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WEB Lab Computing Grid @Brooklyn College

posted Apr 18, 2015, 4:59 PM by Emilio Gallicchio   [ updated Apr 18, 2015, 7:49 PM ]

By Holly Tancredi & Emilio Gallicchio

Did you know that the computers in the WEB student PC lab never rest? When they are done with their day job they go on computing on science projects, such as discovering new drugs against HIV, cancer, and autism. This is made possible by the WEB Lab Computing Grid.

What is Grid Computing?

In this context grid computing is a type of distributed computing in which an organization uses its computers when they are idle to run large research computations. This system of distributing computing resources is especially useful for Universities because computers that already exist for student use can also provide resources to scientific progress. Brooklyn College's computing grid is maintained by the Information Technology Service (ITS) and the Computational Molecular Biophysics Laboratory at the Department of Chemistry. The system is based on the BOINC grid coordination software. Heavy numerical calculations are setup on a dedicated server. Computers at the WEB lab contact the server to download work. When they are done they upload the results back to the server. 

Brooklyn College's WEB Computer Lab

Brooklyn College's WEB PC lab is a public computing facility that provides students with access to over 300 computers on campus. Instead of letting these computers sit idle during nights and weekends when usage is down, researchers are running simulations and collecting data on protein-drug interactions. The grid has entered full production in December 2014 and has since provided hundreds of thousand of CPU computing hours.

Science Projects

The grid is being used to model protein interactions involved in diseases such as HIV, cancer and autism, as well as to test the next generation of chemical models. Proteins are made up of thousands of atoms. Computing all of their interactions and following their motion is extremely computationally intensive. Normally supercomputers are used for this purpose. One project involves to model the interaction between proteins involved in the Fragile X Mental Retardation Syndrome (FXS), one of the major causes of autism in children. The figure on the left represents the interaction between a peptide (CYFIP1p) interacting with a protein called eIF4E part of the same protein networks disrupted in children affected by FXS. Related protein complexes are being modeled to find peptide inhibitors as potential cancer drugs. This research is conducted in collaboration with Daniele Di Marino in Switzerland and Claudia Bagni in Belgium.

Another exciting project running on the grid involves screening potential drugs against the HIV virus. We are conducting hundreds of calculations in parallel on a family of compounds synthesized in the group of Ryan Murelli here at the department of Chemistry at Brooklyn College. The aim is to inhibit a specific function of the virus (RNAseH) that existing drugs do not yet target, thereby creating additional obstacles against the insurgence of resistant mutations. We also plan to screen this family of compounds against other viruses.

The Team

The computer models are developed at the Computational Molecular Biophysics Laboratory headed by Emilio Gallicchio, in collaboration with Ronald Levy's lab at Temple University. Part of the the research is conducted by Holly Tancredi (undergraduate student) and Baofeng Zhang (research associate).  Another undergraduate student, Sade Samlalsingh, helped to set up the initial implementation of the WEB grid. The computational grid is based on the BOINC infrastructure developed at the University of California at Berkeley. James Roman and John Stephen (Brooklyn College ITS) are managing the WEB lab grid computers.