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Course Info |
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1st Course Survey Due Jan 12th,2025
2nd Course Survey Please finish by Jan 13th,2025
cbb752 (at) gersteinlab.org
(Please use this in preference to mailing individually the TFs or the instructors.)
| Name | Abbr | Office | |
|---|---|---|---|
| Mark Gerstein | MG | Bass 432A | contact.gerstein.info |
| Name | Abbr | Office | |
|---|---|---|---|
| Corey O'Hern | CO | Mason Laboratory | corey.ohern (at) yale.edu |
| Jesse Rinehart | JR | West Campus | jesse.rinehart (at) yale.edu |
| Matthew Simon | MDS | West Campus | matthew.simon (at) yale.edu |
| Kei Cheung | KC | 300 George St | kei.cheung (at) yale.edu |
| Martin Renqiang Min | RM | renqiang (at) gmail.com | |
| Carl Zimmer | CZ | 266 Whitney Ave | carl.zimmer (at) yale.edu |
Consultation is available UPON REQUEST or according to times stipulated by the individual instructors. Prof. Gerstein's office office hours will usually be right after some the classes.
| Name | Abbr | Office | |
|---|---|---|---|
| Zhiyuan Chu | ZC | Bass 437 | zhiyuan.chu (at) yale.edu |
| Suchen Zheng | SZ | 100 College St (9/F) | suchen.zheng (at) yale.edu |
| Michelle Yu | MY | 100 College St (9/F) | michelle.yu (at) yale.edu |
| Donglu Bai | DB | 100 College St (9/F) | donglu.bai (at) yale.edu |
The first lecture will be held on Mon. Jan 13th, 2025.
We expect that this year the weighting scheme will be to a first approximation:
| Category | % of Total Grade |
|---|---|
| Quiz 1 | 13% |
| Quiz 2 | 13% |
| Lecture Summary | 10% |
| Discussion Section | 18% |
| Homeworks | 18% |
| Final Project | 28% |
If you want to get more background for the course, here are some resources. All of the following textbooks you can access online through Yale's e-library. Many of them cover the same material, but these should cover the core background that you need:
Essentials of Molecular Biology by Malathi V
important: chapters 1-5, 7, 11
recommended: everything else
Biochemistry: Essential Concepts by Hardin, Charles
chapters 1-6
For the class you can choose to do assignments in either R or python. Here are some resources for both:
The Python Tutorial - Official guide and documentation for Python3.
Learn Python with Google Colab - An interactive guide to python. Useful if you are familiar with basic programming, but not python language.
Learning Python: Powerful Object-Oriented Programming (5th edition) by Mark Lutz
The R book (2nd edition) by Michael J. Crawley
R for Data Science by Hadley Wickam
We will follow the default FAS policy on recording where the instructor’s lectures will be recorded, and student contributions in seminars and sections will not be recorded.
Students may have questions concerning end-of-term matters. Links to further information about these regulations can be found below:
- http://catalog.yale.edu/ycps/academic-regulations/reading-period-final-examination-period/
- http://catalog.yale.edu/ycps/academic-regulations/completion-of-course-work/
- Brief presentation on how to cite correctly : http://archive.gersteinlab.org/mark/out/log/2012/06.12/cbb752b12/cbb752_cite.ppt
Students may use AI tools for the following purposes:
- Research and Learning Support:
- Help in understanding complex topics and questions.
- Assisting with coding or debugging programming assignments -- yes, this is allowed!
- Proofreading and enhancing written assignments for clarity and grammar.
- Creative Brainstorming:
- Exploring different perspectives or approaches to a topic.
- Developing outlines or rough drafts for essays or presentations.
- Efficiency Tools:
- Managing references, citations, and bibliographies.
Students must not use AI tools for the following:
- Academic Dishonesty: (The below list is somewhat redundant, but we want to make this very clear.)
- Using AI to generate submitted lecture summaries, paper summaries, projects, and assignments.
- Submitting AI-generated code, writing, or solutions as their own work without substantial modifications or understanding.
- Copying and pasting AI-generated content directly into assignments.
- Bypassing Learning Objectives: (This is more conceptual in spirit and meant as more of an overall guide.)
- Avoiding critical thinking by relying entirely on AI to generate answers.
- Using AI to bypass coursework designed to assess student understanding and creativity.
- Unethical Behavior:
- Misrepresenting AI output as one's own intellectual work (see attribution requirements below).
If AI tools are used in any capacity, students must:
- Clearly acknowledge their use in the assignment or project. Example:
- "This assignment used ChatGPT for brainstorming and improving grammatical accuracy."
- "Python debugging assistance was obtained via Copilot."
- Specify which parts of the work were influenced by AI and ensure the final submission reflects their understanding.
Failure to adhere to this policy will result in substantial points off on an assignment.
Please note that much of this content was, in fact, generated by chatGPT but with very substantial revision and discussion by the course instructors and TFs.
We are committed to creating a course that is inclusive in its design. If you encounter barriers, please let us know immediately so that we can determine if there is a design adjustment that can be made or if an accommodation might be needed to overcome the limitations of the design. We are always happy to consider creative solutions as long as they do not compromise the intent of the assessment or learning activity. You are also welcome to contact Student Accessibility Services to begin this conversation or to establish accommodations for this or other courses. We welcome feedback that will assist us in improving the usability and experience for all students.
Below is a message from the Dean of Yale College about citing your references and sources of information and plagiarism:
" You need to cite all sources used for papers, including drafts of papers, and repeat the reference each time you use the source in your written work. You need to place quotation marks around any cited or cut-and-pasted materials, IN ADDITION TO footnoting or otherwise marking the source. If you do not quote directly – that is, if you paraphrase – you still need to mark your source each time you use borrowed material. Otherwise you have plagiarized. It is also advisable that you list all sources consulted for the draft or paper in the closing materials, such as a bibliography or roster of sources consulted. You may not submit the same paper, or substantially the same paper, in more than one course. If topics for two courses coincide, you need written permission from both instructors before either combining work on two papers or revising an earlier paper for submission to a new course. It is the policy of Yale College that all cases of academic dishonesty be reported to the chair of the Executive Committee.... "
" Academic integrity is a core institutional value at Yale. It means, among other things, truth in presentation, diligence and precision in citing works and ideas we have used, and acknowledging our collaborations with others. In view of our commitment to maintaining the highest standards of academic integrity, the Graduate School Code of Conduct specifically prohibits the following forms of behavior: cheating on examinations, problem sets and all other forms of assessment; falsification and/or fabrication of data; plagiarism, that is, the failure in a dissertation, essay or other written exercise to acknowledge ideas, research, or language taken from others; and multiple submission of the same work without obtaining explicit written permission from both instructors before the material is submitted. Students found guilty of violations of academic integrity are subject to one or more of the following penalties: written reprimand, probation, suspension (noted on a student’s transcript) or dismissal (noted on a student’s transcript). "
Also, it might be of interest to people, to look at this recent article regarding academic dishonesty.