Peter.Rice%EMBL@PUCC.PRINCETON.EDU (Peter Rice) (02/15/91)
Bio-matrix has been quiet for so long, it is sad to see a spate of "please remove me" messages as soon as a lively discussion springs to life. Perhaps I can dilute the effect, and increase the number of postings, by starting a new discussion. There are now several "genome projects" under way, either (1) to map and sequence (Caenorhabditis elegans, alias the nematode or the worm) (Drosophila melanogaster, alias "the fly"), (Saccharomyces cerevisiae, or "yeast"), (Schizosaccharomyces pombe, or "the other yeast"). (Arabidopsis thaliana, or "the plant") (and others becoming too numerous to mention) or (2) simply to finish the job that individual labs have done pretty well already (Escherichia coli, or E.coli for short, which is already over 30% sequenced and pretty well mapped both genetically and physically). I was wondering what the current status is of each of these projects, and also what their aims should be; in particular what the biological community sees as the needs for the storage of the data, and how to access it in individual labs. In the case of E.coli for example the data is already there in a large number of publications but online access to it is a serious problem. The other projects are just starting and have the opportunity to get things right from the beginning. Enough for starters. If this turns you off too, please say what you want to see on bio-matrix. ----------------------------------------------------------------------------- Peter Rice, EMBL | Post: Computer Group | European Molecular Internet: Peter.Rice@EMBL-Heidelberg.DE | Biology Laboratory EARN/Bitnet: rice@embl.bitnet | Postfach 10-2209 | D-6900 Heidelberg Phone: +49-6221-387247 | Germany
gilbertd@cricket.bio.indiana.edu (Don Gilbert) (02/15/91)
In article <9102142237.AA11441@genbank.bio.net> Peter.Rice%EMBL@PUCC.PRINCETON.EDU (Peter Rice) writes: > >There are now several "genome projects" under way, either (1) to map and ... >I was wondering what the current status is of each of these projects, and also >what their aims should be; in particular what the biological community sees as >the needs for the storage of the data, and how to access it in individual labs. >In the case of E.coli for example the data is already there in a large number of >publications but online access to it is a serious problem. The other projects >are just starting and have the opportunity to get things right from the >beginning. The Worm sequencing project includes much software development. There is now a working, X-Window based worm data base browser that integrates sequence data, physical / contig maps, genetic and other descriptive data and references. It also includes an "annotation" facility where worm researchers can interactively add or change data in the primary, remotely-located data files. The Fly sequencing project is gearing up for some kind of similar integrated data management which will be available to fly biologists with Internet (tcp/ip) network access. I'll leave it to others to provide more details (I'm not directly involved in these). But you can expect to hear more on these in the coming months. This would be a good time for people to discuss what their needs are for access to such data, and in what form. E.g., is X-Window software running on central computers that host the data, and that allows groups of researchers scattered around the globe to view and add to the data, a viable way to proceed? Some of the recent news (minutes of JITF?) on the genome-program newsgroup touches on this. -- Don -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405