Difference between revisions of "2016-2017 AMS-532 Fall-Spring"

From Rizzo_Lab
Jump to: navigation, search
(→‎Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring))
 
(12 intermediate revisions by the same user not shown)
Line 30: Line 30:
 
|-
 
|-
  
−
| 2016.09.07 Wed || Shapiro, Max || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.09.07 Wed || Shapiro, Max || -- || -- || Samuel, C.; Adenosine Deaminases Acting on RNA (ADARs) are both Antiviral and Proviral Dependent upon the Virus. ''Virology'' '''2011''', 411(2): 180–193. doi:10.1016/j.virol.2010.12.004.
 
|-
 
|-
  
Line 42: Line 42:
 
|-
 
|-
  
−
| 2016.10.05 Wed || Ignatov, Mikhail || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.10.05 Wed || -- || -- || -- || No meeting
 
|-
 
|-
  
−
| 2016.10.12 Wed || Jones, George || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.10.12 Wed || Ignatov, Mikhail || -- || -- || Wallach, I., et al.; AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Design. arXiv:1510.02855v1 [cs.LG]
 
|-
 
|-
  
−
| 2016.10.19 Wed || O'Connell, Dan || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.10.19 Wed || -- || -- || -- || No meeting
 
|-
 
|-
  
−
| 2016.10.26 Wed || Nassar, Roy || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.10.26 Wed || O'Connell, Dan || -- || -- || Lopez-Otin, C., et al.; The Hallmarks of Aging. ''Cell.'' '''2013''', ''153'', 1194-1217.
 
|-
 
|-
  
−
| 2016.11.02 Wed || Telehany, Stephen || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.11.02 Wed || Nassar, Roy || -- || -- || Knowles, T.J.P, Vendruscolo, M, Dobson, C.M. The Amyloid State and Its Association with Protein Misfolding Diseases. ''Nat. Rev. Mol. Cell Biol.'' '''2014''', ''15'', 384-396.
 
|-
 
|-
  
−
| 2016.11.09 Wed || Cao, Xin || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.11.09 Wed || Telehany, Stephen || -- || -- || Ucisik, M. and Hammes-Schiffer S. (2015) Comparative Molecular Dynamics Studies of Human DNA Polymerase η. J. Chem. Inf. Model., 55 (12), 2672–2681. DOI: 10.1021/acs.jcim.5b00606
 +
 
 
|-
 
|-
  
−
| 2016.11.16 Wed || Last name, First name || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
| 2016.11.16 Wed || Cao, Xin || -- || -- || Coutsias, E.A., et al.; A Kinematic View of Loop Closure. ''J. Compute. Chem.'' '''2004''', ''25'', 510-528.
 
|-
 
|-
  
−
| 2016.11.23 Wed || - || -- || -- || THANKSGIVING BREAK
+
| 2016.11.23 Wed || -- || -- || -- || THANKSGIVING BREAK
 
|-
 
|-
−
| 2016.11.30 Wed || Last name, First name || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
 
 +
| 2016.11.30 Wed || Jones, George || -- || -- || Wang, Z., et al.; Drug-induced adverse events prediction with LINCS L100 data. ''Bioinformatics'' '''2016''', ''32'', 2338-2345.
 
|-
 
|-
−
| 2016.12.07 Wed || Last name, First name || -- || -- || Shao, J., et al.; Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
+
 
 +
| 2016.12.07 Wed || Fallon, Zachary || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
 
|-
 
|-
 +
 
|- style="background:lightgreen"
 
|- style="background:lightgreen"
 
| '''2017 Spring'''
 
| '''2017 Spring'''
Line 77: Line 81:
 
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
|-
 
|-
−
| 2017.01.27 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||
+
| 2017.01.25 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||
  
 
Discussion of Overall Course Requirements which include:  
 
Discussion of Overall Course Requirements which include:  
Line 85: Line 89:
 
|-
 
|-
  
−
| 2017.02.03 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
+
| 2017.02.01 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]
Line 102: Line 106:
 
|-
 
|-
  
−
| 2017.02.10 Wed || Class discussion  || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
+
| 2017.02.08 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]
Line 118: Line 122:
 
|-
 
|-
  
−
| 2017.02.17 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||  
+
| 2017.02.15 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]
Line 134: Line 138:
 
|-
 
|-
  
−
| 2017.02.24 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
+
| 2017.02.22 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]
Line 152: Line 156:
 
|-
 
|-
  
−
| 2017.03.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
+
| 2017.03.01 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]
Line 166: Line 170:
 
|-
 
|-
  
−
| 2017.03.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
+
| 2017.03.08 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]
Line 181: Line 185:
 
*How many years past a publication, if asked, should a researcher be able provide "raw data"?   
 
*How many years past a publication, if asked, should a researcher be able provide "raw data"?   
 
|-
 
|-
−
| 2017.03.16 Wed || -- || -- || -- || SPRING BREAK
+
| 2017.03.15 Wed || -- || -- || -- || SPRING BREAK
 
|-
 
|-
  
−
| 2017.03.23 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
+
| 2017.03.22 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]
Line 199: Line 203:
 
|-
 
|-
  
−
| 2017.03.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
+
| 2017.03.29 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]
Line 214: Line 218:
 
|-
 
|-
  
−
| 2017.04.13 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
+
| 2017.04.05 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]
Line 233: Line 237:
 
*Is our class for or against Animal testing?
 
*Is our class for or against Animal testing?
 
|-
 
|-
−
| 2017.04.20 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
+
| 2017.04.12 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 +
|-
 +
| 2017.04.19 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
|-
 
|-
−
| 2017.04.27 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
+
| 2017.04.26 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
|-
 
|-
−
| 2017.05.04 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
+
| 2017.05.03 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
|}
 
|}

Latest revision as of 09:28, 11 July 2017

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 P122, 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)

2016 Fall Participant Rotations or Research Group Topic References

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

2016.08.31 Wed Rizzo, Robert -- -- Organizational Meeting
2016.09.07 Wed Shapiro, Max -- -- Samuel, C.; Adenosine Deaminases Acting on RNA (ADARs) are both Antiviral and Proviral Dependent upon the Virus. Virology 2011, 411(2): 180–193. doi:10.1016/j.virol.2010.12.004.
2016.09.14 Wed -- -- -- AMS Grad Student BBQ
2016.09.21 Wed Tang, Cathy -- -- Sheng Z, Schramm CA, Connors M, Morris L, Mascola JR, Kwong PD, et al. (2016) Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection. PLoS Comput Biol 12(5): e1004940. doi:10.1371/journal.pcbi.1004940.
2016.09.28 Wed Tuznik, Stan -- -- Lowe, D.; Object Recognition from Local Scale-Invariant Features. Proc. of the International Conference on Computer Vision Sept 1999.
2016.10.05 Wed -- -- -- No meeting
2016.10.12 Wed Ignatov, Mikhail -- -- Wallach, I., et al.; AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Design. arXiv:1510.02855v1 [cs.LG]
2016.10.19 Wed -- -- -- No meeting
2016.10.26 Wed O'Connell, Dan -- -- Lopez-Otin, C., et al.; The Hallmarks of Aging. Cell. 2013, 153, 1194-1217.
2016.11.02 Wed Nassar, Roy -- -- Knowles, T.J.P, Vendruscolo, M, Dobson, C.M. The Amyloid State and Its Association with Protein Misfolding Diseases. Nat. Rev. Mol. Cell Biol. 2014, 15, 384-396.
2016.11.09 Wed Telehany, Stephen -- -- Ucisik, M. and Hammes-Schiffer S. (2015) Comparative Molecular Dynamics Studies of Human DNA Polymerase η. J. Chem. Inf. Model., 55 (12), 2672–2681. DOI: 10.1021/acs.jcim.5b00606
2016.11.16 Wed Cao, Xin -- -- Coutsias, E.A., et al.; A Kinematic View of Loop Closure. J. Compute. Chem. 2004, 25, 510-528.
2016.11.23 Wed -- -- -- THANKSGIVING BREAK
2016.11.30 Wed Jones, George -- -- Wang, Z., et al.; Drug-induced adverse events prediction with LINCS L100 data. Bioinformatics 2016, 32, 2338-2345.
2016.12.07 Wed Fallon, Zachary -- -- Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. J. Med. Chem. 2016, 59, 4171-4188.
2017 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2017.01.25 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) 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
2017.02.01 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?
2017.02.08 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?
  • Why do people commit scientific misconduct?
  • What are some consequences of committing scientific misconduct?
2017.02.15 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?
  • What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?
2017.02.22 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?
  • 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?
2017.03.01 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?
2017.03.08 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.
  • How many years past a publication, if asked, should a researcher be able provide "raw data"?
2017.03.15 Wed -- -- -- SPRING BREAK
2017.03.22 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 run hospital which might violate patients privacy?
2017.03.29 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, 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 ?
2017.04.05 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?
  • What are some advantages of using Animals in experiments?
  • Discuss the three R's?
  • Is our class for or against Animal testing?
2017.04.12 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2017.04.19 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2017.04.26 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2017.05.03 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2016-2017_AMS-532_Fall-Spring&oldid=10483"