From owner-schistosoma@net.bio.net Wed Apr 01 23:00:00 1998 Path: biosci!biosci!not-for-mail From: David Johnston Newsgroups: bionet.organisms.schistosoma Subject: Call for registration of interest - Schisto Genome Network 1998 Meeting Date: 2 Apr 1998 03:16:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 79 Sender: daemon@net.bio.net Approved: greveld@rz.uni-duesseldorf.de Distribution: world Message-ID: <6fvs2u$dpp@net.bio.net> NNTP-Posting-Host: net.bio.net Dear Collegues, WHO has provided funds to its Schisto Genome Network to hold a Meeting to review progress in the Schisto Genome Initiative, to identify and resolve limitations arising from current strategies and to decide the future agenda for the Network's research. With respect to the future direction of research activities, WHO-TDR's Genome Committee, has indicated that it would like to see the initiation of "post-genomic" studies and that it is willing to receive applications for such projects in the next funding round (deadline for new applications, 15th July 1998). This potential shift in emphasis of Network activity may make participation in the Genome Network more attractive to various research groups. WHO defines "post-genomic" initiatives as projects investigating DNA sequence information for the identification of molecules important for parasite virulence and host survival. Since this is a relatively new area, the Committee does not wish to restrict the scope of such proposals but stipulates that they must: * be of innovative approach * ultimately include whole genome analysis to provide valuable information about function of all genes and the genome; preliminary studies should be extendable to the whole genome * contain detailed analysis, showing that the research is both cost- and time-effective * not simply a be major scale up of currently practiced analysis by single investigators The purpose of this mailing is, therefore, to invite laboratories interested in either "pre-genomic" (gene discovery, physical mapping, informatics etc.) or "post genomic" analyses (as above) to register their interest in attending the 1998 Network Meeting. This is currently scheduled for 9th - 12th May 1998 at Angra dos Reis, Brazil (100 km south of Rio de Janeiro). These dates have been chosen after consultation with WHO and with consideration of the deadlines for reports and new applications. We anticipate that funds will be made available to help support representatives of several new groups attend the Meeting. Please reply, as soon as possible, to David Johnston, Network Secretary (daj@nhm.ac.uk), with details of your potential interests in the generation, analysis and exploitation of genome data. Further details of the TDR-Genome Workplan can be obtained from TDR's WWW site (http://www.who.ch/tdr/) Further information about the WHO Schistosoma Genome Network can be obtained from its WWW site (http://www.nhm.ac.uk/schisto) or by email to the Network Secretary. Thank you, in advance, David Johnston Phil LoVerde (Network co-ordinator) Jucara Parra (local organiser - CPqRR (FIOCRUZ), Belo Horizonte, Brazil) David A. Johnston, Secretary to the WHO Schistosoma Genome Network, Biomedical Parasitology Division, Dept. of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, England, UK. Tel: 0171 9389297 (from outside the UK: 44 171 9389297) Fax: 0171 9388754 (from outside the UK: 44 171 9388754) eMail daj@nhm.ac.uk http://www.nhm.ac.uk/schisto The Biomedical Parasitology Division is a WHO Collaborating Centre for the identification of schistosomes and their snail hosts. From owner-schistosoma@net.bio.net Mon Apr 06 23:00:00 1998 Path: biosci!biosci!not-for-mail From: David Johnston Newsgroups: bionet.organisms.schistosoma Subject: Assessing the usefulness of the WHO Schisto Gene Discovery Initiative Date: 7 Apr 1998 07:50:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 46 Sender: daemon@net.bio.net Approved: greveld@rz.uni-duesseldorf.de Distribution: world Message-ID: <6gdefq$glc@net.bio.net> NNTP-Posting-Host: net.bio.net Dear Researchers, For the past 3 years, WHO has sponsored a gene discovery initiative for Schistosoma mansoni and S. japonicum, with a fourth year just starting. This initiative has resulted in many thousands of Expressed Sequence Tags (ESTs) being deposited in the public databases (with the clones from which they were generated available on request to anyone who wants them for further characterisation). Each year, the gene discovery labs have to re-apply to WHO for continuation of funding and we would like to gather information on how useful the data is to the wider community in order to support our reapplication. Obviously, in cases where we are requested to supply a clone, we know the data is useful. However, in many circumstances, it makes sense for workers to design primers from sequences in the databases and use these primers to amplify up probes to screen their own libraries with, rather than request the clones from us. Obviously, in such cases we have no idea that the data is being used /useful and we would like to try to determine how often this happens. If you have used schisto EST data in this way, please could you reply to me, saying (1) that you have done so and (2) how often you have done it. ALL REPLIES WILL BE TREATED IN THE STRICTEST CONFIDENCE AND WE DO NOT NEED TO KNOW WHAT GENES YOU ARE WORKING WITH, just that you are utilising the EST data. Only summary statistics will be used in any reports to WHO. Any other supporting statements will also be gratefully received. Thank you, in advance, for your co-operation. David A. Johnston, Secretary to the WHO Schistosoma Genome Network, Biomedical Parasitology Division, Dept. of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, England, UK. Tel: 0171 9389297 (from outside the UK: 44 171 9389297) Fax: 0171 9388754 (from outside the UK: 44 171 9388754) eMail daj@nhm.ac.uk http://www.nhm.ac.uk/schisto The Biomedical Parasitology Division is a WHO Collaborating Centre for the identification of schistosomes and their snail hosts. From owner-schistosoma@net.bio.net Mon Apr 06 23:00:00 1998 Path: biosci!biosci!not-for-mail From: David Johnston Newsgroups: bionet.organisms.schistosoma Subject: Computing support for WHO's Parasite Genome Projects Date: 7 Apr 1998 04:29:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 141 Sender: daemon@net.bio.net Approved: greveld@rz.uni-duesseldorf.de Distribution: world Message-ID: <6gd2m1$ksi@net.bio.net> NNTP-Posting-Host: net.bio.net Dear all, the following document written by Mark Blaxter relates to the future development of computing resources to service the WHO Parasite Genome Initiatives (including that for schisto). It is of potential relevance to anyone who uses data generated by the schisto initiative (potentially anyone doing molecular work on schisto or other platyhelminthes. We would appreciate any comments that you might have on the proposals / options outlined in the document. Please reply to Mark Blaxter (mark.blaxter@ed.ac.uk) ********************************************************************** Currently, we have a WHO TDR funded post [staffed by Martin Aslett], based at the EBI, Hinxton, which provides a core support role in developing and maintaining parasite genome databases, and keeping the parasite-genome world wide web site available and up-to-date. We also have most of the parasite-genome acedb databases on the www via HGMP at Hinxton. This post is supplemented by individual parasite genome research labs which are generating and analysing genome data, and initiating and carrying out database and other informatics projects. The WHO grant for this work is up for renewal this year and if we are to reapply for funding it is essential that we have a clear strategy for the next three years. As each genome project starts reaping is successes, and thus enters a "second generation" of activity [with megabases to kilobases of genome sequence each on the cards for the next years] our needs for genome computing resources will soon outstrip current capacity. Obviously it is possible for each project to go it alone and develop and maintain expertise and resources independently. An alternative model is to continue to co-operate [as we have done so far] and to pool scarce resources in some way to yield better returns [services, outcomes] for all. I can see three possible sectors where the different genome projects could co-operate in genome bioinformatics: 1 a core world wide web site with on-line access to databases, maintained at a single location but mirrored elsewhere 2 analysis of EST and genome sequence [the role of finishers and analysts/annotators] 3 development and testing of new genome analysis tools geared to the specific needs of the genomes [base composition, gene organisation] and researchers [antigen identification, metabolic nets for drug target identification, etc]. There are [at least] two ways these needs could be met: through a core computing resource centre [all genomes analysed at one site] or by a distributed network of bioinformatics workers. Both approaches have benefits and costs/bugs - the proper route is most probably in-between these extremes. The core centre might offer benefits in: 1 a single site for access to all information 2 shared costs [e.g. of staff who might be only partially employed on a single genome project] 3 critical mass [basing a number of staff at a single site will both allow fruitful cross-fertilisation and attract better candidates] and access to peer group 4 being more attractive to external funding agencies [a funding body may be more likely to fund half a salary for one particular genome if the staff member will be in a recognised centre] The core might also be able to be based in a larger unit, such as the EBI or NCBI, thus using the leverage of the other bioinformatics expertise to advance parasitic interests. The core centre idea also has disadvantages: a the centre would have a geographical location which might be unattractive to some funding agencies b the centre would be based outside the labs where the data was being generated [in many cases] and thus would be less well integrated with the overall effort. This problem might be acute in the interpretation of data with respect to the particular biology of the parasites. c there may be issues of priority and co-ordination [If two cosmids get sequenced, which gets analysed first? How do the genome projects ensure that their priorities are recognised?] The distributed network of bioinformatics might have the following benefits: 1 the informatics expertise would be based in the genome labs allowing rapid transfer of concepts and data in both directions [biology -> bioinformatics and vice versa] 2 appropriate for local funding, particularly in building up local expertise in genomic computing 3 a greater variety of approaches would be tried and thus potential pitfalls and problems identified more readily Problems from the distributed model might be: a the individual bioinformatics workers would be relatively isolated, having to reinvent wheels already designed by others b the lack of a clear peer group [e.g. a major bioinformatics centre] might stifle innovation and application of advances c costs might be higher [each centre requiring hardware, etc] We am not currently biased towards either approach, but feel that it is timely to discuss this. Can we devise a scheme which will give us most of the benefits and little of the disadvantages? Perhaps a sensible outcome would be to promote a concentration of bioinformaticists in a core facility being achieved when and where possible [e.g. with the Sanger Centre involvement in several projects it might make sense to co-ordinate bioinformatics efforts there or at the EBI next door?], but there being a distributed effort based in other sequencing genome labs. We could have an annual gathering / workshop for all the informaticists, so that some of the benefits of the global informal college / peer group / critical mass can be reaped. This might also be achieved through the funding of a core resource staff who could train other informaticists (say over a 6 month period) at the core site, before they set themselves up in their home labs/countries. This revolving door would both bring new ideas and resources into the projects and keep links between projects alive. One issue is of course funding. We can ask the WHO to continue to fund the support post, and perhaps also other informatics posts per genome. These funding requests could include in them funds for the six months rotation idea. In Europe we could approach European or country-based funding bodies to supplement these posts with full time positions at the Sanger/EBI [if that was the chosen centre]. We would also appreciate any comments you have on the current role/performance of the WHO genomes computing support. Thanks Mark Blaxter *********************************************************** David A. Johnston, Secretary to the WHO Schistosoma Genome Network, Biomedical Parasitology Division, Dept. of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, England, UK. Tel: 0171 9389297 (from outside the UK: 44 171 9389297) Fax: 0171 9388754 (from outside the UK: 44 171 9388754) eMail daj@nhm.ac.uk http://www.nhm.ac.uk/schisto The Biomedical Parasitology Division is a WHO Collaborating Centre for the identification of schistosomes and their snail hosts. From owner-schistosoma@net.bio.net Mon Apr 06 23:00:00 1998 Path: biosci!biosci!not-for-mail From: David Johnston Newsgroups: bionet.organisms.schistosoma Subject: Computing support for WHO's Parasite Genome Projects Date: 7 Apr 1998 08:18:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 141 Sender: daemon@net.bio.net Approved: greveld@rz.uni-duesseldorf.de Distribution: world Message-ID: <6gdg4v$k1i@net.bio.net> NNTP-Posting-Host: net.bio.net Dear all, the following document written by Mark Blaxter relates to the future development of computing resources to service the WHO Parasite Genome Initiatives (including that for schisto). It is of potential relevance to anyone who uses data generated by the schisto initiative (potentially anyone doing molecular work on schisto or other platyhelminthes. We would appreciate any comments that you might have on the proposals / options outlined in the document. Please reply to Mark Blaxter (mark.blaxter@ed.ac.uk) ********************************************************************** Currently, we have a WHO TDR funded post [staffed by Martin Aslett], based at the EBI, Hinxton, which provides a core support role in developing and maintaining parasite genome databases, and keeping the parasite-genome world wide web site available and up-to-date. We also have most of the parasite-genome acedb databases on the www via HGMP at Hinxton. This post is supplemented by individual parasite genome research labs which are generating and analysing genome data, and initiating and carrying out database and other informatics projects. The WHO grant for this work is up for renewal this year and if we are to reapply for funding it is essential that we have a clear strategy for the next three years. As each genome project starts reaping is successes, and thus enters a "second generation" of activity [with megabases to kilobases of genome sequence each on the cards for the next years] our needs for genome computing resources will soon outstrip current capacity. Obviously it is possible for each project to go it alone and develop and maintain expertise and resources independently. An alternative model is to continue to co-operate [as we have done so far] and to pool scarce resources in some way to yield better returns [services, outcomes] for all. I can see three possible sectors where the different genome projects could co-operate in genome bioinformatics: 1 a core world wide web site with on-line access to databases, maintained at a single location but mirrored elsewhere 2 analysis of EST and genome sequence [the role of finishers and analysts/annotators] 3 development and testing of new genome analysis tools geared to the specific needs of the genomes [base composition, gene organisation] and researchers [antigen identification, metabolic nets for drug target identification, etc]. There are [at least] two ways these needs could be met: through a core computing resource centre [all genomes analysed at one site] or by a distributed network of bioinformatics workers. Both approaches have benefits and costs/bugs - the proper route is most probably in-between these extremes. The core centre might offer benefits in: 1 a single site for access to all information 2 shared costs [e.g. of staff who might be only partially employed on a single genome project] 3 critical mass [basing a number of staff at a single site will both allow fruitful cross-fertilisation and attract better candidates] and access to peer group 4 being more attractive to external funding agencies [a funding body may be more likely to fund half a salary for one particular genome if the staff member will be in a recognised centre] The core might also be able to be based in a larger unit, such as the EBI or NCBI, thus using the leverage of the other bioinformatics expertise to advance parasitic interests. The core centre idea also has disadvantages: a the centre would have a geographical location which might be unattractive to some funding agencies b the centre would be based outside the labs where the data was being generated [in many cases] and thus would be less well integrated with the overall effort. This problem might be acute in the interpretation of data with respect to the particular biology of the parasites. c there may be issues of priority and co-ordination [If two cosmids get sequenced, which gets analysed first? How do the genome projects ensure that their priorities are recognised?] The distributed network of bioinformatics might have the following benefits: 1 the informatics expertise would be based in the genome labs allowing rapid transfer of concepts and data in both directions [biology -> bioinformatics and vice versa] 2 appropriate for local funding, particularly in building up local expertise in genomic computing 3 a greater variety of approaches would be tried and thus potential pitfalls and problems identified more readily Problems from the distributed model might be: a the individual bioinformatics workers would be relatively isolated, having to reinvent wheels already designed by others b the lack of a clear peer group [e.g. a major bioinformatics centre] might stifle innovation and application of advances c costs might be higher [each centre requiring hardware, etc] We am not currently biased towards either approach, but feel that it is timely to discuss this. Can we devise a scheme which will give us most of the benefits and little of the disadvantages? Perhaps a sensible outcome would be to promote a concentration of bioinformaticists in a core facility being achieved when and where possible [e.g. with the Sanger Centre involvement in several projects it might make sense to co-ordinate bioinformatics efforts there or at the EBI next door?], but there being a distributed effort based in other sequencing genome labs. We could have an annual gathering / workshop for all the informaticists, so that some of the benefits of the global informal college / peer group / critical mass can be reaped. This might also be achieved through the funding of a core resource staff who could train other informaticists (say over a 6 month period) at the core site, before they set themselves up in their home labs/countries. This revolving door would both bring new ideas and resources into the projects and keep links between projects alive. One issue is of course funding. We can ask the WHO to continue to fund the support post, and perhaps also other informatics posts per genome. These funding requests could include in them funds for the six months rotation idea. In Europe we could approach European or country-based funding bodies to supplement these posts with full time positions at the Sanger/EBI [if that was the chosen centre]. We would also appreciate any comments you have on the current role/performance of the WHO genomes computing support. Thanks Mark Blaxter *********************************************************** David A. Johnston, Secretary to the WHO Schistosoma Genome Network, Biomedical Parasitology Division, Dept. of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, England, UK. Tel: 0171 9389297 (from outside the UK: 44 171 9389297) Fax: 0171 9388754 (from outside the UK: 44 171 9388754) eMail daj@nhm.ac.uk http://www.nhm.ac.uk/schisto The Biomedical Parasitology Division is a WHO Collaborating Centre for the identification of schistosomes and their snail hosts.