Difference between revisions of "2018-2019 AMS-532 Fall-Spring"

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| '''Course No.''' || AMS-532  
 
| '''Course No.''' || AMS-532  
 
|-
 
|-
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| '''Location/Time''' || Physics Bldg. P117, Wed 12:00PM - 12:53PM  
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| '''Location/Time''' || PHYSICS P122 WESTCAMPUS, Wed 12:00PM - 12:53PM  
 
|-
 
|-
 
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics
 
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics
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|-
 
|-
  
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| 2018.08.30 Wed || Rizzo, Robert || -- || -- || Organizational Meeting
+
| 2018.08.29 Wed || Rizzo, Robert || -- || -- || Organizational Meeting
 
|-
 
|-
  
−
| 201809.06 Wed || Fallon, Zach || -- || -- || Morin et al; Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. ''Nucleic Acids Research'' '''2015''', ''43'', 3643-3652.
+
| 2018.09.05 Wed || Mudiyansel, Lakshan || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
|-
 
|-
  
−
| 2018.09.13 Wed || -- || -- || -- || AMS Grad Student BBQ
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| 2018.09.12 Wed || -- || -- || -- || AMS Grad Student BBQ
 
|-
 
|-
  
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| 2018.09.20 Wed || Nassar, Roy || -- || -- || MacCallum et al; Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. ''PNAS'' '''2015''', ''112'', 6985-6990.
+
| 2018.09.19 Wed || Talis, Emma || -- || -- || Rietkerk et al; Regular pattern formation in real ecosystems. ''Trends in Ecology & Evolution'' '''2008''', ''23'', 169-175.
 
|-
 
|-
  
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| 2018.09.27 Wed || Ignatov, Misha || -- || -- || Smith et al; ANI-1: An extensible neural network potential with DFT accuracy at force field computational cost. ''Chemical Science'' '''2017''', ''8'', 3192–3203.
+
| 2018.09.26 Wed || Singh, Niven || -- || -- || Jiang et al; Cholinergic Signaling Controls Conditioned Fear Behaviors and Enhances Plasticity of Cortical-Amygdala Circuits. ''Neuron'' '''2016''', ''90'', 1057-1070.
 
|-
 
|-
  
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| 2018.10.04 Wed || Cao, Xin || -- || -- || Coutsias et al; Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. ''J. Chem. Theory. Comp.'' '''2016''', ''12'', 4674-4687.
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| 2018.10.03 Wed || Liang, Tong || -- || -- || Schneidman et al; Weak pairwise correlations imply strongly correlated network states in a neural population. ''Nature'' '''2016''', ''440'', 1007-1012.
 
|-
 
|-
  
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| 2018.10.11 Wed || Tang, Cathy || -- || -- || Sheng et al; Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation. ''Frontiers in Immunology'' '''2017''', ''8'', Article 537.
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| 2018.10.10 Wed || Kotelnikov, Sergei || -- || -- || Cai et al; A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation. ''J Comput Phys'' '''2008''', ''227'', 10162-10177.
 
|-
 
|-
  
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| 2018.10.18 Wed || Jones, George || -- || -- || Martin-Garcia et al; Serial femtosecond crystallography: A revolution in structural biology. ''Archives of Biochemistry and Biophysics'' '''2016''', ''602'', 32-47.
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| 2018.10.17 Wed || Bickel, John || -- || -- || Miller et al; Molecular dynamics study of the opening mechanism for DNA polymerase I. ''PLOS Comp Bio'' '''2014''', ''10'', e1003961.
 
|-
 
|-
  
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| 2018.10.25 Wed || Carter, Jason || -- || -- || Li et al; Landscape of tumor-infiltrating T cell repertoire of human cancers. ''Nature Genetics'' '''2016''', ''48'', 725-732.
+
| 2018.10.24 Wed || Crosser, Jacob || -- || -- || Boerlin et al; Predicting Coding of Dynamic Variables in Balanced Spiking Networks. ''PLOS Comp Bio'' '''2013''', ''9'', e1003258.
 
|-
 
|-
  
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| 2018.11.01 Wed || Telehany, Steve || -- || -- || Schmidt et al; Small-Molecule Inhibitors of Dengue-Virus Entry. ''PLOS Pathogens'' '''2012''', ''8'', e1002627
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| 2018.10.31 Wed || Ashizawa, Ryota || -- || -- || Decherchi et al; The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning. ''Nature communications'' '''2015''', ''6'', 1-10.
 
|-
 
|-
  
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| 2018.11.08 Wed || Taouil, Adam || -- || -- || Woodcock et al; MSCALE: A General Utility for Multiscale Modeling. ''J. Chem. Theory. Comp.'' '''2011''', ''7'', 1208-1219.
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| 2018.11.07 Wed || Wang, Yuzhang || -- || -- || Miao et al; Improved Reweighing of Accelerated Molecular Dynamics Simulations for Free Energy Calculations. ''JCTC'' '''2014''', ''10'', 2677-2689.
  
 
|-
 
|-
  
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| 2018.11.15 Wed || Manathunga, Lakshan || -- || -- || Philips et al; LigandRNA: computational predictor of RNA-ligand interactions. ''RNA' '''2013''', ''19'', 1605-1616.
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| 2018.11.14 Wed || Bickel, John & Crosser, Jacob || -- || -- || Lab Rotation Presentations
 
|-
 
|-
  
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| 2018.11.22 Wed || -- || -- || -- || THANKSGIVING BREAK
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| 2018.11.21 Wed || -- || -- || -- || THANKSGIVING BREAK
 
|-
 
|-
  
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| 2018.11.29 Wed || Talis, Emma || -- || -- || Oprea et al; Somatic Mutations Leads to Efficient Affinity Maturation When Centrocytes Recycle Back to Centroblasts. ''J. Immunology.'' '''1997''', ''158'', 5155-5162.
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| 2018.11.28 Wed || Ashizawa, Ryota & Wang, Yuzhang || -- || -- || Lab Rotation Presentations
 
|-
 
|-
  
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| 2018.12.06 Wed || Maria Spyrou, Ioanna || -- || -- || Berg et al; Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplication. ''BMC Evolutionary Biology.'' '''2004''', ''4'', 51.
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| 2018.12.05 Wed || -- || -- || -- || AMS Holiday Party
 
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|-
  
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SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
|-
 
|-
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| 2019.01.24 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||
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| 2019.01.30 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:  
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|-
 
|-
  
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| 2019.01.31 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
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| 2019.02.06 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
 
Stony Brook Lecture
 
Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p42411560 Peter Williams Lecture]
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*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture]
  
  
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|-
 
|-
  
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| 2019.02.07 Wed || Class discussion  || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
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| 2019.02.13 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]
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*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture]
  
  
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|-
 
|-
  
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| 2019.02.14 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||  
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| 2019.02.20 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||  
 
Stony Brook Lecture
 
Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p20134531 Clinton Rubin Lecture]
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*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture]
  
  
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|-
  
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| 2019.02.21 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
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| 2019.02.27 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
 
Stony Brook Lecture
 
Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p32819600 Peter Gergen Lecture]
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*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture]
  
  
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|-
 
|-
  
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| 2019.02.28 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
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| 2019.03.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
 
Stony Brook Lecture
 
Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
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*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture]
  
  
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|-
 
|-
  
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| 2019.03.07 Wed || -- || -- || -- || SNOW DAY
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| 2019.03.13 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
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|-
 
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| 2019.03.14 Wed || -- || -- || -- || SPRING BREAK
 
−
|-
 
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| 2019.03.21 Wed || -- || -- || -- || SNOW DAY
 
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|-
 
−
 
 
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| 2019.03.28 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
 
 
Stony Brook Lecture
 
Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
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*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture]
  
  
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*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"?   
 
|-
 
|-
−
 
+
| 2019.03.20 Wed || -- || -- || -- || SPRING BREAK
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| 2019.04.04 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
+
|-
 +
| 2019.03.27 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]
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*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture]
  
  
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|-
  
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| 2019.04.11 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
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| 2019.04.03 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]
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*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture]
  
  
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|-
  
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| 2018.04.18 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
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| 2019.04.10 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
 
Stony Brook Lecture
 
Stony Brook Lecture
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*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
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*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture]
  
  
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*Is our class for or against Animal testing?
 
*Is our class for or against Animal testing?
 
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|-
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| 2019.04.25 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| 2019.04.17 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| 2019.04.24 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 +
|-
 +
| 2019.05.01 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 +
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| 2019.05.08 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
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| 2019.05.02 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
 
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Latest revision as of 15:45, 17 August 2021

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 WESTCAMPUS, 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)

2018 Fall Participant Rotations or Research Group Topic References

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

2018.08.29 Wed Rizzo, Robert -- -- Organizational Meeting
2018.09.05 Wed Mudiyansel, Lakshan -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.09.12 Wed -- -- -- AMS Grad Student BBQ
2018.09.19 Wed Talis, Emma -- -- Rietkerk et al; Regular pattern formation in real ecosystems. Trends in Ecology & Evolution 2008, 23, 169-175.
2018.09.26 Wed Singh, Niven -- -- Jiang et al; Cholinergic Signaling Controls Conditioned Fear Behaviors and Enhances Plasticity of Cortical-Amygdala Circuits. Neuron 2016, 90, 1057-1070.
2018.10.03 Wed Liang, Tong -- -- Schneidman et al; Weak pairwise correlations imply strongly correlated network states in a neural population. Nature 2016, 440, 1007-1012.
2018.10.10 Wed Kotelnikov, Sergei -- -- Cai et al; A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation. J Comput Phys 2008, 227, 10162-10177.
2018.10.17 Wed Bickel, John -- -- Miller et al; Molecular dynamics study of the opening mechanism for DNA polymerase I. PLOS Comp Bio 2014, 10, e1003961.
2018.10.24 Wed Crosser, Jacob -- -- Boerlin et al; Predicting Coding of Dynamic Variables in Balanced Spiking Networks. PLOS Comp Bio 2013, 9, e1003258.
2018.10.31 Wed Ashizawa, Ryota -- -- Decherchi et al; The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning. Nature communications 2015, 6, 1-10.
2018.11.07 Wed Wang, Yuzhang -- -- Miao et al; Improved Reweighing of Accelerated Molecular Dynamics Simulations for Free Energy Calculations. JCTC 2014, 10, 2677-2689.
2018.11.14 Wed Bickel, John & Crosser, Jacob -- -- Lab Rotation Presentations
2018.11.21 Wed -- -- -- THANKSGIVING BREAK
2018.11.28 Wed Ashizawa, Ryota & Wang, Yuzhang -- -- Lab Rotation Presentations
2018.12.05 Wed -- -- -- AMS Holiday Party
2019 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2019.01.30 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
2019.02.06 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?
2019.02.13 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?
  • Who are some of your mentors?
2019.02.20 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?
2019.02.27 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?
2019.03.06 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?
2019.03.13 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"?
2019.03.20 Wed -- -- -- SPRING BREAK
2019.03.27 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?
2019.04.03 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 ?
2019.04.10 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?
2019.04.17 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2019.04.24 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2019.05.01 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2019.05.08 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
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