Hands-on Workshop on Computational Biophysics 2018

Dates: May 21 - 25, 2018
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA

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Early Application Deadline: April 1 2018
Application Deadline April 15 2018

 

mmbios-CompBiophysics2016This workshop will cover a wide range of physical models and computational approaches for the simulation of biological systems at  multiple scales, using cutting edge technology including ProDy, NAMDVMD, iGNM and ANM.  The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways and druggability simulations. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, elastic network models, and steered molecular dynamics simulations.

It will be presented by members of the Theoretical and Computational Biophysics Group (www.ks.uiuc.edu) from the University of Illinois at Urbana-Champaign (UIUC) and the National Center for Multiscale Modeling of Biological Systems (MMBioS) from the University of Pittsburgh.

The workshop is designed for students and researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations.

Participants are encouraged to bring their own laptops for use in workshop tutorial sessions but computer workstations are also available.

Agenda

See the tentative workshop agenda (subject to change).

Workshop Instructors:

Ivet Bahar (University of Pittsburgh)
Emad Tajkhorshid (UIUC)
João Ribeiro (UIUC)

Assistant Instructors:

James Kreiger (University of Pittsburgh)
Hongchun Li (University of Pittsburgh)
Karolina Mikulska-Ruminska (University of Pittsburgh)
She (John) Zhang (Carnegie Mellon University/University of Pittsburgh)

Fees

Registration fee for accepted participants*: $150 fee for students; $250 non-student academics; $350 all others. The fee is non-refundable.

Housing and directions

Workshop housing for participants will be at Ruskin Hall (120 Ruskin Avenue) on the University of Pittsburgh campus. Check-in/Check Out for Ruskin Hall will be at Panther Central. Panther Central is located in the main lobby of Litchfield Towers (3990 Fifth Ave) and is open 24 hours a day, seven days a week. If you are driving and staying in the workshop housing, you may park at Soldiers and Sailors Garage (4101 Fifth Ave, enter on Bigelow) and pay for a weekly permit at the Pitt Parking office on Monday.

The workshop is held at the Pittsburgh Supercomputing Center (PSC), 300 South Craig Street, Room 103, Pittsburgh PA, 15213.  If you have trouble finding the building, call 412.268.4960.

A Pitt campus map is available here, a Carnegie Mellon campus map is available here, and the Pittsburgh Supercomputing Center can be found via Google Maps. Pittsburgh Supercomputing Center is located in the same building as, and in between, Quiznos and Razzy Fresh.

Meals

Breakfast and lunch will be provided at the workshop, and ample evening restaurant options are available along Forbes Avenue and South Craig Street. PSC is also very close to a pleasant recreational area, Schenley Plaza and Schenley Park (shown in the Google Maps link).

Transportation

There are several ground transportation options available to and from campus.  You may use bus service, specifically the 28X Airport Flyer, which will take you from Pittsburgh International Airport and drop you in Oakland.  Likewise, you can take this bus back to the airport.  Uber and Lyft are also options.  Taxi/shuttle service is also available by calling Yellow Cab/zTrip (412.321.8100) or Super Shuttle (1.800.258.3826).

There are several paid lots and garages in the Oakland area, should you need to obtain parking for your vehicle.  More details and maps are available here and here.  Parking is not provided as a part of workshop registration or housing services.

Addresses and Contacts

Pittsburgh Supercomputing Center (Workshop): 412.268.4960
300 South Craig Street, Room 103, Pittsburgh PA, 15213

You can also contact This email address is being protected from spambots. You need JavaScript enabled to view it. with any questions.