Difference between revisions of "2011-2012 AMS-532 Fall-Spring"

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'''Announcement'''
 
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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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| '''Topic'''
 
| '''Topic'''
 
| '''References
 
| '''References
−
NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT'''
+
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT'''
 
|-
 
|-
  
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|-
 
|-
  
−
| 2011.11.23 || - || -- || THANKSGIVING BREAK || THANKSGIVING BREAK
+
| 2011.11.23 || - || -- || -- || THANKSGIVING BREAK
 
|-
 
|-
  
−
| 2011.11.30 || Chen, Jeff and Sinayev, Roman || -- || topic || ROTATION/RESEARCH PRESENTATIONS
+
| 2011.11.30 || Sin, Jeewoen and Xia, Yunting and Chen, Jeff || -- || topic || FIRST ROTATION/RESEARCH PRESENTATIONS
 
|-
 
|-
 +
| 2011.12.07 (last class) || Sinayev, Roman and Zhou, Yuchen || -- || topic || FIRST ROTATION/RESEARCH PRESENTATIONS
 +
|-
 +
|- style="background:lightgreen"
 +
| '''2012 Spring'''
 +
| '''Participant'''
 +
| '''Rotations or Research Group'''
 +
| '''Topic'''
 +
| '''References
 +
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 +
|-
 +
| -- || Work to be Done Outside of class|| Responsible Conduct of Research (RCR) || (0) Additional requirements to fulfill RCR training ||
 +
 +
Requirements
 +
*View the Responsible Conduct of Research and Scholarship - Presentation given to department chairs by professor Michael Hadjiargyrou [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
 +
|-
 +
| 2012.01.25 || Class discussion|| Responsible Conduct of Research (RCR) || (1) Integrity in Scholarship (Introduction to Ethics and Science) ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p42411560 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?
 +
|-
 +
 +
| 2012.02.01 || Class discussion  || Responsible Conduct of Research (RCR) || (2) Scientific Misconduct ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p30629381 Michael Hadjiargyrou Lecture]
 +
 +
 +
Reading
 +
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct 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?
 +
*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
 +
*[https://meeting.sinc.stonybrook.edu/p20134531 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?
 +
 +
|-
 +
| 2012.02.15 || Class discussion || Responsible Conduct of Research (RCR) || (4) Ownership and Authorship ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p32819600 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?
 +
*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
 +
*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
 +
 +
 +
Readings
 +
*[http://www.stonybrook.edu/uaa/academicjudiciary/policies.shtml Stony Brook's Policy on Academic Dishonesty]
 +
 +
 +
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
 +
*[https://meeting.sinc.stonybrook.edu/p68134598 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. 
 +
|-
 +
 +
| 2012.03.07 || Class discussion || Responsible Conduct of Research (RCR) || (7) Journalism and Science ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
 +
 +
 +
Readings (3 Case Studies)
 +
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2011-2010_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]
 +
  
−
| 2011.12.07 || Xia, Yunting and Zhou, Yuchen || -- || topic || ROTATION/RESEARCH PRESENTATIONS
+
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
 +
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
 +
 +
 +
Readings: (Background Information, Case Studies, Helsinki manuscript)
 +
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]
 +
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/helsinki.pdf 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 ?
 +
 +
  
−
| 2011.12.14 || Sin, Jeewoen || -- || topic || ROTATION/RESEARCH PRESENTATIONS
 
 
|-
 
|-
 +
| 2012.03.21 || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Laboratory Animals ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
 +
 +
 +
Readings (Case Studies)
 +
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_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?
 +
  
−
| 2012.01.  || Last name, First name || -- || topic || paper
 
 
|-
 
|-
 +
| 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 || --
 +
|-
 +
|}

Latest revision as of 15:08, 5 August 2013

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

2011 Fall Participant Rotations or Research Group Topic References

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

2011.00.00 Last name, First name -- topic paper
2011.09.07 Cao，Yiwei Green Protein Design Georgiev, I., et al., Algorithm for backrub motions in protein design. Bioinformatics 2008, 24(13), i196-i204.
2011.09.14 Yao， Yuan Wang topic Siegel, J., et al., Computational Design of an Enzyme Catalyst for a Stereoselective Biomolecular Diels-Alder Reaction. Science 2010, 329, 309-313
2011.09.21 Gardin，Justin futcher topic Exact Discovery of Time Series Motifs. 2008
2011.09.28 - -- topic followed a Friday schedule
2011.10.05 Fochtman, Brian Rizzo topic Efficient Inclusion of Receptor Flexibility in Grid-Based Protein-Ligand Docking. J. of Comp. Chem. 2011
2011.10.12 Chen, Jeff -- topic Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10(3), R25.1-10
2011.10.19 Sinayev, Roman -- topic Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin. Science 2011, 332, 816-821
2011.10.26 Xia, Yunting -- topic paper
2011.11.02 Zhou, Yuchen -- topic paper
2011.11.09 Yuan, Joanna -- topic paper
2011.11.16 Sin, Jeewoen -- topic paper
2011.11.23 - -- -- THANKSGIVING BREAK
2011.11.30 Sin, Jeewoen and Xia, Yunting and Chen, Jeff -- topic FIRST ROTATION/RESEARCH PRESENTATIONS
2011.12.07 (last class) Sinayev, Roman and Zhou, Yuchen -- topic FIRST ROTATION/RESEARCH PRESENTATIONS
2012 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

-- Work to be Done Outside of class Responsible Conduct of Research (RCR) (0) Additional requirements to fulfill RCR training

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
2012.01.25 Class discussion Responsible Conduct of Research (RCR) (1) 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?
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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