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"Designing Computational Biology Workflows with Perl Part 2
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CC BY-NC-SA
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This material briefly reintroduces the DNA double Helix structure, explains SNP and INDEL mutations in genes and describes FASTA, FASTQ, BAM and VCF file formats. It also explains the index creation, alignment, sorting, marking duplicates and variant calling steps of a simple preprocessing workflow and how to write a Perl script to automate the execution of these steps on a Virtual Machine Image.

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Esma Yildirim
Date Added:
06/15/2019
Designing Computational Biology Workflows with Perl Part 2b
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CC BY-NC-SA
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This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Esma Yildirim
Date Added:
06/15/2019
Elementary College Geometry
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CC BY-NC-SA
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This text is intended for a brief introductory course in plane geometry. It covers the topics from elementary geometry that are most likely to be required for more advanced mathematics courses. The only prerequisite is a semester of algebra.

The emphasis is on applying basic geometric principles to the numerical solution of problems. For this purpose the number of theorems and definitions is kept small. Proofs are short and intuitive, mostly in the style of those found in a typical trigonometry or precalculus text. There is little attempt to teach theorem-proving or formal methods of reasoning. However the topics are ordered so that they may be taught deductively.

The problems are arranged in pairs so that just the odd-numbered or just the even-numbered can be assigned. For assistance, the student may refer to a large number of completely worked-out examples. Most problems are presented in diagram form so that the difficulty of translating words into pictures is avoided. Many problems require the solution of algebraic equations in a geometric context. These are included to reinforce the student's algebraic and numerical skills, A few of the exercises involve the application of geometry to simple practical problems. These serve primarily to convince the student that what he or she is studying is useful. Historical notes are added where appropriate to give the student a greater appreciation of the subject.

This book is suitable for a course of about 45 semester hours. A shorter course may be devised by skipping proofs, avoiding the more complicated problems and omitting less crucial topics.

Subject:
Geometry
Mathematics
Material Type:
Textbook
Provider:
CUNY Academic Works
Provider Set:
New York City College of Technology
Author:
Henry Africk
Date Added:
01/01/2013
General Astronomy 110 Syllabus (Zero Textbook Cost)
Unrestricted Use
CC BY
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The spring 2017 syllabus for the General Astronomy Course (AST 110), developed as part of the textbook free courseware initiative at Borough of Manhattan Community College.

Subject:
Astronomy
Physical Science
Material Type:
Syllabus
Provider:
CUNY Academic Works
Provider Set:
Borough of Manhattan Community College
Author:
Carlos E. Chaparro
Date Added:
05/07/2017
Guidelines on how to analyze a social science article (or social science documentary film)
Unrestricted Use
CC BY
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A guide on how to read an article, for undergraduate students. It’s designed for anthropology classes but might work for other social sciences as well.

Subject:
Social Science
Material Type:
Reading
Provider:
CUNY Academic Works
Provider Set:
John Jay College of Criminal Justice
Date Added:
01/01/2017
Human Anatomy and Physiology Preparatory Course
Conditional Remix & Share Permitted
CC BY-NC-SA
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The overall purpose of this preparatory course textbook is to help students familiarize with some terms and some basic concepts they will find later in the Human Anatomy and Physiology I course.

The organization and functioning of the human organism generally is discussed in terms of different levels of increasing complexity, from the smallest building blocks to the entire body. This Anatomy and Physiology preparatory course covers the foundations on the chemical level, and a basic introduction to cellular level, organ level, and organ system levels. There is also an introduction to homeostasis at the beginning.

Subject:
Anatomy/Physiology
Life Science
Material Type:
Textbook
Provider:
CUNY Academic Works
Provider Set:
Bronx Community College
Author:
Carlos Liachovitzky
Date Added:
01/01/2015
Introduction to the History of Modern Art
Conditional Remix & Share Permitted
CC BY-NC-SA
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Modern art begins in the middle of the 19th Century, in the 1850s, and lasts until approximately the 1960s. After that, once the vocabulary of modernism has been established and fully explored, the art made in the 1970s and 1980s is called post-modern art. Art made within the last 15-20 years is generally called contemporary art.

Subject:
Art History
Arts and Humanities
Material Type:
Full Course
Provider:
CUNY Academic Works
Author:
Sharon Jordan
Date Added:
09/08/2021
Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
Conditional Remix & Share Permitted
CC BY-NC-SA
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The exercises in this laboratory manual are designed to engage students in hand-on activities that reinforce their understanding of the microbial world. Topics covered include: staining and microscopy, metabolic testing, physical and chemical control of microorganisms, and immunology. The target audience is primarily students preparing for a career in the health sciences, however many of the topics would be appropriate for a general microbiology course as well.

Subject:
Life Science
Material Type:
Activity/Lab
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Joan Petersen
Susan McLaughlin
Date Added:
06/15/2019
List Comprehensions
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CC BY-NC-SA
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List Comprehensions

This is a tutorial on list comprehensions in Python, suitable for use in an Intro or CS0 course. We also briefly mention set comprehensions and dictionary comprehensions.

https://cocalc.com/share/bde99afd-76c8-493d-9608-db9019bcd346/171/list_comprehensions?viewer=share/

This OER material was produced as a result of the CS04ALL CUNY OER project

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
John Jay College of Criminal Justice
Author:
Johnson Hunter R
Date Added:
06/15/2019
Machine Learning Module
Conditional Remix & Share Permitted
CC BY-NC-SA
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These are materials that may be used in a CS0 course as a light introduction to machine learning.

The materials are mostly Jupyter notebooks which contain a combination of labwork and lecture notes. There are notebooks on Classification, An Introduction to Numpy, and An Introduction to Pandas.

There are also two assessments that could be assigned to students. One is an essay assignment in which students are asked to read and respond to an article on machine bias. The other is a lab-like exercise in which students use pandas and numpy to extract useful information about subway ridership in NYC. This assignment uses public data provided by NYC concerning entrances and exits at MTA stations.

This OER material was produced as a result of the CS04ALL CUNY OER project

Subject:
Applied Science
Computer Science
Material Type:
Activity/Lab
Lecture Notes
Provider:
CUNY Academic Works
Provider Set:
John Jay College of Criminal Justice
Author:
Johnson Hunter R
Date Added:
06/15/2019
The Mathematics of Nutrition Science
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CC BY-NC-SA
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The Mathematics of Nutrition Science is a workbook designed to integrate and contextualize developmental mathematics into an introductory college level Nutrition class. Definitions and skills from Community College Level Elementary Algebra and Quantitative Literacy courses are explained through examples analyzing the nutritional content of different foods. The book contains exercises for students to practice these skills, and also to reflect on the concepts through short writing assignments aligned with developmental English. These materials could be used by Nutrition course instructor in many different ways, and are designed to be self-contained and require minimal mathematical instruction.

Subject:
Life Science
Nutrition
Material Type:
Textbook
Provider:
CUNY Academic Works
Provider Set:
Queensborough Community College
Author:
Jennifer Maloy
Jonathan Cornick
Lana Zinger
Date Added:
03/03/2017
Music: Its Language, History, and Culture
Unrestricted Use
CC BY
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This text is designed to introduce students to works representative of a variety of music traditions including the repertoires of Western Europe from the Middle Ages through the present; of the United States, including art music, jazz, folk, rock, musical theater; and from at least two non-Western world areas (Africa, Asia, Latin America, the Caribbean, the Middle East, Indian subcontinent). A primary goal is to enable students to speak and write about the features of the music, employing vocabulary and concepts of melody, rhythm, harmony, texture, timbre,and form used by musicians. The texts explores the historic, social, and cultural contexts and the role of class, ethnicity, and gender in the creation and performance of music, including practices of improvisation and the implications of oral and notated transmission. Similarly, the text aims to acquaint students with the sources of musical sounds—instruments and voices from different cultures, found sounds, electronically generated sounds; basic principles that determine pitch and timbre. Lastly, the text aims to examine students to the influence of technology, mass media, globalization, and transnational currents on the music of today.

Subject:
Arts and Humanities
Performing Arts
Material Type:
Textbook
Provider:
CUNY Academic Works
Provider Set:
Brooklyn College
Author:
Douglas Cohen
Date Added:
06/19/2019