California State University Stanislaus
CS 4010 Section 1 and 2: Computing for the Sciences
Welcome to CS 4010, Computing for the Sciences
The purpose of this class is to provide students with the background and training in computational methods and programming to gain the skills necessary to work with this modern scientific data. In this course, we will cover topics such as simple command line computing environments, object-oriented programming, relational databases, and data analysis using statistical tools. We will use a variety of computing tools and environments such as UNIX, Python, R and the SQL query language. No prior background in programming is required. The goal for this course is that by the end of the semester you will all be able to apply computational tools and skills to analyzing and managing biological data that will be invaluable in your careers as scientists.
Student Learning Outcomes:
1) Students will be proficient in UNIX environment and be able to script, navigate, and use high-performance computing tools to execute biological analyses.
2) Students will be able to implement object-oriented programming using the computer language Python and write programs or scripts to process and analyze data.
3) Students will be able to set-up, query, and generate reports from a relational database.
4) Students will be able to use either Python packages or statistical software to visualize data.
5) Students will have learned the application of these programming concepts well enough to complete a significant project and solve data analysis/management problems on their own.
Announcements and Upcoming Events
Welcome to CS 4010!
Required Textbook is Practical Computing for Biologists by Steven Haddock and Casey Dunn
Dr. Melanie Martin
Email: firstname.lastname@example.org Office Phone: (209) 667-3787 or (209) 667-3269
Web Page: www.cs.csustan.edu/~mmartin
Monday 3:00 – 4:00 pm DBH 278
Tuesday 1:00 – 2:00 pm Naraghi 375
Wednesday 3:00 – 4:00 pm DBH 278
Thursday 2:00 – 4:00 pm Naraghi 375
and by appointment.
Warning: I reserve the right to make changes to the
syllabus at any time during the term by announcing them in class
and on my web page.
Class generally will be structured by starting with the presentation of a specific computing or programming concept, followed by a demonstration of this topic using a scientific example. This will probably take between 30 minutes to an hour. Subsequently, the remainder of class will be dedicated to students using the previously demonstrated concept to do either other in-class exercises or class assignments. IT IS VERY IMPORTANT TO ATTEND CLASS. Class participation is part of your grade (described below) and the structure of class is additive - meaning we will constantly be building on concepts through in-class lectures, examples, and practical applications. If you miss class, you will miss the invaluable time you will need to figure out how to do what I am teaching. The majority of your grades in this course will be practical in nature (either assignments or a “practical” final) and it will be important to regularly practice the applications of skills we go over in class. The good thing is that if you come to class, keep a proper notebook of class examples, and make use of after-lecture time to do examples and ask me questions, you should do very well in this course and be able to meet the learning outcomes I have outlined for each class as well as the course overall.
Grading for this course will consist of assignments, participation, notebook, and a final practical exam. All assignments and quizzes will be on a 0-10 point scale and all other grades will be on a 0-100 point scale.
Assignments (50%): There will likely be approximately 6 assignments although I reserve the right to change this depending on how the class is proceeding. You must turn in a working version of all assignments to pass the course.
Participation and Quizzes (10%):
Simply put, this is a grade based largely on class attendance. Attend class and make proper use of class time and you will get this. There will be short quizzes to ensure that students are keeping pace with, and understanding the material presented in class
Notebook (10%): You must keep a notebook of all in class examples I demonstrate in class. It is best-practice for all scientists to keep a daily log of their work so that they can actually track what it was they did, when it was, and how they accomplished it. For you, these notebooks will have invaluable resources for your assignments.
Final Project (30%): The final project will allow individual or groups of students to work in more depth on a computational problem in their own discipline.
Please be respectful and professional in how you interact with both myself and your classmates. I plan on acting the same way with you. No food or beverage allowed in the computer lab.
Academic Honesty: The work you do for this
course will be your own, unless otherwise specified. You are not
to submit other people's work and represent it as your own. I
consider academic honesty to be at the core of the University's
activities in education and research. Academic honesty is expected
at all times in this course. Cheating is an attack on the efforts
of myself and fellow students and, above all, on the cheater's
integrity. Those caught cheating will be dealt with to the full
extent allowed under University policy. If you have questions,
University Disability Services: CSU Stanislaus respects all forms of diversity. By university commitment and by law, students with disabilities are entitled to participate in academic activities and to be tested in a manner that accurately assesses their knowledge and skills. They also may qualify for reasonable accommodations that ensure equal access to lectures, labs, films, and other class-related activities. Please see the instructor if you need accommodations for a registered disability. Students can contact the Disability Resource Services office for additional information. The Disability Resource Services website can be accessed at http://www.csustan.edu/DRS/ Phone: (209) 667-3159
of Courses or Academic Calendar)
Last day to add a class:
|Last day to drop or change
grade options (CR/NC):
March 18-22, April 1.