Difference between revisions of "2013-2014 AMS-532 Fall-Spring"

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(→‎Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring))
(→‎Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring))
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*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
 
*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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| 2014.02.05 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
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| 2014.02.05 Wed || - || -- || -- || SNOW STORM, CLASS CANCELLED
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| 2014.02.12 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p42411560 Peter Williams Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p42411560 Peter Williams Lecture]
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| 2014.02.12 Wed || Class discussion  || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
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| 2014.02.19 Wed || Class discussion  || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p30629381 Michael Hadjiargyrou Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p30629381 Michael Hadjiargyrou Lecture]
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| 2014.02.19 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||  
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| 2014.02.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||  
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p20134531 Clinton Rubin Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p20134531 Clinton Rubin Lecture]
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| 2014.02.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
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| 2014.03.05 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p32819600 Peter Gergen Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p32819600 Peter Gergen Lecture]
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| 2014.03.05 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
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| 2014.03.12 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
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| 2014.03.19 Wed || -- || -- || -- || SPRING BREAK
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| 2014.03.12 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
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| 2014.03.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
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|-
 
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| 2014.03.19 Wed || -- || -- || -- || SPRING BREAK
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| 2014.04.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
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| 2014.03.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
 
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
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| 2014.04.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
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| 2014.04.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
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| 2014.04.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
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| 2014.04.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
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| 2014.04.16 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
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| 2014.04.23 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
| 2014.04.23 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS

Revision as of 12:09, 11 February 2014

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage


Instructor Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
Course No. AMS-532
Location/Time Physics P124 Wed 12:00PM - 12:53PM
Office Hours Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics


Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)

2013 Fall Participant Rotations or Research Group Topic References

REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT

2013.08.28 Wed Last name, First name -- Topic paper
2013.09.04 Wed Krantsevich, Nikolay Green topic Travers, SA. Conservation, compensation, and evolution of N-linked glycansin the HIV-1 group M subtypes and circulating recombinant forms. ISRN AIDS. 2012 Nov.
2013.09.11 Wed Yuan, Chaohui MacCarthy topic Oprea, M. and Perelson, AS. Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. J Immunology. 1997 Jun. 158(11). 5155-5162.
2013.09.18 Wed Lee, Xindi (Cindy) Green topic Eklund, R. and Widmalm, G. Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. Carbohydrate Reasearch. 2002 Nov. 338(2003). 393-398.
2013.09.25 Wed Last name, First name -- topic paper
2013.10.02 Wed Krantsevich, Artem Green topic Kim, Pan-Jun. et al. Centralized modularity of N-linked glycosylation pathways in mammalian cells. PLoS ONE. 2009 Oct. 4(10). e7317.
2013.10.09 Wed Amgalan, Anar Dill topic Pang, Tin Yau. and Maslov, Sergei. Universal distribution of component frequencies in biological and technological systems. P.N.A.S. 2013 Feb. 110(52). 21054-21058.
2013.10.16 Wed Shan, Jiahui (Emma) -- topic Alexandrov, LB. et al. Signatures of mutational processes in human cancer. Nature. 2013 Aug. 500. 415-421.
2013.10.23 Wed Zou, Junjie -- topic Lill, MA. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. Biochemistry. 2011 Jun. 50. 6157-6169.
2013.10.30 Wed Li, Fangfei -- topic Forli, S. and Olson, AJ. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. J Med Chem. 2012. 55. 623-638.
2013.11.06 Wed Yu, Bihua -- topic Green, DF. A statistical framework for hierarchical methods in molecular simulation and design. J Chem Theory Comput. 2010 Apr. 6. 1682-1697.
2013.11.13 Wed Kennedy, Chelsea -- -- ROTATION/RESEARCH PRESENTATIONS
2013.11.20 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
2013.11.27 Wed - -- -- THANKSGIVING BREAK
2013.12.04 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
2014 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2014.01.29 Wed Class discussion Responsible Conduct of Research (RCR) (1) Course Overview: Discussion of work to be done outside of class to fulfill RCR training

Overall Course Requirements

  • View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou 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
2014.02.05 Wed - -- -- SNOW STORM, CLASS CANCELLED
2014.02.12 Wed Class discussion Responsible Conduct of Research (RCR) (2) Integrity in Scholarship (Introduction to Ethics and Science)

Stony Brook Lecture


Readings (Nature articles)


Discussion

  • Why is the class important?
  • How should we behave as scientists?
  • How is science a social enterprise?
2014.02.19 Wed Class discussion Responsible Conduct of Research (RCR) (3) Scientific Misconduct

Stony Brook Lecture


Reading


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?
  • How can the pressure to publish influence the conduct of research?
2014.02.26 Wed Class discussion Responsible Conduct of Research (RCR) (4) Mentoring

Stony Brook Lecture


Readings


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?
2014.03.05 Wed Class discussion Responsible Conduct of Research (RCR) (5) Ownership and Authorship

Stony Brook Lecture


Readings


Discussion (also from the above Columbia course)

  • Is it ever appropriate for authorship to change during a project or potential paper?
  • Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?
2014.03.12 Wed Class discussion Responsible Conduct of Research (RCR) (6) Plagiarism

Stony Brook Lecture


Readings


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?
2014.03.19 Wed -- -- -- SPRING BREAK
2014.03.26 Wed Class discussion Responsible Conduct of Research (RCR) (7) Data Management

Stony Brook Lecture


Readings


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.
2014.04.02 Wed Class discussion Responsible Conduct of Research (RCR) (8) Journalism and Science

Stony Brook Lecture


Readings (3 Case Studies)


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 hospital which might violate patients privacy?
2014.04.09 Wed Class discussion Responsible Conduct of Research (RCR) (9) Responsible Conduct of Research Involving Human Subjects

Stony Brook Lecture


Readings: (Background Information, Case Studies, Helsinki manuscript)

Discussion

  • From Human Subjects handout, Background History: Why does the Helsinki Declaration limit the use of Placebo's?
  • From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?
  • From Helsinki manuscript: Do you agree with the authors that placebo-controlled trails are in many cases necessary ? Why ?
2014.04.16 Wed Class discussion Responsible Conduct of Research (RCR) (10) Responsible Conduct of Research Involving Laboratory Animals

Stony Brook Lecture


Readings (Case Studies)


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?
2014.04.23 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
2014.04.30 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
2014.05.07 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
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