2011-2012 AMS-532 Fall-Spring

Announcement

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

2011 Fall	Participant	Rotations or Research Group	Topic	References NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS 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	Chen, Jeff and Sinayev, Roman	--	topic	ROTATION/RESEARCH PRESENTATIONS
2011.12.07	Xia, Yunting and Zhou, Yuchen	--	topic	ROTATION/RESEARCH PRESENTATIONS
2011.12.14	Sin, Jeewoen	--	topic	ROTATION/RESEARCH PRESENTATIONS
2012.01.	Last name, First name	--	topic	paper
2011 Spring	Participant	Rotations or Research Group	Topic	References NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT
--	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 under the POLICY heading located at http://www.stonybrook.edu/research/orc/rcr/index.shtml 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
2011.02.02 (first class)	Class Cancelled due to Ice Storm	--	--	--
2011.02.09	Class discussion	Responsible Conduct of Research (RCR)	(1) Introduction to Ethics and Science	Stony Brook Lecture 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?
2011.02.16	Class discussion	Responsible Conduct of Research (RCR)	(2) Scientific Misconduct	Stony Brook Lecture Hadjiargyrou Lecture Reading Introduction and Case Study 1 Sections from Columbia University online RCR course 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?
2011.02.23	Class discussion	Responsible Conduct of Research (RCR)	(3) Mentorship	Stony Brook Lecture Rubin Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR course 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?
2011.03.02	Class discussion	Responsible Conduct of Research (RCR)	(4) Authorship	Stony Brook Lecture Gergen Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR course 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?
2010.03.09	Class discussion	Responsible Conduct of Research (RCR)	(5) Plagiarism	Stony Brook Lecture 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?
2011.03.16	Class discussion	Responsible Conduct of Research (RCR)	(6) Managing Data	Stony Brook Lecture Huddy Lecture Readings Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR course 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.
2010.03.23	Class discussion	Responsible Conduct of Research (RCR)	(7) Journalism	Stony Brok Lecture 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 hospital which might violate patients privacy?
2011.03.30	Grinshpun, B; Gardin, J	--	Second rotation presentations	--
2011.04.06	Yao, Y; Cao, Y	--	Second rotation presentations	--
2011.04.13	Chen, J;	--	Second rotation presentations	--
2011.04.20	Spring Break	Spring Break	Spring Break	Spring Break
2011.04.27	URECA Celebration	URECA Celebration	SAC Ballrooms A&B	10am-4 pm ALL DAY
2011.05.04	Cao, Y	--	Second & Third rotation presentations	--
2011.05.11 (last class)	Yao, Y; Chen, J; Gardin, J; Grinshpun, B	--	Third rotation presentations	--