. Suggestions for further research that should be undertaken are given throughout the grammar. The approach is theory-informed rather than theory-driven, but an underlying functional-typological framework is assumed. Diachronic development is taken into account, particularly in the area of morphology, and comparisons with other languages and references to areal phenomena are included insofar as they are motivated and available. The description also provides a brief introduction to the speaker community and their immediate environment.