View source for 2023-2024 AMS-532 Fall-Spring

=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===
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! style="width:10%" | '''Instructor''' 
|Dr. Robert C. Rizzo    [631-632-9340, rizzorc -at- gmail (dot) com]
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| '''Course No.''' || AMS-532 
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| '''Location/Time''' || Wed 12:00PM - 12:53PM, Math Tower AMS seminar room (122A, First Floor)
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| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics
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'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects.  In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.

'''Learning Objectives:'''
*(1) Actively participate in Journal Club discussions on Computationally Biology literature.  
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531).   
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections: 
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training
**(ii) Integrity in Scholarship
**(iii) Scientific Misconduct
**(iv) Mentoring
**(v) Ownership and Authorship
**(vi) Plagiarism
**(vii) Data Management
**(viii) Journalism and Science
**(ix) Responsible Conduct of Research Involving Human Subjects
**(x) Responsible Conduct of Research Involving Laboratory Animals



'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.  If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?


'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals.  Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies.  The RCR meetings will be run as small group breakout sessions followed by group discussion.  To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org.  See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings.  
   

'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.


'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.
      
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== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==

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| '''2023 Fall
| '''Participant''' 
| '''Rotations or Research Group'''
| '''Topic'''
| '''References
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''
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| 2023.08.30 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).
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| 2023.09.06 Wed || -- || -- || -- || First year students will attend AMS-539 meeting (Faculty research presentations).
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| 2023.09.13 Wed || Li, Stan || FIRST DAY of CLASS || -- || Ignatov et al; High Accuracy Prediction of PROTAC Complex Structure. ''JACS'' '''2023''', ''145'', 7123-7135
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| 2023.09.20 Wed || Glukhov, Ernest || -- || -- || Greener et al; A guide to machine learning for biologists. ''Nature Reviews: Molecular Cell Biology'' '''2022''', ''23'', 40
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| 2023.09.27 Wed || Cheung, Andrew || -- || -- || Luecken et al; Current best practices in single-cell RNA-seq analysis: a tutorial. ''Molecular Systems Biology'' '''2019''', ''15'', e8746
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| 2023.10.04 Wed || Zhu, Zeru || -- || -- || Fimmel et al; Mathematical fundamentals for the noise immunity of the genetic code. ''BioSystems'' '''2018''', ''164'', 186-198
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| 2023.10.11 Wed || Moy, Olivia || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163
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| 2023.10.18 Wed || Li, Stan || -- || -- || Wang et al et al; Predicting Biomolecular Binding Kinetics: A Review. ''Journal of Chemical Theory and Computation'' '''2023''', ''19'', 2135-2148
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| 2023.10.25 Wed || Cheung, Andrew || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163
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| 2023.11.01 Wed ||  Glukhov, Ernest || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163
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| 2023.11.08 Wed || Zhu, Zeru || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163
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| 2023.11.15 Wed || Moy, Olivia || -- || -- || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163
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| 2023.11.22 Wed || -- || -- || -- || THANKSGIVING BREAK
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| 2023.11.29 Wed || TBD || -- || -- || TBD
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| 2023.12.06 Wed || TBD || LAST DAY OF CLASS || -- || TBD
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|- style="background:lightgreen"
| '''2024 Spring'''
| '''Participant''' 
| '''Rotations or Research Group'''
| '''Topic'''
| '''NOTE: This semester (Spring 2024) students will fulfill RCR training by registering for AMS-500 instead of AMS-532.  Please resgister for AMS-500 and follow that schedule:'''
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500
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| 2024.01.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||

Discussion of Overall Course Requirements which include: 
*View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]
*Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org
*Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics
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| 2024.02.02 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
Stony Brook Lecture
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]


Readings (Nature articles)
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]


Discussion
*Why is the class important?
*How should we behave as scientists?
*How is science a social enterprise?
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| 2024.02.09 Wed || Class discussion  || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
Stony Brook Lecture
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]


Reading 
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]


Discussion
*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?
*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?
*Why do people commit scientific misconduct?
*What are some consequences of committing scientific misconduct?
*Who are some of your mentors?
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| 2024.02.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || 
Stony Brook Lecture
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]


Readings 
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]


Discussion
*What qualities do you want in a mentor?
*What are the challenges associated with being a mentor?
*What does Professor Rubin mean when he says it is very important not to burn bridges?
*What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?
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| 2024.02.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
Stony Brook Lecture
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]


Readings 
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]


Discussion (also from the above Columbia course)
*Is it ever appropriate for authorship to change during a project or potential paper?
*How should authorship roles be defined?
*What are some abuses of authorship?
*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?
*Why are acknowledgments so important?
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| 2024.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
Stony Brook Lecture
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]


Readings 
*[https://www.stonybrook.edu/commcms/academic_integrity/policies_procedures/index.php Stony Brook University Academic Integrity Policy]

 
Discussion
*Is plagiarism really that bad?
*If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism?  How many words do you need to change?
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| 2024.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
Stony Brook Lecture
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]


Readings 
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]


Discussion
*From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?
*From Case Study 2: Under what condition is copying allowed?
*Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results.  Include in your discussion how you you will be able to share "raw" results.
*How many years past a publication, if asked, should a researcher be able provide "raw data"?  
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| 2024.03.16 Wed || -- || -- || -- || SPRING BREAK
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| 2024.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
Stony Brook Lecture
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]


Readings (3 Case Studies)
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]


Discussion
*From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?
*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?
*From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly run hospital which might violate patients privacy?  
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| 2024.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
Stony Brook Lecture
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]


Readings: (Background Information, Case Studies, Helsinki Manuscript)
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]

Discussion
*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?
*From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?
*From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ?  Why ?
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| 2024.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
Stony Brook Lecture
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]


Readings (Case Studies)
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]



Discussion
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?
*From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?
*From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?
*What are some advantages of using Animals in experiments?
*Discuss the three R's?
*Is our class for or against Animal testing?
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| 2024.04.13 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| 2024.04.20 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| 2024.04.27 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| 2024.05.04 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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