The bioinformatics facility at NCCS provides access to high-performance compute resources and programming expertise. The compute infrastructure serves scientists at NCCS to master the informatics needs of their research in a proficient and cost-effective manner.
Hardware infrastructure SGI Altix XE 1300 Cluster
Head Node SGI Altix XE 270 Server Dual Quad Core XEON 5620 @ 2.4GHz / 12MB cache 12GB Memory 5 x 2TB SATA Disk @ 7.2K RPM RAID 5
Compute Nodes SGI Altix 340 Servers 2 x HEXA Core XEON 5670 @ 2.93GHz / 12MB cache 24GB Memory 250GB SATA Disk @ 7.2K RPM Dual Gigabit Ethernet Card SGI Cluster Software Stack: SLES Ver 11 SGI ProPack 7 SGI Foundation Software Ver 2.0 Interconnect: 24-Ports Gigabit Ethernet Switch
Sunfire X 4150 (Intel Xeon 2.33 GHz Quad Core Dual Processor) Standard Libraries and compilers.
Specialized Workstations HP workstations of Intel Core 2 Duo @3.00GHz with 8 GB of DDR2 memory, 320 GB of SATA storage and 19" LCD wide Display with Linux operating system
Desktop Computers Desktop computers with Intel core 2 duo processor @1.8Ghz to 2.8GHz with 2 GB to 4 GB of DRR2 memory, 160GB to 320GB of SATA storage with 17" wide and normal LCD display and loaded with Windows XP. Apple iMac PC for running specialized programs and softwares
Printer HP Laserjet M1136MFP UPS: 10KVA (APC make) to run clusters
Software infrastructure Bioinformatics Facility at NCCS has procured several software for scientific research with commercial and/or academic licenses.
Sequence analysis BLAST, CLUSTAL-W, MEGA, Eisen
Molecular Modeling Modeler Protein Families Protein Health Protein Refine Profiles-3D
Molecular Docking Flexible Docking LibDock Ludi LigPrep LigandFIT LigandScore AUTODOCK, Database of 1.5million Compound Library
Pharmacophore Modeling Auto Pharmacophore generation Receptor-ligand pharmacophore egeneration 3D QSAR pharmacophore generation Steric Refinements with excluded volumes
Toxicity Prediction ADMET TOPKAT
QSAR Create Bayesian Model Recusrive Partioning Model Multiple Linear Regression Model partial least squares model genetic function approximation model 3D QSAR model Intelligent QSAR using molecular fragments of interest and their features, evaluation of descriptors from template scaffold to form relationship with the activity.
Quantum Mechanics and Molecular Mechanics GAUSSIAN
Molecular Dynamics CHARMM, GROMACS, NAMD, MOIL
Molecular Visualisation Rasmol, MolMol, WinCoot, Swiss PDB viewer, MolScript, VMD
Systems Biology Tools Virtual Cell, M-cell, Cell Designer, GEPASI, Cytoscape, Osprey,E-Cell, COPASI Artificial Intelligence: SVMlight and SNNS
Material Modeling and Simulation Material Studio 5.5
Graphs and Graphics Sigma Plot, GNU Plot, Corel Draw and Adobe PhotoShop
Statistical packages: MATLAB and R
Incharge Dr. Shailza Singh