This material introduces Linux File System structures and demonstrates how to use commands to communicate with the operating system through a Terminal program. Basic program structures and system() function of Perl are discussed. A brief introduction to gene-sequencing terminology and file formats are given.
This manual guides the instructor to combine the partial files of the virtual machine image and construct sequencer.ova file. It is accompanied by the partial files of the virtual machine image.
This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided, connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to enter the data folder, which includes gene-sequencing input files and print the first five line of each file remotely. 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.
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.
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.
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.
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.
My Math GPS: Elementary Algebra Guided Problem Solving is a textbook that aligns to the CUNY Elementary Algebra Learning Objectives that are tested on the CUNY Elementary Algebra Final Exam (CEAFE). This book contextualizes arithmetic skills into Elementary Algebra content using a problem-solving pedagogy. Classroom assessments and online homework are available from the authors.