Difference between revisions of "2012-2013 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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| 2012.12.05 (last class) || -- || -- || Group Study || Test Preparation for AMS 535
 
| 2012.12.05 (last class) || -- || -- || Group Study || Test Preparation for AMS 535
 
|-
 
|-
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|- style="background:lightgreen"
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| '''2012 Spring'''
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| '''Participant'''
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| '''Rotations or Research Group'''
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| '''Topic'''
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| '''References
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SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
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|-
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| 2012.01.30 || -|| -- || --||--
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| 2012.02.01 || Class discussion  || Responsible Conduct of Research (RCR) || (2) Scientific Misconduct ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p30629381 Michael Hadjiargyrou Lecture]
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Reading
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*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]
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Discussion
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*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?
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*From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?
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*How can the pressure to publish influence the conduct of research?
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|-
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| 2012.02.08 || Class discussion || Responsible Conduct of Research (RCR) || (3) Mentoring ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p20134531 Clinton Rubin Lecture]
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 +
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Readings
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*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]
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 +
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Discussion
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*What qualities do you want in a mentor?
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*What are the challenges associated with being a mentor?
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*What does Professor Rubin mean when he says it is very important not to burn bridges?
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|-
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| 2012.02.15 || Class discussion || Responsible Conduct of Research (RCR) || (4) Ownership and Authorship ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p32819600 Peter Gergen Lecture]
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Readings
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*[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]
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 +
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Discussion (also from the above Columbia course)
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*Is it ever appropriate for authorship to change during a project or potential paper?
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*Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?
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|-
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| 2012.02.22|| Class discussion || Responsible Conduct of Research (RCR) || (5) Plagiarism ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
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Readings
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*[http://www.stonybrook.edu/uaa/academicjudiciary/policies.shtml Stony Brook's Policy on Academic Dishonesty]
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 +
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Discussion
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*Is plagiarism really that bad?
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*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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|-
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| 2012.02.29|| Class discussion || Responsible Conduct of Research (RCR) || (6) Data Management ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
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 +
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Readings
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*[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]
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 +
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Discussion
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*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?
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*From Case Study 2: Under what condition is copying allowed?
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*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. 
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|-
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| 2012.03.07 || Class discussion || Responsible Conduct of Research (RCR) || (7) Journalism and Science ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
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 +
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Readings (3 Case Studies)
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2011-2010_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]
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 +
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Discussion
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*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?
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*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?
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*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? 
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|-
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| 2012.03.14 || Class discussion || Responsible Conduct of Research (RCR) || (8) Responsible Conduct of Research Involving Human Subjects ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
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 +
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Readings: (Background Information, Case Studies, Helsinki manuscript)
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]
 +
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Discussion
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*From Human Subjects handout, Background History: Why does the Helsinki Declaration limit the use of Placebo's?
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*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?
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*From Helsinki manuscript: Do you agree with the authors that placebo-controlled trails are in many cases necessary ?  Why ?
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|-
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| 2012.03.21 || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Laboratory Animals ||
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Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
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Readings (Case Studies)
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]
 +
 +
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Discussion
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*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?
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|-
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| 2012.03.28 || Sin, Jeewoen and Xia, Yunting and Chen, Jeff || -- || Second rotation presentations || --
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|-
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| 2012.04.04 || Spring Break || Spring Break  || Spring Break || Spring Break
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|-
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| 2012.04.11 || URECA Celebration || URECA Celebration || SAC Ballrooms A&B || 10am-4 pm ALL DAY
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|-
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| 2012.04.18 || Sinayev, Roman and Zhou, Yuchen || -- || Second rotation presentations || --
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|-
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| 2012.04.25 || Sin, Jeewoen and Xia, Yunting and Chen, Jeff || -- || Third rotation presentations || --
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|-
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| 2012.05.02 (last class) || Sinayev, Roman and Zhou, Yuchen || -- || Third rotation presentations || --
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|-
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|}

Revision as of 12:32, 28 January 2013

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

2012 Fall Participant Rotations or Research Group Topic References

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

2012.08.29 -- -- -- --
2012.09.05 Zhou, Yuchen Rizzo Topic Armstrong, MS., et al., ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics. J Comput Aided Mol Des. 2010 Sep, 24(9), 789-801.
2012.09.12 Chen, Jeffrey MacCarthy Topic Hershberg, U., et al., Differences in potential for amino acid change after mutation reveals distinct strategies for κ and λ light-chain variation. PNAS 2006 Oct, vol. 103 no. 43, 15963-15968.
2012.09.19 Sin, Jeewoen MacCarthy Topic Leclerc, RD., Survival of the sparsest: robust gene networks are parsimonious. Mol Syst Biol. 2008 4:213.
2012.09.26 Krantsevich, Nikolay Rizzo Topic Barrciro, G., et al., From Docking False-Positive to Active Anti-HIV Agent. J. Med. Chem. 2007, 50, 5324-5329.
2012.10.03 -- -- Postponed AMS Graduate Party
2012.10.10 Li, Xindi Rizzo Topic Chang, C., et al., Pharmacophore-based discovery of ligands for drug transporters. Adv Drug Deliv Rev. 2006 Nov, 58(12-13), 1431-1450.
2012.10.17 Krantsevich, Artyom MacCarthy Topic MacCarthy, T., et al., Differential regulation drives plasticity in sex determination gene networks. BMC Evolutionary Biology. 2010 10:388.
2012.10.25 Yuan, Chaohui MacCarthy Topic Cohen, RM., Somatic hypermutation targeting is influenced by location within the immunoglobulin V region. Molecular Immunology 2011, 48, 1477-1483.
2012.10.31 -- -- -- No Class: Hurricane Sandy
2012.11.07 -- -- Group Study Test Preparation for AMS 535
2012.11.14 Li, Xindi and Yuan, Chaohui -- Topic FIRST ROTATION/RESEARCH PRESENTATIONS
2012.11.21 - -- -- THANKSGIVING BREAK
2012.11.28 -- -- Group Study Test Preparation for AMS 535
2012.12.05 (last class) -- -- Group Study Test Preparation for AMS 535
2012 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2012.01.30 - -- -- -- 2012.02.01 Class discussion Responsible Conduct of Research (RCR) (2) 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?
2012.02.08 Class discussion Responsible Conduct of Research (RCR) (3) 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?
2012.02.15 Class discussion Responsible Conduct of Research (RCR) (4) 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?
2012.02.22 Class discussion Responsible Conduct of Research (RCR) (5) 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?
2012.02.29 Class discussion Responsible Conduct of Research (RCR) (6) 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.
2012.03.07 Class discussion Responsible Conduct of Research (RCR) (7) 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?
2012.03.14 Class discussion Responsible Conduct of Research (RCR) (8) 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 ?


2012.03.21 Class discussion Responsible Conduct of Research (RCR) (9) 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?


2012.03.28 Sin, Jeewoen and Xia, Yunting and Chen, Jeff -- Second rotation presentations --
2012.04.04 Spring Break Spring Break Spring Break Spring Break
2012.04.11 URECA Celebration URECA Celebration SAC Ballrooms A&B 10am-4 pm ALL DAY
2012.04.18 Sinayev, Roman and Zhou, Yuchen -- Second rotation presentations --
2012.04.25 Sin, Jeewoen and Xia, Yunting and Chen, Jeff -- Third rotation presentations --
2012.05.02 (last class) Sinayev, Roman and Zhou, Yuchen -- Third rotation presentations --
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