Difference between revisions of "2010-2011 AMS-532 Fall-Spring"

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(→‎Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring))
 
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'''Announcement'''
 
'''Announcement'''
−
*Posted on 12/01 by Trent:
+
*Posted on 09/01 by Trent:
 
:#Each participant please update the Wiki as required
 
:#Each participant please update the Wiki as required
  
−
*Posted on 12/02 by Lingling:
+
*Posted on 09/10 by Lingling:
 
:#Lab rotation is a very important part of this course. It is recommended （required for PhD track) that every new student in Computational Biology track to do three rotations in research groups of his/her special interests. Student must contacted four professors and get their permissions to do a rotation in their group. If you have any questions in regard to choosing a lab, please feel free to talk to professor Rizzo and his students （Trent Balius and Lingling Jiang）.  Rizzo lab is located in Room 3-129, Math Tower.
 
:#Lab rotation is a very important part of this course. It is recommended （required for PhD track) that every new student in Computational Biology track to do three rotations in research groups of his/her special interests. Student must contacted four professors and get their permissions to do a rotation in their group. If you have any questions in regard to choosing a lab, please feel free to talk to professor Rizzo and his students （Trent Balius and Lingling Jiang）.  Rizzo lab is located in Room 3-129, Math Tower.
 +
*Posted on 09/15 by Lingling:
 +
:#Since some students find that the presentation is scheduled close to their AMS535 presentation, I modified the schedule so that people can prepare one at a time.
  
−
== Journal Club Participants, Topics, References, and Schedule ==
+
*Posted on 11/17 by Lingling:
 +
:#I set up the rotation presentation schedule. Please prepare for a 15 minutes talk about your first rotation.
 +
:#We won't have journal club next Wednesday as it will follow a Friday schedule then.
 +
 
 +
== Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring) ==
  
  
Line 19: Line 25:
 
|-
 
|-
  
−
| 2010.09.08 || Adler, Jeremy || -- || -- || --  
+
| 2010.09.08 || Adler, Jeremy || -- || Network identification || Chu LH, Chen BS. Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targetsBMC Syst Biol. 2008 Jun 30;2:56.
 +
|-
 +
| 2010.09.15 || Vo, Emily || -- || GWAS || Liu, J. Z.; et al., A versatile gene-based test for genome-wide association studies. ''Am. J. Hum. Genet.'' '''2010''', ''87'', 139-145.
 +
|-
 +
| 2010.09.22 || Jiang, Lingling || -- || HIV-gp41 || Shi, W. X.; et al., Structural Characterization of HIV gp41 with the Membrane-proximal External Region. ''J. Bio. Che.'' '''2010''', ''285'', 24290-24298.
 +
|-
 +
| 2010.09.29 || Grinshpun, Boris || Maslov || Prokaryotic Metabolic Networks - Quadratic Scaling|| Maslov, S.; et al., Toolbox model of evolution of prokaryotic metabolic networks and their regulation. ''Proc. Natl. Acad. Sci.'' '''2009''', ''106'', 9743-9748.
 +
|-
 +
| 2010.10.06 || Liu, Jiangyang || -- || -- || --
 +
|-
 +
| 2010.10.13 || Li, Miao || Wei Zhu || Normalization and DE Evaluation|| Bullard et al.: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. ''BMC Bioinformatics'' ''' 2010 11:94'''.
 +
|-
 +
| 2010.10.20 || Yao, Yuan || Wang || Enzyme Conformation || Wei Min; et al., Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction: Effects of Protein Conformational Dynamics on Enzyme Catalysis. J. Phys. Chem. B '''2008''', 112, 454-466
 +
|-
 +
| 2010.10.27 || Gardin, Justin Michael || -- || -- || --
 +
|-
 +
| 2010.11.03 || Chen, Jia Ruo || -- || -- || --
 +
|-
 +
| 2010.11.10 || Cao, Yiwei || Green || Protein Design || Shannon A. M.; et al., One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. ''Protein Sci.'' '''2005''', ''14'', 1293-1304.
 +
|-
 +
| 2010.11.17 || Balius, Trent  || Rizzo || Drug design ||
 +
Jorgensen W. L., Efficient Drug Lead Discovery and Optimization. Acc. Chem. Res. '''2009''', ''42'', ''(6)'', 724-733
 +
|-
 +
| 2010.12.01 || Grinshpun, B; Liu, J; Li, M || -- || First rotation presentations || --
 +
|-
 +
| 2010.12.08 || Gardin, J; Chen, J; Cao, Y; Yao, Y || -- || First rotation presentations || --
 +
 
 +
|- style="background:lightgreen"
 +
| '''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
 +
*[https://meeting.sinc.stonybrook.edu/p42411560 Williams Lecture]
 +
 
 +
 
 +
Readings (Nature articles)
 +
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]
 +
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]
 +
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf 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
 +
*[https://meeting.sinc.stonybrook.edu/p30629381 Hadjiargyrou Lecture]
 +
 
 +
 
 +
Reading
 +
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct 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
 +
*[https://meeting.sinc.stonybrook.edu/p20134531 Rubin Lecture]
 +
 
 +
 
 +
Readings
 +
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring 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?
 +
 
 
|-
 
|-
−
| 2010.09.15 || Vo, Emily || -- || GWAS || Liu, J. Z.; et al., A versatile gene-based test for genome-wide association studies. ''Am. J. Hum. Genet.'' '''2010''', ''87, 139-145.  
+
| 2011.03.02 || Class discussion || Responsible Conduct of Research (RCR) || (4) Authorship ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p32819600 Gergen Lecture]
 +
 
 +
 
 +
Readings
 +
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship 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?
 
|-
 
|-
−
| 2010.09.22 || Jiang, Lingling || -- || -- || --
+
 
 +
| 2010.03.09 || Class discussion || Responsible Conduct of Research (RCR) || (5) Plagiarism ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p41971516 Clark Lecture]
 +
 
 +
 
 +
Readings
 +
*[http://www.stonybrook.edu/uaa/academicjudiciary/policies.shtml 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?
 
|-
 
|-
−
| 2010.09.29 || Cao, Yiwei || -- || -- || --
+
 
 +
 
 +
| 2011.03.16 || Class discussion || Responsible Conduct of Research (RCR) || (6) Managing Data ||
 +
Stony Brook Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p68134598 Huddy Lecture]
 +
 
 +
 
 +
Readings
 +
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data 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. 
 
|-
 
|-
−
| 2010.10.06 || Chen, Jia Ruo || -- || -- || --
+
 
 +
| 2010.03.23 || Class discussion || Responsible Conduct of Research (RCR) || (7) Journalism ||
 +
Stony Brok Lecture
 +
*[https://meeting.sinc.stonybrook.edu/p99353453 Schneider Lecture]
 +
 
 +
 
 +
Readings (3 Case Studies)
 +
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2011-2010_AMS532_Fall_and_Spring/scientists_and_reporters.pdf 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? 
 +
 
 
|-
 
|-
−
| 2010.10.13 || Gardin, Justin Michael || -- || -- || --
+
| 2011.03.30 || Grinshpun, B; Gardin, J || -- || Second rotation presentations || --
 
|-
 
|-
−
| 2010.10.20 || Grinshpun, Boris || -- || -- || --
+
| 2011.04.06 || Yao, Y; Cao, Y || -- || Second rotation presentations || --
 
|-
 
|-
−
| 2010.10.27 || Li, Miao || -- || -- || --
+
| 2011.04.13 || Chen, J; || -- || Second rotation presentations || --
 
|-
 
|-
−
| 2010.11.03 || Liu, Jiangyang || -- || -- || --
+
| 2011.04.20 || Spring Break || Spring Break  || Spring Break || Spring Break
 
|-
 
|-
−
| 2010.11.10 || Yao, Yuan || -- || -- || --
+
| 2011.04.27 || URECA Celebration || URECA Celebration || SAC Ballrooms A&B || 10am-4 pm ALL DAY
 
|-
 
|-
−
| 2010.11.17 || Balius, Trent || -- || -- || --
+
| 2011.05.04 || Cao, Y || -- || Second & Third rotation presentations || --
 
|-
 
|-
−
| 2010.12.01 || Last, First || -- || -- || --
+
| 2011.05.11 (last class) || Yao, Y; Chen, J; Gardin, J; Grinshpun, B || -- || Third rotation presentations || --
 
|-
 
|-
−
| 2010.12.08 || Last, First || -- || -- || --
+
|}

Latest revision as of 14:22, 5 August 2013

Announcement

  • Posted on 09/01 by Trent:
  1. Each participant please update the Wiki as required
  • Posted on 09/10 by Lingling:
  1. Lab rotation is a very important part of this course. It is recommended （required for PhD track) that every new student in Computational Biology track to do three rotations in research groups of his/her special interests. Student must contacted four professors and get their permissions to do a rotation in their group. If you have any questions in regard to choosing a lab, please feel free to talk to professor Rizzo and his students （Trent Balius and Lingling Jiang）. Rizzo lab is located in Room 3-129, Math Tower.
  • Posted on 09/15 by Lingling:
  1. Since some students find that the presentation is scheduled close to their AMS535 presentation, I modified the schedule so that people can prepare one at a time.
  • Posted on 11/17 by Lingling:
  1. I set up the rotation presentation schedule. Please prepare for a 15 minutes talk about your first rotation.
  2. We won't have journal club next Wednesday as it will follow a Friday schedule then.

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

2010 Fall Participant Rotations or Research Group Topic References

NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT

2010.09.08 Adler, Jeremy -- Network identification Chu LH, Chen BS. Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targetsBMC Syst Biol. 2008 Jun 30;2:56.
2010.09.15 Vo, Emily -- GWAS Liu, J. Z.; et al., A versatile gene-based test for genome-wide association studies. Am. J. Hum. Genet. 2010, 87, 139-145.
2010.09.22 Jiang, Lingling -- HIV-gp41 Shi, W. X.; et al., Structural Characterization of HIV gp41 with the Membrane-proximal External Region. J. Bio. Che. 2010, 285, 24290-24298.
2010.09.29 Grinshpun, Boris Maslov Prokaryotic Metabolic Networks - Quadratic Scaling Maslov, S.; et al., Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc. Natl. Acad. Sci. 2009, 106, 9743-9748.
2010.10.06 Liu, Jiangyang -- -- --
2010.10.13 Li, Miao Wei Zhu Normalization and DE Evaluation Bullard et al.: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010 11:94.
2010.10.20 Yao, Yuan Wang Enzyme Conformation Wei Min; et al., Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction: Effects of Protein Conformational Dynamics on Enzyme Catalysis. J. Phys. Chem. B 2008, 112, 454-466
2010.10.27 Gardin, Justin Michael -- -- --
2010.11.03 Chen, Jia Ruo -- -- --
2010.11.10 Cao, Yiwei Green Protein Design Shannon A. M.; et al., One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Protein Sci. 2005, 14, 1293-1304.
2010.11.17 Balius, Trent Rizzo Drug design

Jorgensen W. L., Efficient Drug Lead Discovery and Optimization. Acc. Chem. Res. 2009, 42, (6), 724-733

2010.12.01 Grinshpun, B; Liu, J; Li, M -- First rotation presentations --
2010.12.08 Gardin, J; Chen, J; Cao, Y; Yao, Y -- First rotation presentations --
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


Readings (Nature articles)


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


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?
  • 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


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?
2011.03.02 Class discussion Responsible Conduct of Research (RCR) (4) 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?
  • 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


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?
2011.03.16 Class discussion Responsible Conduct of Research (RCR) (6) Managing Data

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.
2010.03.23 Class discussion Responsible Conduct of Research (RCR) (7) Journalism

Stony Brok 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 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 --
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