Linux cluster

Main Cluster: bioservx

• Master node: Intel Xeon Six Core E5-2620 (2GHz x 2; 64GB; 120GBx2 SSD+ 3TBx6 HD; CentOS 7.5)

• Compute nodes: node15 - node20
  (Intel Xeon Quad or Six Core; 2.4 - 2.93GHz x 2; 24 - 256GB)
• Stand-alone node: node251
  (Intel Xeon Eight Core E5-3601; 2.4GHz x 2; 512GB; 80GB SSD + 4TBx8 HD)

Web Servers

• bioinfolab: Intel Xeon Ten Core E5-2630 (2.2GHz x 2; 64GB; 200GBx2 SSD+ 4TBx2 HD; CentOS 7.5)

• crridb: Intel Xeon Ten Core E5-2630 (2.2GHz x 2; 32GB; 240GBx2 SSD+ 6TBx8 HD; CentOS 7.5)

TORQUE distributed resource manager

• Start using Torque/PBS (a quick guide; more information is available in the Lab Use Only page)
• Torque/PBS FAQ (Some more note on Torque/PBS)
• Torque overview at IU
• Torque Resource Manager Documentation

Databases available on our servers

Note: Information below has not been updated

BAliBASE: A benchmark alignment database

• Version: 2.01 (directory: /data/permanent/databases/BAliBASE2.01)
• BAliBASE web page
• Publications: BAliBASE 1.0, BAliBASE 2.0

GPCRDB: Information system for G protein-coupled receptors (GPCRs)

• Main database files (directory: /data/permanent/programs/GPCRDB)
  • GPCRDB (GPCR sequences)
  • GPCRDB_fragments (GPCR fragments)
  • GPCRDB_gprota (G protein sequences)
  • GPCRDB_gprota_frag (G protein fragments)
• GPCRDB web page
• Publication: Horn et al. (2001) Nucleic Acids Res. 29:346-349

NCBI databases

• Main database files:
  • Unformatted: FASTA format w/ annotations (directory: /home/data/databases/blast/db/UnformattedDB)
  • Formatted: Used for BLAST search (directory: /home/data/databases/blast/db/OurFormattedDB)
• Update: weekly (and monthly full download from NCBI)
• NCBI Blast web page
• Associated program: BLAST (see Software section below)
• Database lists:
  • Nucleotide Sequence Databases
  • Protein Sequence Databases

Pfam: Database of protein domains and HMMs

• Main database files (directory: /data/permanent/programs/Pfam)
  • Pfam_ls (The PFAM HMM library, glocal alignment models)
  • Pfam_fs (The PFAM HMM library, local alignment models)
• Pfam web page
• Publications: Bateman et al. (2002) Nucleic Acids Res. 30:276-280
• Associated program: HMMER (see Software section below)

PRINTS: Protein Fingerprint Database

• Main database file (directory: /data/permanent/programs//data/permanent/programs/prints/P35.0)
  • prints.dat
• PRINTS web page
• Publication: Attwood et al. (2002) Nucleic Acids Res. 30:239-241
• Associated program: FingerPRINTScan

PROSITE: Database of protein families and domains

• Main database files (directory: /data/permanent/programs/prosite/release_with_updates)
  • prosite.dat (PROSITE data file)
  • prosite.doc (PROSITE documentation file)
• Update: weekly
• PROSITE web page
• Publication: Falquet et al. (2002) Nucleic Acids Res. 30:235-238
• Associated program: ps_scan.pl

SWISS-PROT: Protein Knowledgebase
TrEMBL: Computer-annotated supplement to SWISS-PROT

• Main database files (directory: /data/permanent/programs/swiss-prot)
  • sprot.dat (SWISS-PROT data file)
  • trembl.dat (TrEMBL data file)
  • trembl_new.dat (New entries to be later integrated into TrEMBL)
• Update: weekly
• SWISS-PROT web page
• Publication: Bairoch and Apweiler (2000) Nucleic Acids Res. 28:45-48

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