Difference between revisions of "Stony Brook Joint Group Meetings in Computational Structural Biology"

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Joint Group Meetings in Computational Structural Biology convene every second Thursday of the month for one hour. There will be a 1/2 hour presentation by a member of one of the partipating research groups followed by discussion after or during the talk.  The focus of the presentation is on the computational and analytical methods used to simulate biological systems as well as the problems and issues concerning these.  Currently particpiating research groups are: [http://www.bnl.gov/csc Davenport], [http://www.ams.sunysb.edu/~deng/ Deng],  [http://www.ams.sunysb.edu/~dfgreen/ Green],  [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/index.html Rizzo],  [http://comp.chem.sunysb.edu/ Simmerling], and [http://www.sunysb.edu/chemistry/faculty/jwang.htm Wang ].  
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Joint Group Meetings in Computational Structural Biology convene every third Monday of the month for one hour. There will be a 1/2 hour presentation by a member of one of the partipating research groups followed by discussion after or during the talk.  The focus of the presentation is on the computational and analytical methods used to simulate biological systems as well as the problems and issues concerning these.  Currently participating research groups are: [http://www.dillgroup.org Dill] [http://www.ams.sunysb.edu/~deng/ Deng],  [http://www.ams.sunysb.edu/~dfgreen/ Green],  [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/index.html Rizzo],  [http://simmerlinglab.org Simmerling], [http://www.sunysb.edu/chemistry/faculty/jwang.htm Wang](past years [http://www.bnl.gov/csc Davenport],  [http://mini.physics.sunysb.edu/~marivi/ Fernandez-Serra]).  
  
== Group Meeting Time and Location ==
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== Group Meeting Time and Location ==  
  
5:30 to 6:30PM in Chemistry Room 410
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TEMPORARILY ON HOLD FOR RESCHEDULING
  
 
== Group Meeting Food ==
 
== Group Meeting Food ==
  
IMPORTANT: The group that is presenting is also is responsible for bringing pizza and soda. We have been ordering seven pizzas (cut into 8 slices) from SAC and bringing three 2-liter bottles of soda. Don't forget plates, napkins, and cups.  
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IMPORTANT: The group that is presenting also is responsible for bringing pizza and soda. We have been ordering seven pizzas (cut into 8 slices) from SAC and bringing three 2-liter bottles of soda. Don't forget plates, napkins, and cups.  
  
SAC pizza needs to be ordered in advance, preferably the day before the meeting. Go to the SAC cafeteria office, just past the entrance door. You can order the pizza there and pay with a credit card. Insist on NOT paying sales sax since it will not be reimbursed. If they give you a hassle tell them to do it anyway and they will agree. Get the receipt then, or make sure that someone gets the receipt when they pick up the pizza later. Since they don't have large soda bottles, you need to get these somewhere else.  Reminder- don't forget plates, napkins, and cups!  
+
SAC pizza needs to be ordered in advance, preferably the day before the meeting. Go to the SAC cafeteria office, just past the entrance door. You can order the pizza there and pay with a credit card. Insist on NOT paying sales tax since it will not be reimbursed. If they give you a hassle tell them to do it anyway and they will agree. Get the receipt then, or make sure that someone gets the receipt when they pick up the pizza later. Since they don't have large soda bottles, you need to get these somewhere else.  Reminder- don't forget plates, napkins, and cups!  
  
 
Also, since each group will need to get reimbursed by their respective departments it is important to save all receipts.
 
Also, since each group will need to get reimbursed by their respective departments it is important to save all receipts.
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For the Rizzo lab members do the following for reimbursement:
 +
 +
(1) Money comes from the stony brook foundation
 +
    (fill out the Stony Brook Foundation Cash Payment Voucher)
 +
(2) Attach all receipts
 +
(3) Attach a copy of the meeting schedule
  
 
== Group Meeting Schedule ==
 
== Group Meeting Schedule ==
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{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; font-weight:bold; text-align:center; width:80%"
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[[Joint Group Meeting 2007-2009]]
|- style="background:lightblue"
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! style="width:15%" | Date
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[[Joint Group Meeting 2010]]
! style="width:25%" | Speaker
+
 
| Group
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[[Joint Group Meeting 2011]]
| Talk Title
+
 
|-
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[[Joint Group Meeting 2012]]
| 13th Nov 2007 || Dan Roe  || Simmerling || Replica Exchange
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|-
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[[Joint Group Meeting 2013]]
| 11th Dec 2007 || Kun Song and Christina Bergonzo || Simmerling || Umbrella Sampling and Nudged Elastic Band Methods
 
|-
 
| 12th Feb 2008 || Sudipto Mukherjee || Rizzo || Docking Testset and Improvements in Docking Protocol
 
|-
 
| 11th Mar 2008 || Vadim Patsalo || Green || Design and Synthesis of Minimal and Persistent Protein Complexes 
 
|-
 
| 08th Apr 2008 || Yongzhi Chen || Deng || Task Mapping Schemes for Parallel Computing
 
|-
 
| 13th May 2008 || AJ Campbell || Simmerling || Parameterization of Damaged DNA for Molecular Dynamics Studies
 
|-
 
| 10th Jun 2008 || Yolanda Small || Davenport || Molecular Dynamics Simulations of Cellulose Degrading Enzymes
 
|-
 
| 08th Jul 2008 || Trent Balius || Rizzo || Inhibition and Conformational Shifts of EGFR Tyrosine Kinase Domain Using Molecular Dynamics
 
|-
 
| 12th Aug 2008 || Chris Marai || Wang || Studies of NTL9 Protein Unfolding
 
|-
 
| 09th Sep 2008 || Yukiji Fujimoto || Green || Carbohydrate recognition by antiviral lectins
 
|-
 
| 16th Oct 2008 || Christina Bergonzo || Simmerling || Combining coarse grained models and atomistic MD simulations to accelerate slow motions
 
|-
 
| 13th Nov 2008 || Jim Davenport || Davenport || Density Functional Theory
 
|-
 
| 11th Dec 2008 || - || - || No Meeting: AMS Holiday Party
 
|-
 
| 08th Jan 2009 || Brian McGillick || Rizzo || HIVgp41 and lipid bilayer simulations
 
|-
 
| 12th Feb 2009 || Reid Powell || Deng || Mapping-Oriented Network Analysis for Supercomputers
 
|-
 
| 12th Mar 2009 || Noel Carrascal || Green || -
 
|-
 
| 09th Apr 2009 || - || Wang || -
 
|-
 
| 14th May 2009 || - || Simmerling || -
 
|-
 
| 11th Jun 2009 || - || Davenport || -
 
|-
 
| 09th Jul 2009 || Yulin Huang || Rizzo || -
 
|-
 
| 13th Aug 2009 || - || Deng || -
 
|-
 
| 10th Sep 2009 || - || Green || -
 
|-
 
| 08th Oct 2009 || - || Wang || -
 
|-
 
| 12th Nov 2009 || - || Simmerling || -
 
|-
 
| 10th Dec 2009 || - || Davenport || -
 
|-
 

Latest revision as of 11:03, 12 March 2012

Joint Group Meetings in Computational Structural Biology convene every third Monday of the month for one hour. There will be a 1/2 hour presentation by a member of one of the partipating research groups followed by discussion after or during the talk. The focus of the presentation is on the computational and analytical methods used to simulate biological systems as well as the problems and issues concerning these. Currently participating research groups are: Dill Deng, Green, Rizzo, Simmerling, Wang(past years Davenport, Fernandez-Serra).

Group Meeting Time and Location

TEMPORARILY ON HOLD FOR RESCHEDULING

Group Meeting Food

IMPORTANT: The group that is presenting also is responsible for bringing pizza and soda. We have been ordering seven pizzas (cut into 8 slices) from SAC and bringing three 2-liter bottles of soda. Don't forget plates, napkins, and cups.

SAC pizza needs to be ordered in advance, preferably the day before the meeting. Go to the SAC cafeteria office, just past the entrance door. You can order the pizza there and pay with a credit card. Insist on NOT paying sales tax since it will not be reimbursed. If they give you a hassle tell them to do it anyway and they will agree. Get the receipt then, or make sure that someone gets the receipt when they pick up the pizza later. Since they don't have large soda bottles, you need to get these somewhere else. Reminder- don't forget plates, napkins, and cups!

Also, since each group will need to get reimbursed by their respective departments it is important to save all receipts.

For the Rizzo lab members do the following for reimbursement:

(1) Money comes from the stony brook foundation 
    (fill out the Stony Brook Foundation Cash Payment Voucher) 
(2) Attach all receipts
(3) Attach a copy of the meeting schedule

Group Meeting Schedule

Each group is responsible for updating the Joint Group Meeting Wiki.


Joint Group Meeting 2007-2009

Joint Group Meeting 2010

Joint Group Meeting 2011

Joint Group Meeting 2012

Joint Group Meeting 2013