2016-2017 AMS-532 Fall-Spring

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	--	--	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	O'Connell, Dan	--	--	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	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 Peter Williams Lecture Readings (Nature articles) Article 1 Article 2 Article 3 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 Michael Hadjiargyrou Lecture Reading 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?
2017.02.15 Wed	Class discussion	Responsible Conduct of Research (RCR)	(4) Mentoring	Stony Brook Lecture Clinton Rubin Lecture Readings 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?
2017.02.22 Wed	Class discussion	Responsible Conduct of Research (RCR)	(5) Ownership and Authorship	Stony Brook Lecture Peter Gergen Lecture Readings 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?
2017.03.01 Wed	Class discussion	Responsible Conduct of Research (RCR)	(6) Plagiarism	Stony Brook Lecture Richard Clark Lecture Readings 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?
2017.03.08 Wed	Class discussion	Responsible Conduct of Research (RCR)	(7) Data Management	Stony Brook Lecture Stefan Judex Lecture Readings 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"?
2017.03.15 Wed	--	--	--	SPRING BREAK
2017.03.22 Wed	Class discussion	Responsible Conduct of Research (RCR)	(8) Journalism and Science	Stony Brook Lecture Howard Schneider Lecture Readings (3 Case Studies) 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?
2017.03.29 Wed	Class discussion	Responsible Conduct of Research (RCR)	(9) Responsible Conduct of Research Involving Human Subjects	Stony Brook Lecture Judy Matuk Lecture Readings: (Background Information, Case Studies, Helsinki Manuscript) Human Subjects handout 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 Tom Zimmerman Lecture Readings (Case Studies) 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?
2017.04.12 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2017.04.19 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2017.04.26 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2017.05.03 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS