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Bioinformatics



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