Syllabus

Course Description

DATA 442 - Continue projects initiated in DATA 441. Team-based design, implementation of bioinformatics solutions and management of development teams. Technical documentation, quality assurance, and systems testing. Design and conduct empirical studies. Data visualization. Oral and written presentation. 2 laboratories.

Required Text

None.

Contact Information

Professor: Dr. Paul Anderson and Dr. Jean Davidson

Dr. Anderson

Office hours:

• Link
• Tuesday: 8:40 AM - 9:40 AM, 11 AM - 12 PM
• Thursday: 11 AM - 12 PM
• By appointment (email)

“Walk” in hours:

• Link
• I will be in my office and available for ad hoc meetings on Fridays. These are different than office hours which I have set aside to focus on my classes. Walk in hours may be used by anyone interested in chatting about anything.

Dr. Davidson

Grading Policy

GitHub Production and Progress Evidence - 30%
Final Report - 20%
Scrum Master Performance (specifically communication with company, instructor, team) - 20%
Midterm Presentation - 10%
Final Presentation - 10%
2-3 minute slick video - 10%

Grading Scale

Grading Scale:

• A 100% to 93%
• A- < 93% to 90%
• B+ < 90% to 87%
• B < 87% to 83%
• B- < 83% to 80%
• C+ < 80% to 77%
• C < 77% to 73%
• C- < 73% to 70%
• D+ < 70% to 67%
• D < 67% to 63%
• D- < 63% to 60%
• F < 60% to 0%

Grading Guidelines

Submitted work requires Analysis, Evaluation, and Creation of ideas, concepts, and materials into various deliverables (e.g., see revised Bloom’s Taxonomy (http://www.nwlink.com/~donclark/hrd/bloom.html) and reference below).

The grade of A is for work that involves high-quality achievement in all three Bloom areas.
The grade of B is for work that involves high-quality achievement in at least two Bloom areas, and mediumlevel achievement in the other.
The grade of C is for work that involves high-quality achievement in at least one Bloom area, and mediumlevel achievement in the others.
The grade of F is for work that does not meet above criteria.

Reference: Errol Thompson, Andrew Luxton-Reilly, Jacqueline L. Whalley, Minjie Hu, and Phil Robbins. 2008. Bloom’s taxonomy for CS assessment. In Proceedings of the tenth conference on Australasian computing education

• Volume 78 (ACE ‘08), Simon Hamilton and Margaret Hamilton (Eds.), Vol. 78. Australian Computer Society, Inc., Darlinghurst, Australia, Australia, 155-161.

Policies

Two Quarter Long Project: This courses revolves around a two quarter long project. All of your learning and therefore grades center on this one task. As such, this course does not operate like a standard lecture course. There will be no lectures. It is a team project, but wherever possible, you will be graded individually. Your success in this course depends on your ability to work well with team members inside and outside of class. Meeting time will not be used to teach you new technology as this will be specific to your project. This course tries to mimic a real-world bioinformatics development team. You can picture yourself as junior bioinformaticians because at this point, well, you are (assuming you pass this course :). You can picture us as your instructors/CTO/CSO. Most of the time we spend together is needed to execute the standup portion of Agile development leaving almost no time for introducing new material. Good thing you’ve had approximately 4 years of new material getting you ready for this course. I will be available digitally and during office hours, and because we like all things nerdy, we will happily try to help with whatever technology your project demands. But you and your team are ultimately responsible for the success of your project.

Industry Partners/Representatives: Each team will work with an industry or academic partner on a real project of importance to their company or research. Each company will provide feedback on your performance that will not be used in your grade in any direct way, but it will be used to corroborate my own observations.

Instructor Role: The instructors of this course act as the overseeing chief technology and chief science officer for all the projects. Our role is to guide you and your interactions with the client (industry partner), and of course help resolve project impediments.

Scrum Master: Each member of the team will rotate as scrum master. So, each team member will have the opportunity to be scrum master for about 3 weeks. As scrum master, you manage the project (project and release backlogs/user-stories, and burndown chart/velocity/timeline-to-finish), make sure all team members are progressing, work with the instructor to resolve impediments, set release dates, sprints, and moderate Daily Scrums.

Other Roles: Other roles on the team include the Scientist, Developer, Tester, DevOps roles. Because we will have small teams, all of these roles will probably not be exclusive to one person. (Scrum masters will still have to code, developers will have to test, etc)

Scrums: Each week the scrum master is to hold a scrum. Once per sprint we will do a full team scrum (including professors). The scrum master is to lead the meeting with formal update slides. Each person will take turns being scribe and taking detailed meeting notes. If you miss a meeting, you lose 33% of your progress report grade. If you are more than 5 minutes late to the meeting, you lose 16% of your grade.

Communication with the company: Each week your scrum master must initiate at least one professional communication with the company via e-mail. These emails MUST be professional (Random internet link about emails). The instructors must be CC-ed on every e-mail with the company. The must begin with Cal Poly Bioinformatics Capstone in the subject line followed by a colon and then the real title (e.g., Cal Poly Bioinformatics Capstone: Question about the database). If they are not professional, not only will we make you resend it with an apology, and you’ll get a 0 for that week’s email grade. At the end of the capstone, you must perform a formal project handoff to the company or researcher that includes any code, artifacts, and documentation. You will receive an incomplete as your final grade until this is done.

GitHub and Grading: We will setup a private repository for each of the teams. If something is not in the GitHub repo or shown during the standup, it doesn’t exist in terms of grading. Therefore, I suggest you use GitHub issues, projects, Wiki, etc as much as possible. You can use other tools like Slack and Trello, but that will not count for your grade unless you copy those interactions into GitHub somehow, which is duplication of effort in my opinion, and I would avoid it. You should be able to have a nice easy life if you stick to e-mails and GitHub for grading purposes.

Presentations: Presentations can NOT be missed and can NOT be made up.

Final Deliverables: The final documentation for the project includes a detailed project report. Also, you must create a slick 2-3 minute video that documents and shows off your project/experience.

Honor Code

Lying, cheating, attempted cheating, and plagiarism are violations of our Honor Code that, when identified, are investigated. Each instance is examined to determine the degree of deception involved.

Incidents where the professor believes the student’s actions are clearly related more to ignorance, miscommunication, or uncertainty, can be addressed by consultation with the student. We will craft a written resolution designed to help prevent the student from repeating the error in the future. The resolution, submitted by form and signed by both the professor and the student, is forwarded to the Dean of Students and remains on file.

Cases of suspected academic dishonesty will be reported directly to the Dean of Students. A student found responsible for academic dishonesty will receive a XF in the course, indicating failure of the course due to academic dishonesty. This grade will appear on the student’s transcript for two years after which the student may petition for the X to be expunged. The student may also be placed on disciplinary probation, suspended (temporary removal) or expelled (permanent removal) from the College by the Honor Board.

It is important for students to remember that unauthorized collaboration–working together without permission– is a form of cheating. Unless a professor specifies that students can work together on an assignment and/or test, no collaboration is permitted. Other forms of cheating include possessing or using an unauthorized study aid (such as a PDA), copying from another’s exam, fabricating data, and giving unauthorized assistance.

Remember, research conducted and/or papers written for other classes cannot be used in whole or in part for any assignment in this class without obtaining prior permission from the professor.

Diversity Statement (Cal Poly official statement)

At Cal Poly we believe that academic freedom, a cornerstone value, is exercised best when there is understanding and respect for our diversity of experiences, identities, and world views. Consequently, we create learning environments that allow for meaningful development of self-awareness, knowledge, and skills alongside attention to others who may have experiences, worldviews, and values that are different from our own. In so doing, we encourage our students, faculty, and staff to seek out opportunities to engage with others who are both similar and different from them, thereby increasing their capacity for knowledge, empathy, and conscious participation in local and global communities.

In the spirit of educational equity, and in acknowledgement of the significant ways in which a university education can transform the lives of individuals and communities, we strive to increase the diversity at Cal Poly. As an institution that serves the state of California within a global context, we support the recruitment, retention, and success of talented students, faculty, and staff from across all societies, including people who are from historically and societally marginalized and underrepresented groups.

Cal Poly is an inclusive community that embraces differences in people and thoughts. By being open to new ideas and showing respect for diverse points of view, we support a climate that allows all students, faculty, and staff to feel valued, which in turn facilitates the recruitment and retention of a diverse campus population. We are a culturally invested university whose members take personal responsibility for fostering excellence in our own and others’ endeavors. To this end, we support an increased awareness and understanding of how one’s own identity facets (such as race, ethnicity, gender, sexual orientation, religion, age, disability, social class, and nation of origin) and the combinations of these identities and experiences that may accompany them can affect our different worldviews.

Disability Accomodations

Any student who feels he or she may need an accommodation based on the impact of a disability should contact me individually to discuss your specific needs. Also, please contact the Disability Resource Center: https://drc.calpoly.edu/content/drc-services.