Centre for Bioinformatics

Infrastructure Facilities – Computers, Networks & Accessories

Servers

• Tesla Software Server(4TF) - 1No.: One Super Micro Tesla Server with 2 x Intel Xeon Quad-Core processor @2.4GHz/12MB L3 Cache,  896 GPU based cores (2 x NVIDIA Tesla C2050), 64 GB of DDR3 memory, 6 TB of storage controlled by 128MB cache SAS RAID, 24” wide LED Display and loaded with CentOS.

• Web Server, File Server, DB Server, DBT Web Server - 4Nos.: Super Micro HCL Server with 2 x Intel Xeon Quad-Core processor @1.6GHz,  4 GB of DDR2 memory, 6 x 146 GB of storage controlled by SAS RAID, 19”wide LCD Display, Integrated KVM 15” LCD switch and loaded with RHEL 5.

• Cluster Server - 3Nos.: HCL Servers with 2 x Intel Xeon @3.2GHz, 4 GB of DDR2 memory, 6 x 146GB of storage controlled by SAS RAID, 17” LCD Display, KVM switch and loaded with RHL Advanced Sever 4. 

• Mail Server - 1Nos. HCL Server with 2 x Itanium 2@1.7GHz, 4 GB of DDR2 memory, 6 x 146GB of storage controlled by SAS RAID, 17” LCD Display with KVM switch and loaded with RHL Advanced Sever 4.

• Domain Name Server - 1Nos.: Wipro Server with Intel Xeon @3.0GHz, 1 GB of memory, 120GB of storage, 17” LCD Display and loaded with RHL Advanced Sever 4.

• Domain Controller Server - 1Nos.: HCL AMD Server with AMD 8131/8111 Motherboard, 1 GB of memory, 100GB of storage, 12/24GB-DAT drive, 17” LCD Display and loaded with Windows 2003 Server R2.

Specialized Workstations

• Docking & Modeling studies - 2Nos: HP workstation with Intel Core 2 Duo @3.00GHz, 4 GB of DDR2 memory, 320 GB of SATA storage, 21” LCD wide Display and loaded with Windows Vista Business Edition.
• 3D and 2D Graphical Analyze - 2Nos: Apple iMac workstation with Intel Core 2 Duo @3.00GHz, 1 GB of DDR2 SD memory, 250 GB of SATA storage, 20” LCD Display loaded with Mac OS.
• Onyx3 Infinite Performance Fuel - 1Nos: SGI workstations of 800Mhz. MIPS R16000 (IP35) with MIPS R16000 FPU with 1 GB of memory, 176 GB of storage with V10 graphics along with 20” CRT Display loaded with IRIX64 Release 6.5 OS.

 Desktop Computers

• Around 105 Nos. of desktop computers with Intel core 2 duo processor @1.8Ghz to 2.8GHz, 1 GB to 4 GB of DRR2 memory, 160GB to 320GB of SATA storage, 17” wide and normal LCD display and loaded with dual OS Windows XP and RHEL5.
• Around 30 Nos. of desktop computers with Intel Pentium D processor @2.8Ghz to 3.0GHz with 1 GB to 3 GB of DRR2 memory, 160GB of SATA storage with 15” LCD display and loaded with dual OS Windows XP and RHEL5.

Network Hardware

• Cisco 1800 with 2 Fast Ethernet ports, 1 AUX port, 1 Console port to manage LAN Connectivity along with 12 manageable 24 port Switches including 5 Giga byte manageable switches. 
• 5 CCTV cam with wide-angle, IR facility technology to monitor function of Students’ Lab since it has been allowed 24x7 for access.

Other Facilities

• Printers: Samsung Color Laser Network Printer -2, HP Color Laser Printer, Samsung Laser Black Network Printer, Samsung Laser Black Printer -5, HP LaserJet Black Network Printer -2, Mono Printer -1, DeskJet Printer -1, Infocus Projectors -4, HP ScanJet -2 
• Photocopier: Toshiba Multi functionality Digital Photocopiers cum Network Printer -1, Toshiba Digital Photocopiers cum Network Printer -2.
• Scanner: HP Scan Jet -2.
• Projectors: Hitachi Multimedia projectors -2 one with wall mount facility for M.Sc. Bioinformatics teaching program, Infocus projectors -2 for M.Sc. Computational Biology teaching program, Toshiba TDP LCD wall mount projector for seminar hall

UPS Backup

• Numeric 75KVA (in total) UPS to provide 4 hours to 12 hours power backup. 15 KVA - 3 Nos. 10 KVA – 3Nos. 0.5 KVA – 5 Nos.

Infrastructure Facilities – Scientific Software

Molecular Modeling:
Modeler (DISCOVERY STUDIO 2.5), Protein Families (DISCOVERY STUDIO 2.5), Protein Health (DISCOVERY STUDIO 2.5), Protein Refine (DISCOVERY STUDIO 2.5)

Molecular Docking:
Flexible Docking (DISCOVERY STUDIO 2.5), LibDock (DISCOVERY STUDIO 2.5), Ludi (DISCOVERY STUDIO 2.5), LigPrep (DISCOVERY STUDIO 1.5), LigandFIT (DISCOVERY STUDIO 1.5), LigandScore (DISCOVERY STUDIO 1.5), GOLD, AUTODOCK, Database of 1.5million Compound Library (DISCOVERY STUDIO 1.5) 

Toxicity Prediction:
ADMET (DISCOVERY STUDIO 2.5), TOPKAT (DISCOVERY STUDIO 2.5)

QSAR:
QSARPlus (VLife)
Rapid calculation of 1000+ descriptors including 2D, 3D alignment independent, atom type count etc., 

GQSAR (VLife)
Intelligent QSAR using molecular fragments of interest and their features, evaluation of descriptors from template scaffold to form relationship with the activity.  

Molecular Dynamics:
AMBER 11, GROMOS96  

Infrastructure Facilities – Wetlab
      Our wet lab is equipped with state of the Art facility, highly sophisticated Akta Purifier for protein purification with various columns (size exclusion, Ion exchange, Affinity).  Each and every student is equipped with both Page and slab gel electrophoresis system, which is also equipped with centrifuges, Spectrophotometer and Elisa Reader. We are also having facilities for Protein cloning, expression and purification.  We are in the process of furnishing cell culture facilities.

Equipments used for Research:

• Invert Fluorescence Microscope -(Model Ti-s)
  Specification:  Inverted fluorescence microscope with fast research grade high resolution CCD with 5 Mega Pixel Camera and image analysis system.

• Galaxy Co2 Incubator-(Model CO170S)
  Specification:  Direct Heat Co2 incubator with fan less design and High Temp Decontamination wit 170 liter capacity, 6.0 cu. Ft on a minimal footprint.

• Bio safety Cabinet - HITECH (Type B2-350 Lts)
  Specification : HEPA-filtered unidirectional (laminar) flow (ISO 5/Class 100) with removable screen for cleaning purpose with UV light for Sterilization and fluorescent light above work space.

• Liquid Nitrogen Container (3L and 25 L)
  Specifiacation: Evaporation :<0.143 Litter Per day is present in this instrument

• Bench Top Freeze Dryer
  Specification: ILSHIN- TFD5505 Table top model
  Used for lyophilization and to stabilize the product, minimizing effects of oxidation and other degradation processes.

• Cold cabinet
  Specification: UNICHROMAT 1500 – PRO
  Equipped with temperature control sensor which helps to maintain temperature constantly at 4ºC. 

• Sonicator
  Specification: Sonics
  To speed up dissolution, disrupt or deactivate a biological material.

• HPLC System
  Specification: AKTA PURIFIER 10
  To identify, quantify and purify individual components from a mixture of biological sample.

• ELISA Reader
  Specification: Versamax Model 2020
  For assays such as ELISA, protein and nucleic acid quantification and for enzyme activity assays (viz. in the MTT assay for cell viability). 

• Deep Freezer-80ºC
  Specification: Premium Upright Model (U4100)
  It is used for quick-freezing and long-term storage of biological samples.

Equipment used for Teaching:

• UV-Visible Spectrophotometer
  Specification: Shimadzu Model - Uv-1800
  Used in quantitative determination of solutions of transition metal ions and highly conjugated organic compounds.

• Thermo Cycler
  Specification: Bangalore Genei
  To amplify a single or a few copies of a piece of DNA across several orders of magnitude. 

• Electrophoresis unit
  Specification: Bangalore Genei
  Used for separation of DNA, RNA or protein molecules using an electric field applied to a gel matrix.

• Refrigerated Centrifuge
  Specification: 5 415 Eppendorf
  Used for isolating and separating suspensions.

Infrastructure Facilities – Other Resourses  

Resources & Services

• A separate website available at www.bicpu.edu.in is being maintained by the Centre. All the activities of the centre are updated regularly
• Web server for sequence analysis, Blast, Predict Protein, Sequence Manipulation suite are available at http://www.bicpu.edu.in
• Web server for offline blast for sequence homology search is available at http://www.bicpu.edu.in/blast
• Web based database administration tool phpmyadmin is available at http://www.bicpu.edu.in
• Free Biosoftware Artemis, Bioedit, Clustal W, Glimmer, Munner, Philip etc. are available at http://www.bicpu.edu.in
• A minor site of all publicly available protein structure co-ordinate in the form of the Protein Data Bank available at http:// www.bicpu.edu.in.pdb
• A full mirror of the SCOP database linked to PDB available at http://www.bicpu.edu.in/ scop
• Micro Array Animation will be available http://www.bicpu.edu.in/Microarray.php

Databases Developed

• Humet database will be at http://hmdb.bicpu.edu.in
• DrugMetZDB database will be at http://dmdb.bicpu.edu.in
• Immune Epitope Prediction database will be at http://iep.bicpu.edu.in
• Membrane Protein database will be at http://memprot.bicpu.edu.in
• E-Learning Module in Bioinformatics will be available at http://dbtel.bicpu.edu.in
• Peptide Binding Protein database will be at http://pepbind.bicpu.edu.in
• FiloBase:A Comprehensive database for filaria will be available at http://filobase.bicpu.edu.in

Books
550 books (In addition to the books available in the Central Library)

Journals
Scientific American, Cell, Current Science.