Workshop 1: Electronic Information Resources
Chair: Mary Anderson, Nottingham Arabidopsis Stock Centre, University of Nottingham, UK.
email: arabidopsis@nottingham.ac.uk
In the last few years there has been a dramatic increase in the amount of information which has been generated due to the success of the Arabidopsis research programme. In keeping with the open philosophy of the programme, where appropriate this information has been made publically available to the community. This workshop provided a forum for the introduction to, and live demonstration of, the various projects which provide electronic access to Arabidopsis information resources.Randy Scholl (Arabidopsis Biological Resource Center, Ohio State University) described the ABRC WWW server, which provides a WWW interface to their database management system AIMS (Arabidopsis Information Management System). Randy combined his demonstration of the workings of the server with a description of the Stock Centre's activities. He demonstrated how to browse the information as well as how to search the server to find stocks and images, how to place orders, check on your own order status or to check on order histories for a particular stock. Randy also described how ABRC intends to acquire large numbers of T-DNA transformants and transposon lines for mutant screens and reverse genetics experiments. DNA isolated from T-DNA lines will also be made available to allow easy PCR-based screening of these populations for mutations.
Mary Anderson (Nottingham Arabidopsis Stock Centre, University of Nottingham) gave a demonstration of the redesigned NASC WWW server. The new layout has incorporated the use of frames to allow for fast and easy access of information. Information is provided as a menu on the left hand side of the screen that drives the loading of information into the main part of the screen on the right. The new search facility for the on-line catalogue and picture book was also demonstrated, using the example of the newly released MOGEN lines, as well as how to interact with the Centre by placing orders or asking questions on-line. Mary also previewed the abstracts from the conference which had been prepared by Mike Arnold and are available from the NASC server to be queried or browsed by session, author or keyword. Mary then changed tack to talk about Weeds World giving a brief description of the types of information the newsletter contains, how regularly it is published and how to submit information for publication.
Ernie Retzel (University of Minnesota), with his designer crutches and brace for his broken foot, spoke about their Arabidopsis EST project which has been conducted in collaboration with Tom Newman at the Michigan State University. The analysis also includes the EST data from the French consortia. Ernie described the suite of tools that they have developed to allow easy analysis of the myriad of data that the ESTs have generated. Most of these tools are made available through the project's WWW server. An exciting development has been the creation of a motif and similarity clustering tool to identify and display relationships between sequences. The relationships are displayed as a "tangled cats cradle" with the close relationships identifed by coloured groups and short distances, so that islands of related genes are linked through lines. The close relationships identified concur with the findings of Steve Rounsley at TIGR (see next speaker) but also bring out additional findings of less related sequences that nevertheless show significant relationships. This will be a useful tool for the discovery of genes and gene-relatedness.
Following on from the EST project at Minnesota, Steve Rounsley from The Institute for Genome Research (TIGR), spoke about the analysis they have been conducting on the US and French EST data which is deposited in dbEST. Inherent to any EST project is a redundancy of information that is generated due to the fact that cDNA clones from the same gene may be sequenced multiple times. Steve described how they assembled the ESTs into tentative consensus sequences to reduce this redundancy. Nucleotide and amino acid similarity searches were then conducted in the public databases for each of the ESTs to allow putative gene identifications. The tentative consensus sequences and homologies are made publically available through the TIGR WWW server.
Changing tack, we moved away from sequence information, to physical mapping. Tony Schaeffner (Institut fuer Biochemie, Muenchen) described their WWW server which has been established to provide information about on-going chromosome walking projects. The idea for the server sprang from discussions at the last meeting at Madison.Tony described how they have set up five pages representing the five Arabidopsis chromosomes. Each page carries a list of ordered markers and a listing of laboratories that are currently working or interested in a particular region. Tony encouraged anyone who was interested in including their data to contact him or submit their information through their WWW server.
David Meinke (Oklahoma State University) started his talk in his capacity as curator of gene symbols for the Arabidopsis community, describing how the Meinke WWW server carries detailed information on rules of nomenclature, mutant gene symbols, linkage data, genetic maps, and e-mail addresses of contributing laboratories. He described the philosophy of gene naming, how to send in data about new gene names and the submission of mapping information. David then went on to describe the other part of the server, which is devoted to his research activities. He described how detailed information is provided on the 250 embryo- defective mutants which have been isolated in the Meinke Lab including the background, mutagen employed, tagging status, seed and embryo phenotype, segregation ratio, chromosome location, and original seed source for mutants in the collection.
David Flanders (AtDB Project, Stanford) brought up the rear, with a "canned" live demonstration (didn't trust UK technology now that he is based at Stanford) of the latest developments from the AtDB Project at Stanford. He described how, as well as making new information available from their WWW server, they are developing a new prototype plant genome database. The database is being developed using the commercial object-orienated database management system, Illustra and will be accessed through the WWW. He demonstrated some early displays that they have been designing for physical map and colleague information. Full details of the project's developments are given in the article "New Directions in Genome Databases at Stanford", in this issue of Weeds World.
A computer demonstration of all the services ran for the entire conference in the LCR. We are grateful to the staff of the UEA Computer Department for their help with the demonstration. Many thanks to Sun Microsystems and Relay Business Systems for the loan of the two Sun machines for the conference.