Difference between revisions of "AMS-532 Journal Club in Computational Biology"

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=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===
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=== <center> Please see https://ringo.ams.stonybrook.edu/~rizzo for Rizzo Group Homepage </center> ===
 
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{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
 
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
 
|- style="background:white"
 
|- style="background:white"
 
! style="width:10%" | '''Instructor'''  
 
! style="width:10%" | '''Instructor'''  
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|Dr. Robert C. Rizzo    [631-632-9340, rizzorc@gmail.com]
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|Dr. Robert C. Rizzo    [631-632-9340, rizzorc -at- gmail.com]
 
|-
 
|-
 
| '''Course No.''' || AMS-532  
 
| '''Course No.''' || AMS-532  
 
|-
 
|-
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| '''Location/Time''' || See Yearly Syllabi
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| '''Location/Time''' || Wed 11:00PM - 11:55PM, Math Tower AMS seminar room (122A, First Floor)
 
|-
 
|-
 
| '''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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'''GENERAL INFORMATION:''' AMS-532 is a two semester course in which students spend at least 8 weeks in each of three different laboratories actively participating in the research of participating Computational Biology faculty.  In addition, students will attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during the rotations.  In the Spring, a third component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Lab Rotations, Journal Club, and Responsible Conduct of Research are required of all PhD students.  For Masters students, Lab Rotations are optional and may be pursued with interested faculty on a case-by-case basis. Students register for AMS-532 each semester.  
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'''GENERAL INFORMATION:''' GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects.  In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.
  
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'''All students (in other tracks, graduate programs, or already in a research group) are fully welcome to participate in the Journal Club component.'''
+
'''Learning Objectives:'''
 +
*(1) Actively participate in Journal Club discussions on Computationally Biology literature. 
 +
*(2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531). 
 +
*(3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).
 +
*(4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections:
 +
**(i) Course Overview: Fulfilling Responsible Conduct in Research Training
 +
**(ii) Integrity in Scholarship
 +
**(iii) Scientific Misconduct
 +
**(iv) Mentoring
 +
**(v) Ownership and Authorship
 +
**(vi) Plagiarism
 +
**(vii) Data Management
 +
**(viii) Journalism and Science
 +
**(ix) Responsible Conduct of Research Involving Human Subjects
 +
**(x) Responsible Conduct of Research Involving Laboratory Animals
  
  
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'''(1) Lab Rotations:'''  The goal of the "Lab Rotations" portion of AMS-532 is for PhD students in the AMS Computational Biology Track to learn in detail what and how research is conducted in at least three groups over the Fall and Spring semesters of the first year.  At the end of each rotation, students give a brief synopsis (~15 minutes) of their lab activities and accomplishments.  The goal of the rotations is to help students choose a research advisor and to help faculty members choose students.  Students should consult the AMS compbio track webpage at http://compbio.ams.sunysb.edu, talk with senior Stony Brook students, and contact potential PI's in an effort to narrow down a list to 3-4 potential laboratories.  Depending on availability, and in conjunction with the AMS-532 instructor, three rotations are then scheduled for the following dates:
 
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*Rotation 1:  Sep 20th – Nov 15th (Fall)
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'''(1) Journal Club:''' The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.
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*Rotation 2: Nov 15th – Feb 14th (Fall-Spring)
 
−
*Rotation 3: Feb 14th – April 18th (Spring)
 
  
  
−
'''(2) Journal Club:'''  The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs.  Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting.  Normally, research papers are suggested by the PI of the laboratory hosting the student.  An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.
+
'''(2) Responsible Conduct of Research (RCR):''' The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals.  Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies.  The RCR meetings will be run as small group breakout sessions followed by group discussion.  To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org.  See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings.   
−
 
+
 
−
 
 
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'''(3) Responsible Conduct of Research (RCR):''' Journal Club meetings in the Spring will initially be devoted to training in "Responsible Conduct of Research" on topics that include Integrity in Science, Scientific Misconduct, Collaborating and Mentoring, Authorship, Plagiarism, Managing Data, and Journalism and Science.  Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials which often include case studies.  The RCR meetings will be run as small group breakout sessions followed by group discussion.  To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org.  See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings.   
 
−
 
 
  
 
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.
 
'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.
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'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.
 
'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.
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'''REQUIRED SYLLABI STATEMENTS:'''  The University Senate has authorized that the following required statements appear in all teaching syllabi on the Stony Brook Campus. This information is also located on the Provost’s website: http://www.stonybrook.edu/commcms/provost/policies.shtml
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== '''Required Syllabi Statements:''' ==
 +
  The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php
  
  
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'''Americans with Disabilities Act:''' If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Disability Support Services, ECC(Educational Communications Center) Building, Room 128, (631)632-6748. They will determine with you what accommodations, if any, are necessary and appropriate. All information and documentation is confidential. https://web.stonybrook.edu/newfaculty/StudentResources/Pages/DisabilitySupportServices.aspx.  
+
'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities  and search Fire Safety and Evacuation and Disabilities.
  
  
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'''Academic Integrity:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/
+
'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html
  
  
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'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.
+
'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php
  
 
== Course Schedules==
 
== Course Schedules==
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*[[2013-2014 AMS-532 Fall-Spring]]
 
*[[2013-2014 AMS-532 Fall-Spring]]
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*[[2014-2015 AMS-532 Fall-Spring]]
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*[[2015-2016 AMS-532 Fall-Spring]]
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*[[2016-2017 AMS-532 Fall-Spring]]
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*[[2017-2018 AMS-532 Fall-Spring]]
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*[[2018-2019 AMS-532 Fall-Spring]]
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*[[2019-2020 AMS-532 Fall-Spring]]
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*[[2020-2021 AMS-532 Fall-Spring]]
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*[[2021-2022 AMS-532 Fall-Spring]]
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*[[2022-2023 AMS-532 Fall-Spring]]
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*[[2023-2024 AMS-532 Fall-Spring]]
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*[[2024-2025 AMS-532 Fall-Spring]]

Latest revision as of 12:37, 5 September 2024

Please see https://ringo.ams.stonybrook.edu/~rizzo for Rizzo Group Homepage


Instructor Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail.com]
Course No. AMS-532
Location/Time Wed 11:00PM - 11:55PM, Math Tower AMS seminar room (122A, First Floor)
Office Hours Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics


GENERAL INFORMATION: GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.

Learning Objectives:

  • (1) Actively participate in Journal Club discussions on Computationally Biology literature.
  • (2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531).
  • (3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).
  • (4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections:
    • (i) Course Overview: Fulfilling Responsible Conduct in Research Training
    • (ii) Integrity in Scholarship
    • (iii) Scientific Misconduct
    • (iv) Mentoring
    • (v) Ownership and Authorship
    • (vi) Plagiarism
    • (vii) Data Management
    • (viii) Journalism and Science
    • (ix) Responsible Conduct of Research Involving Human Subjects
    • (x) Responsible Conduct of Research Involving Laboratory Animals


(1) Journal Club: The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.


(2) Responsible Conduct of Research (RCR): The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings.


LITERATURE DISCLAIMER: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.


PRESENTATION DISCLAIMER: Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.

Required Syllabi Statements:

The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php


Student Accessibility Support Center Statement: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.


Academic Integrity Statement: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html


Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php

Course Schedules

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