AMS-531 Laboratory Rotations in Computational Biology

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage

Instructor	Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail.com]
Course No.	AMS-531
Location/Time	Individual
Office Hours	Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics

GENERAL INFORMATION: This is two semester course in which first year PhD students spend at least 8 weeks in each of three different laboratories actively participating in the research of participating Computational Biology faculty. At the end of each rotation, students give a presentation of their lab activities and accomplishments. The primary goal of rotations is to help students choose a research advisor and to help faculty members choose students. Students register for AMS 531 in both the Fall and Spring semesters of the first year. Fall and Spring, 0 - 3 credits, S/U grading. Crosslisted with PHY 584.

Learning Objectives:

• (1) Learn how research is conducted at a "very high research" University.
• (2) Actively participate in research of three Computational Biology faculty.
• (3) Gain experience working as a part of a team.
• (4) Learn to use cutting edge research tools in Computational Biology.
• (5) Explore research projects that could lead to dissertation work.
• (6) Gain experience giving group-meeting presentations on lab activities and accomplishments.

The goal of "Lab Rotations" 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. Note that Lab Rotations 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. 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://www.ams.sunysb.edu/CB/CBOverview.shtml, 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-531 instructor, three rotations are then scheduled for the following dates:

• Rotation 1: ~ Sep 29 – Nov 28 (Fall)
• Rotation 2: ~ Dec 01 – Feb 27 (Fall-Spring)
• Rotation 3: ~ Mar 02 – May 01 (Spring)

Lab Rotation Guidelines: The goal of lab rotations is to help students choose a research advisor and to help faculty members choose students. In particular, faculty members use rotations as a way to help gauge how a student will work in a laboratory setting and if they would be a productive team member of the lab. With this objective in mind it is important to consider the following points when doing each rotation.

• Become fully engaged in the lab during your rotation. Make arrangements with the group leader to have a desk or other place at which you can work and be sure to go to the lab everyday. If you need to work on class assignments do your homework in the lab. Students that rarely show up leave a less than favorable impression.

• Show interest in the lab's research. Ask questions.

• Read key papers from the lab. Become well-acquainted with tools being used in the group.

• Be proactive in communicating with others in the lab. Ask for help and guidance to get started.

• Attend lab meetings. Ask questions.

• Be proactive in asking your rotation advisor to discuss with you research projects which could be pursued should you join the group permanently.

• Keep in mind that faculty members must devote considerable time, effort, as well as provide financial assistance when they commit to becoming an advisor to a student. Thus, faculty members want to be sure that before they make such a commitment a student has good work habits, can communicate, is easy to work with, is interested in the lab's research, and wants to succeed in graduate school. Lab rotations can be used to show to potential advisors you have such qualities.

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 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

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.

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/

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.

Rotation Schedules

Academic Year	Participant	Track	Rotation 1 (~ Sep 20 to Nov 15)	Rotation 2 (~ Nov 15 to Feb 14)	Rotation 3 (~ Feb 14 to Apr 18)
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2016-2015	-, -	PhD -	-	-	-
2015-2014	Belfon, Kellon	PhD CHE	Simmerling	-	Rizzo
2015-2014	Cortes, Michael	PhD AMS	Rizzo	Balazsi	Green
2015-2014	Elkin, Rena	PhD AMS	MacCarthy	Tannenbaum	Balazsi
2015-2014	Lee, Stella	PhD AMS	Levy	MacCarthy	Dill
2015-2014	Sam-Ang, Panu	PhD AMS	Balazsi	Green	Reuter
2015-2014	Santos, Ruda	PhD BSB	Green	Li	Rizzo
2015-2014	Hassan, Mosavverul	MS AMS	Seeliger	Coutsias	Simmerling
2015-2014	Yin, Xingyu	PhD BSB	Glyn	Rizzo	Garcia-Diaz
2014-2013	Kennedy, Chelsea	PhD AMS	Zhu	Rizzo	Green
2014-2013	Li, Fangfei	PhD AMS	Rizzo	Green	Coutsias
2014-2013	Yu, Bihua	PhD AMS	Green	Coutsias	Zhu
2014-2013	Zhou, Junjie	PhD CHE	Rizzo	Raleigh	Simmerling
2013-2012	Krantsevich, Artyom	PhD AMS	MacCarthy	Schatz	Green
2013-2012	Krantsevich, Nick	PhD AMS	Rizzo	MacCarthy	Schatz
2013-2012	Li, Xindy	PhD AMS	Rizzo	Green	MacCarthy
2013-2012	Yuan, Chaohui	PhD AMS	MacCarthy	Rizzo	Green
2013-2012	Guo, Jiaye	PhD BSB	Boon	Rizzo	-
2013-2012	Shan, Emma	MS AMS	-	MacCarthy	-
2013-2012	Chen, Ye	MS AMS	-	-	MacCarthy
2013-2012	Amgalan, Anar	PhD PHY	Dill	Rizzo	Maslov
2012-2011	Jeewon, Sin	PhD AMS	Rizzo	Green	MacCarthy
2012-2011	Chen, Jeff	PhD AMS	Schatz	Maslov	MacCarthy
2012-2011	Sinayev, Roman	AMS MS	Green	Rizzo	Simmerling
2012-2011	Xia, Yunting	AMS MS	Rizzo	MacCarthy	Green
2012-2011	Zhou, Yuchen	AMS MS	Green	Rizzo	MacCarthy