At Genoscope, informatics is based on a high-performance and high-availability UNIX computing environment.

The main calculation system is a cluster of 4 Digital 4-way SMP (AXP 21264 (EV6) @ 525 MHz) computers (Compaq GS60, ex AS 8200) with 4 Go of memory each. The main stocking system is a set of disk racks with a total capacity of about 3 To (3,000 Go). Backup functions are ensured by a 330 cartridges robot (DLT7000 tape drives), with a 35 to 70 Gb capacity for each cartridge.

Physical security of data is ensured through a combination of the following :

• The disk rack has a RAID5 organisation, and the memory is backed-up;
• a few disks are reserved for immediate automatic replacement, in case of material failure
• daily incremental backup
• double weekly complete backup (one of which is stored outside of Genoscope)
• on-line (or nearly on-line, i.e. on site) conservation of back-ups for six months quickly accessible
• definitive backups are made each month

Moreover, several functions are ensured by dedicated servers :

• a general purpose (X-term support, mail, PC's and Macintosh integration) Digital DS20 (2 EV6 CPU @ 500 MHz) server
• a cluster of 2 Digital AS 1000 servers interfacing the sequencers with the main calculation structure
• a Digital AS 255 public server (FTP and HTTP)
• a dedicated Digital server for logistic support
• two machines (Linux/Intel and DEC) as part of the Firewall
• a CCD coupled SUN workstation running the Millipore BioImage software
• a NCD WinCenter equiped PC for the distribution of office softwares to the X terminals

Human/machine interfaces include 70 X-terminals and 40 PCs.

All this equipment is connected through several virtual 10 Mps and 100 Mps ethernet-switched networks. Internet access is via a 2 Mps link with RERIF/Renater. Genoscope actively participates in the metropolitan network of the Evry area (RMRE) project, associating Genoscope with the Evry University, GENOPOLE, Généthon, INT, IEE-CNAM and ENSMP-Centre des Matériaux.

Together with the GCG and Staden software packages, more than 240 programs are installed and used at Genoscope. Their main application area is, of course, sequence analysis and genetic and physical mapping.

The first category includes :

• phred for base calling
• phrap and consed for assembly (Acembly is currently under evaluation)
• fasta, blast and Smith and Waterman algorithm-based sequence comparison software, along with LASSAP (Large Scale Sequence compArison Package).

This is complemented with locally developed software and databases :

• tafie for contig analysis
• scf2ps for chromatogram visualisation
• orfs for open reading frame determination
• contigprobe for consensus validation
• local maintenance of public sequence databases
• sequence production and manipulation tool databases
• automatic creation and delivery of Licor-sequencer sample sheets
• "projects" database with processing specifications (filtering, quality checking, etc) to be applied during the production
• automated transfer process, from production to analysis :
1. sample sheet creation
2. sample sheet distribution
3. automatic harvesting of electrophoresis data (ABI) along with base calling results (Licor) to UNIX calculation systems
4. base calling (phred) for ABI datas
5. control of sequence nomenclature correctness
6. quality control
7. database updating
8. sequence delivery for the projects

Early error detection procedures are under development.

These programs make use of reusable object module libraries (C, Perl).