Physical Sciences and Mathematics Commons^™

Cs+Sociology: Global Inequality Lab 2, Elin Waring, Janet Michello

Open Educational Resources

These materials include background for the instructor and a lab that engages student in an analysis of global inequality while learning and using the R language (a programming language for statistics). Students ultimately write a function to access country level data from the CIA World Factbook.

Cs+Sociology: Global Inequality Lab 1, Elin Waring, Janet Michello

Open Educational Resources

These materials include background for the instructor and a lab that engages student in an analysis of global inequality while learning and using the R language (a programming language for statistics). Students obtain data on the US and two other countries (one more developed and one less developed).

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

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.

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

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.

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

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 …

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

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.

Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim

Open Educational Resources

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.

Python Working With Files, Natalia Novak

Open Educational Resources

This is an introduction to work with files in Python.

Prior knowledge of variables, assignments, expressions, input-output, lists, conditionals, and loops is recommended.

For CS0 students. Part of the CUNY CS04All project.

Python Loops, Natalia Novak

Open Educational Resources

The following topics are covered:

• While Loops
• For Loops
• Nested loops
• Break and continue
• Loops else
• enumerate()

Applications: Turtle library with loops and decision procedures.

Prior knowledge of variables, assignments, expressions, input-output, lists, and conditionals is recommended.

For CS0 students. Part of the CUNY CS04All project.

Python Dictionary, Natalia Novak

Open Educational Resources

This is an introduction Python dictionary, using Python 3.

Prior knowledge of input/output in Python, and Python list is recommended.

For CS0 students. Part of the CUNY CS04All project.

Python Functions, Natalia Novak

Open Educational Resources

An introduction to functions in Python.

Prior knowledge of variables, assignments, expressions, input-output, lists, conditionals, and loops is recommended.

For CS0 students. Part of the CUNY CS04All project.

Python If Statements, Natalia Novak

Open Educational Resources

Python If-else branches, equality and relational operators, and some additional topics: Boolean operators and expressions, membership and identity operators.

Prior knowledge of variables, assignments, and expressions is recommended.

For CS0 students. Part of the CUNY CS04All project.