Network-centric computing in genomics

Biology is becoming increasingly dependent on information resources. Large-scale projects generate enormous amounts of mapping and sequencing data. Complex analytical methods are required to work with these data. Lab groups create databases which encode combined expertise of lab members into object-oriented knowledge bases. The desktop-centric personal computer is an impediment, rather than an asset, for most of these tasks because it is oriented towards a single user on a single computer, rather than multiple users sharing resources. BIRCH is a network-centric resource providing a comprehensive set of databases and software for molecular biologists. BIRCH is integrated into a larger campus-wide Unix system so that all computing, including molecular biology, Internet access and office tasks can be done in an easy-to-use graphic desktop, accessible anywhere on campus, at home, or when travelling. The network-centric approach makes all resources accessible in a consistent fashion, minimizing costs and software administration, and promoting reliability, data integrity, security and scalability. See http://home.cc. umanitoba.ca/~psgendb. Desktop computing: what we’ve gained and what we’ve lost Starting up a new lab is an opportunity to make a fresh, start, to do things right the first time. This idea was at the front of my mind when I set up my lab at the University of Manitoba in 1990. The late 1980s was the period when the PC became a necessity for most biologists. Resources like GenBank were only available if enough members of a department had the will and the money to keep the databases on a minicomputer or mainframe. Among biologists, only hard-core computer aficionados like myself knew about the Internet, and almost no one appreciated why email was useful. Communication between PCs was by modem. The desktop PC, thorough its relative ease of use and moderate cost enabled biologists to take advantage of computers for data analysis, writing, and making figures. The small group of us who had learned computing on mainframes appreciated the “user-friendliness” of PCs. However, we also noted that PCs lacked the discipline, consistency and reliability of mainframes. Of fundamental importance was the fact that mainframes and minis allowed any user to do any task from any terminal. Much like the Protestant Reformation, in which every believer became a theologian, every PC user became a system administrator. And, as in the Reformation, numerous denominations sprang up, peppering labs with PCs, Macs, some UnixPCs, Amigas, which still had to talk to the Vax and Unix minis or workstations. People learned to take for granted that a program that would run on one PC could not run on another. Data, documents, and drawings became scattered across these machines like samples in a -70oC freezer. Files accumulated with no one in charge, most older files being of little value, but at the same time not easily distinguishable from those few that were great value, due to inconsistent or incomplete labelling. Since m biologists had never used mainframes, things such as havin reboot several times a week were just a normal part of using a P The demands of 21st century biotechnology In recent years, the isolated lab with a group leader and a few dents has given way to megaprojects with many collaborat sharing data, clones, cultures and strains. At the same time, the from publicly-funded projects is increasingly used by others in t research community: complete genomic sequences, genetic m and expression data. Researchers need access to complex me such as gene prediction, phylogenetic analysis and recognitio patterns among groups of sequences or expression datasets. Because each PC is a unique combination of hardware, softw configurations and data, it is actually an impediment to progress particular, fragmentation of data across many PCs allows for inc sistent organization of data and makes it difficult for data to shared, or even located. Differences in software and configura from machine to machine results in competition among lab work for use of specific computers. When expensive software is insta on a single machine, workers can only use it on that machine. W many users use a given machine, changes or deletions made by user affect all other users. Like the -70oC freezer, no one is resp ible for keeping the PC organized. In summary, the standalone makes what you can do strongly dependent on which machine yo using. 2 AgBiotechNet 1999, Vol. 1 November, ABN 032