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Systems Biology and Pharmacology Lab

Systems biology and pharmacology involves the application of systems biology approaches, integrating high throughput experimental data from different experimental techniques such as genomics and proteomics involving computational analytical approaches, to understand the mechanism of action of drugs, identify potential drug targets, use existing drugs for other disease indications and study adverse drug reactions. 

The significance of using integrated approach is that it allows drug action and drug response to be studied in the context of whole genome or proteome. Basically, a strong and simplified platform for the development of systems pharmacology is provided by information from genetic studies, disease pathophysiology, pharmacology, protein-protein and protein-drug interactions. 

Network analyses of interactions involved in disease pathophysiology and drug response will allow the integration of the systems-level understanding of drug action with genetic information enabling personalized medicine. Developments and insights from merging systems pharmacology and pharmacogenomics studies will provide new information on the complexities of disease associated with the identification of multiple targets for drug treatment and understanding adverse events caused by off-targets of drugs.

Reserach Focus

  • Predicting drug-target/drug/adverse drug reaction based on multi-scale systems biology model
  • The study of multi-scale modeling approaches and key questions in systems pharmacology
  • The study of the chemometrics algorithms solving pairwise data and its applications to the compound-protein interaction recognition
  • Database and computation plaform construction

Dell Precision Tower 5810 Workstation

Intel® Xeon® processors: Power through the most demanding, interactive applications quickly with a new generation of single-socket performance with the Intel® Xeon® processor E5-1600 v3 series. The Dell Precision Tower 5810 delivers up to 75 percent better performance than previous generations for iterative design and prototyping.

Powerful graphics and memory: The latest NVIDIA® Quadro® and AMD FirePro™ graphics deliver the muscle you need to run the most demanding software applications. New Quadro and FirePro graphics offer larger dedicated graphics memory for your large data sets. System memory is expandable up to 256GB using the latest DDR4 RDIMM memory technology. The Dell Precision Tower 5810 delivers up to 5.5x higher graphics performance than previous generations on SolidWorks, 3.7x on CATIA, 5.5x on CREO, 6.8x on MAYA and 3.6x on Siemens NX.

High-performance storage: Choose the Dell actively cooled PCIe SSD storage solution for the fastest and most reliable way to store your content, up to 180% faster than traditional SATA SSD storage. If you prefer traditional storage options, choose the optional 12 Gb/s RAID controllers, doubling the I/O speed of our previous-generation Workstation.

The Milky Way II Supercomputer System

  • The Milky Way II supercomputer system, developed by the National University of Defense Technology (NUDT), is the outstanding achievement of the National 863 Program.
  • With 16,000 computer nodes, each comprising two Intel Ivy Bridge Xeon processors and three Xeon Phi coprocessor chips, it represents the world"s largest installation of Ivy Bridge and Xeon Phi chips, counting a total of 3,120,000 cores. Each of the 16,000 nodes possess 88 gigabytes of memory (64 used by the Ivy Bridge processors, and 8 gigabytes for each of the Xeon Phi processors). The total CPU plus coprocessor memory is 1,375 TiB (approximately 1.34 PiB).
  • During the testing phase, the Milky Way II supercomputer system was laid out in a non-optimal confined space. When assembled at its final location, the system will have a theoretical peak performance of 54.9 petaflops. At peak power consumption, the system itself would draw 17.6 megawatts of power. Including external cooling, the system would draw an aggregate of 24 megawatts. The computer complex would occupy 720 square meters of space.
  • The front-end system consists of 4096 Galaxy FT-1500 CPUs, a SPARC derivative designed and built by NUDT. Each FT-1500 has 16 cores and a 1.8 GHz clock frequency. The chip has a performance of 144 gigaflops and runs on 65 watts. The interconnect, called the TH Express-2, designed by NUDT, utilizes a fat tree topology with 13 switches each of 576 ports.
Chemoffice: ChemOffice Professional is a scientifically intelligent, integrated suite of personal productivity tools that enables scientists and researchers to capture, store, retrieve and share data and information on compounds, reactions, materials and their properties.
Cytoscape: Cytoscape is an platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
MATLAB: MATLAB is a multi-paradigm numerical computing environment and fourth-generation programming language.
COPASI: COPASI is an software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.
PyMOL: PyMOL is a user-sponsored molecular visualization system on an open-source foundation.
Chimera: Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
GROMACS: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.