Difference between revisions of "2013-2014 AMS-532 Fall-Spring"
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(→Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)) |
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− | | 2013.08.28 Wed || | + | | 2013.08.28 Wed || Last name, First name || -- || Topic || paper |
|- | |- | ||
− | | 2013.09.04 Wed || Krantsevich, Nikolay || Green || topic || Travers, SA. Conservation, compensation, and evolution of N-linked glycansin the HIV-1 group M subtypes and circulating recombinant forms. ''ISRN AIDS.'' '''2012 Nov''' | + | | 2013.09.04 Wed || Krantsevich, Nikolay || Green || topic || Travers, SA. Conservation, compensation, and evolution of N-linked glycansin the HIV-1 group M subtypes and circulating recombinant forms. ''ISRN AIDS.'' '''2012 Nov'''. |
|- | |- | ||
− | | 2013.09.11 Wed || | + | | 2013.09.11 Wed || Yuan, Chaohui || MacCarthy || topic || Oprea, M. and Perelson, AS. Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. ''J Immunology''. '''1997 Jun'''. ''158(11)''. 5155-5162. |
|- | |- | ||
− | | 2013.09.18 Wed || | + | | 2013.09.18 Wed || Lee, Xindi (Cindy) || Green || topic || Eklund, R. and Widmalm, G. Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. ''Carbohydrate Reasearch''. '''2002 Nov'''. ''338(2003)''. 393-398. |
|- | |- | ||
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− | | 2013.10.02 Wed || | + | | 2013.10.02 Wed || Krantsevich, Artem || Green || topic || Kim, Pan-Jun. ''et al.'' Centralized modularity of N-linked glycosylation pathways in mammalian cells. ''PLoS ONE''. '''2009 Oct'''. ''4(10)''. e7317. |
|- | |- | ||
− | | 2013.10.09 Wed || | + | | 2013.10.09 Wed || Amgalan, Anar || Dill || topic || Pang, Tin Yau. and Maslov, Sergei. Universal distribution of component frequencies in biological and technological systems. ''P.N.A.S.'' '''2013 Feb'''. ''110(52)''. 21054-21058. |
|- | |- | ||
− | | 2013.10.16 Wed || | + | | 2013.10.16 Wed || Shan, Jiahui (Emma) || -- || topic || Alexandrov, LB. ''et al.'' Signatures of mutational processes in human cancer. ''Nature''. '''2013 Aug'''. ''500''. 415-421. |
|- | |- | ||
− | | 2013.10.23 Wed || | + | | 2013.10.23 Wed || Zou, Junjie || -- || topic || Lill, MA. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. ''Biochemistry''. '''2011 Jun'''. ''50''. 6157-6169. |
|- | |- | ||
− | | 2013.10.30 Wed || | + | | 2013.10.30 Wed || Li, Fangfei || -- || topic || Forli, S. and Olson, AJ. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. ''J Med Chem''. '''2012'''. ''55''. 623-638. |
|- | |- | ||
− | | 2013.11.06 Wed || | + | | 2013.11.06 Wed || Yu, Bihua || -- || topic || Green, DF. A statistical framework for hierarchical methods in molecular simulation and design. ''J Chem Theory Comput''. '''2010 Apr'''. ''6''. 1682-1697. |
|- | |- | ||
− | | 2013.11.13 Wed || | + | | 2013.11.13 Wed || Kennedy, Chelsea || -- || -- || ROTATION/RESEARCH PRESENTATIONS |
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|- style="background:lightgreen" | |- style="background:lightgreen" | ||
− | | ''' | + | | '''2014 Spring''' |
| '''Participant''' | | '''Participant''' | ||
| '''Rotations or Research Group''' | | '''Rotations or Research Group''' | ||
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SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH''' | SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH''' | ||
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− | | 2014.01.29 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: | + | | 2014.01.29 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training || |
− | Overall Course Requirements | + | Discussion of Overall Course Requirements which include: |
− | *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] | + | *View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [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 | *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 | *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 | ||
|- | |- | ||
− | | 2014.02.05 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) || | + | |
+ | | 2014.02.05 Wed || - || -- || -- || SNOW STORM, CLASS CANCELLED | ||
+ | |- | ||
+ | |||
+ | | 2014.02.12 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] | ||
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− | | 2014.02. | + | | 2014.02.19 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] | ||
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Reading | Reading | ||
− | *[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct] | + | *[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct] |
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− | | 2014.02. | + | | 2014.02.26 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] | ||
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− | | 2014. | + | | 2014.03.05 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] | ||
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*Is it ever appropriate for authorship to change during a project or potential paper? | *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? | *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? | ||
|- | |- | ||
− | | 2014.03. | + | | 2014.03.12 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] | ||
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+ | | 2014.03.19 Wed || -- || -- || -- || SPRING BREAK | ||
+ | |- | ||
− | | 2014.03. | + | | 2014.03.26 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] | ||
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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? | *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? | *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. | + | *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"? | ||
|- | |- | ||
− | | 2014. | + | | 2014.04.02 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] | ||
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Readings (3 Case Studies) | Readings (3 Case Studies) | ||
− | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/ | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout] |
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− | | 2014.04. | + | | 2014.04.09 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] | ||
− | Readings: (Background Information, Case Studies, Helsinki | + | Readings: (Background Information, Case Studies, Helsinki Manuscript) |
− | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/ | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout] |
− | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/ | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript] |
Discussion | 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 1: Was this an ethical trial? If so, why? If not, why not? | ||
− | *From Helsinki | + | *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 ? | ||
|- | |- | ||
− | | 2014.04. | + | | 2014.04.16 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] | ||
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Readings (Case Studies) | Readings (Case Studies) | ||
− | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/ | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout] |
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| 2014.04.23 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS | | 2014.04.23 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS |
Latest revision as of 15:25, 9 April 2014
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 P124 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)
2013 Fall | Participant | Rotations or Research Group | Topic | References
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT |
2013.08.28 Wed | Last name, First name | -- | Topic | paper |
2013.09.04 Wed | Krantsevich, Nikolay | Green | topic | Travers, SA. Conservation, compensation, and evolution of N-linked glycansin the HIV-1 group M subtypes and circulating recombinant forms. ISRN AIDS. 2012 Nov. |
2013.09.11 Wed | Yuan, Chaohui | MacCarthy | topic | Oprea, M. and Perelson, AS. Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. J Immunology. 1997 Jun. 158(11). 5155-5162. |
2013.09.18 Wed | Lee, Xindi (Cindy) | Green | topic | Eklund, R. and Widmalm, G. Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. Carbohydrate Reasearch. 2002 Nov. 338(2003). 393-398. |
2013.09.25 Wed | Last name, First name | -- | topic | paper |
2013.10.02 Wed | Krantsevich, Artem | Green | topic | Kim, Pan-Jun. et al. Centralized modularity of N-linked glycosylation pathways in mammalian cells. PLoS ONE. 2009 Oct. 4(10). e7317. |
2013.10.09 Wed | Amgalan, Anar | Dill | topic | Pang, Tin Yau. and Maslov, Sergei. Universal distribution of component frequencies in biological and technological systems. P.N.A.S. 2013 Feb. 110(52). 21054-21058. |
2013.10.16 Wed | Shan, Jiahui (Emma) | -- | topic | Alexandrov, LB. et al. Signatures of mutational processes in human cancer. Nature. 2013 Aug. 500. 415-421. |
2013.10.23 Wed | Zou, Junjie | -- | topic | Lill, MA. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. Biochemistry. 2011 Jun. 50. 6157-6169. |
2013.10.30 Wed | Li, Fangfei | -- | topic | Forli, S. and Olson, AJ. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. J Med Chem. 2012. 55. 623-638. |
2013.11.06 Wed | Yu, Bihua | -- | topic | Green, DF. A statistical framework for hierarchical methods in molecular simulation and design. J Chem Theory Comput. 2010 Apr. 6. 1682-1697. |
2013.11.13 Wed | Kennedy, Chelsea | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
2013.11.20 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
2013.11.27 Wed | - | -- | -- | THANKSGIVING BREAK |
2013.12.04 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
2014 Spring | Participant | Rotations or Research Group | Topic | References
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH |
2014.01.29 Wed | Class discussion | Responsible Conduct of Research (RCR) | (1) Course Overview: Fulfilling Responsible Conduct in Research Training |
Discussion of Overall Course Requirements which include:
|
2014.02.05 Wed | - | -- | -- | SNOW STORM, CLASS CANCELLED |
2014.02.12 Wed | Class discussion | Responsible Conduct of Research (RCR) | (2) Integrity in Scholarship (Introduction to Ethics and Science) |
Stony Brook Lecture
|
2014.02.19 Wed | Class discussion | Responsible Conduct of Research (RCR) | (3) Scientific Misconduct |
Stony Brook Lecture
|
2014.02.26 Wed | Class discussion | Responsible Conduct of Research (RCR) | (4) Mentoring |
Stony Brook Lecture
|
2014.03.05 Wed | Class discussion | Responsible Conduct of Research (RCR) | (5) Ownership and Authorship |
Stony Brook Lecture
|
2014.03.12 Wed | Class discussion | Responsible Conduct of Research (RCR) | (6) Plagiarism |
Stony Brook Lecture
|
2014.03.19 Wed | -- | -- | -- | SPRING BREAK |
2014.03.26 Wed | Class discussion | Responsible Conduct of Research (RCR) | (7) Data Management |
Stony Brook Lecture
|
2014.04.02 Wed | Class discussion | Responsible Conduct of Research (RCR) | (8) Journalism and Science |
Stony Brook Lecture
|
2014.04.09 Wed | Class discussion | Responsible Conduct of Research (RCR) | (9) Responsible Conduct of Research Involving Human Subjects |
Stony Brook Lecture
Discussion
|
2014.04.16 Wed | Class discussion | Responsible Conduct of Research (RCR) | (10) Responsible Conduct of Research Involving Laboratory Animals |
Stony Brook Lecture
Discussion
|
2014.04.23 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
2014.04.30 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
2014.05.07 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |