From dan.bolser at gmail.com Sat Dec 1 05:56:48 2007 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 1 Dec 2007 11:56:48 +0100 Subject: [BiO BB] Extracting GeneNames from a GO class and their syblings In-Reply-To: <1C6586068DF1054DA3899159C38B32C9245FD3@um-mail0136.unimaas.nl> References: <1C6586068DF1054DA3899159C38B32C9245FD3@um-mail0136.unimaas.nl> Message-ID: <2c8757af0712010256t5fa85f55w59dcf15f866b76cf@mail.gmail.com> On 28/11/2007, Gaj Stan (BIGCAT) wrote: > Dear all, > > > > My question today concerns GeneOntology annotation extraction. Is it > possible to extract a list of genes which belong to a specific > GO-process and it's children? > > > > Or, to put it in a more clearer context: > > > > - I'm interested in all genes belonging to the Lipid Metabolic process > category (GO:0006629 : lipid metabolic process > constraint=terms&depth=0&query=GO:0006629&session_id=4045b1196258143&sho > w_associations=list> ). > > - I aim to have a list of ALL genes that belong to this GO category or > below, up untill the smallest, most specific node (i.e. cellular lipid > metabolic process > constraint=terms&depth=0&query=GO:0044255&session_id=4045b1196258143&sho > w_associations=list> -> cellular lipid catabolic process > constraint=terms&depth=0&query=GO:0044242&session_id=4045b1196258143&sho > w_associations=list> --> etc) > > - This list can afterwards be filtered for duplicate names / IDs using > Perl or something similar (can do that part myself (-; ) > > - In the end, I would like to have a list that consists of gene names or > any other usable ID(i.e. like EnsEMBL, UniProt, EntrezGene, ...) which > are classfied as having a Lipid Metabolic activity! > > > > Is there a specific GO-Tool available (or am I unaware that this is even > possible in GO itself) that can do this? If the solution presents itself > by using R and specific GO-libraries, then I'm eager to hear about it as > well (-: (since I know it is possible to extract both parent and > children nodes, but am unaware on how to do this for gene names/IDs). Sounds like an interesting (if not uncommon) request.... You should be able to achieve this using the 'go-database', which you can find under here; http://www.geneontology.org/ Seems that you need to traverse the hierarchy, querying a specific mapping as you go (performing iterative SQL queries via Perl should allow you to do this). I don't know why the database dump isn't provided in a convenient tab delimited format. You can try asking for a more direct solution on either the "GO Friends" mailing list or the "GO Database" mailing list, here; http://www.geneontology.org/GO.mailing.lists.shtml Which reminds me... (more in the next email). Dan. -- Join the # bioinformatics fun! irc://freenode.net/#bioinformatics or http://www.acm.jhu.edu/cgi-irc/irc.cgi?chan=%23bioinformatics From dan.bolser at gmail.com Sat Dec 1 06:02:02 2007 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 1 Dec 2007 12:02:02 +0100 Subject: [BiO BB] Mailing lists for biologists? Message-ID: <2c8757af0712010302q2ab865bdnedfc516edeb78e60@mail.gmail.com> Hi, Together with some friends I started to put together this page; List of mailing lists for biologists; http://biodatabase.org/index.php/List_of_mailing_lists_for_biologists I am not sure if there is a better place for this kind of list somewhere on http://Bioinformatics.Org, http://BiO.CC or even on Wikipedia, as I know all these sites maintain related projects. I don't even know if such lists already exist elsewhere on the internet (preliminary searching didn't turn anything up). Can anyone point me towards related resources to integrate or transfer effort to? Alternatively, please feel free to edit, add or update the existing (rather limited) list of mailing lists on the above page. Cheers, Dan. -- Join the #bioinformatics fun! irc://freenode.net/#bioinformatics or http://www.acm.jhu.edu/cgi-irc/irc.cgi?chan=%23bioinformatics From cjm at fruitfly.org Sat Dec 1 15:19:08 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Sat, 1 Dec 2007 12:19:08 -0800 Subject: [BiO BB] Extracting GeneNames from a GO class and their syblings In-Reply-To: <2c8757af0712010256t5fa85f55w59dcf15f866b76cf@mail.gmail.com> References: <1C6586068DF1054DA3899159C38B32C9245FD3@um-mail0136.unimaas.nl> <2c8757af0712010256t5fa85f55w59dcf15f866b76cf@mail.gmail.com> Message-ID: <9FC1123A-F2ED-4A0E-B6DF-58D8C239D26B@fruitfly.org> On Dec 1, 2007, at 2:56 AM, Dan Bolser wrote: > On 28/11/2007, Gaj Stan (BIGCAT) wrote: >> Dear all, >> >> >> >> My question today concerns GeneOntology annotation extraction. Is it >> possible to extract a list of genes which belong to a specific >> GO-process and it's children? >> >> >> >> Or, to put it in a more clearer context: >> >> >> >> - I'm interested in all genes belonging to the Lipid Metabolic >> process >> category (GO:0006629 : lipid metabolic process >> > view=details&search_ >> constraint=terms&depth=0&query=GO: >> 0006629&session_id=4045b1196258143&sho >> w_associations=list> ). >> >> - I aim to have a list of ALL genes that belong to this GO >> category or >> below, up untill the smallest, most specific node (i.e. cellular >> lipid >> metabolic process >> > view=details&search_ >> constraint=terms&depth=0&query=GO: >> 0044255&session_id=4045b1196258143&sho >> w_associations=list> -> cellular lipid catabolic process >> > view=details&search_ >> constraint=terms&depth=0&query=GO: >> 0044242&session_id=4045b1196258143&sho >> w_associations=list> --> etc) >> >> - This list can afterwards be filtered for duplicate names / IDs >> using >> Perl or something similar (can do that part myself (-; ) >> >> - In the end, I would like to have a list that consists of gene >> names or >> any other usable ID(i.e. like EnsEMBL, UniProt, EntrezGene, ...) >> which >> are classfied as having a Lipid Metabolic activity! >> >> >> >> Is there a specific GO-Tool available (or am I unaware that this >> is even >> possible in GO itself) that can do this? If the solution presents >> itself >> by using R and specific GO-libraries, then I'm eager to hear about >> it as >> well (-: (since I know it is possible to extract both parent and >> children nodes, but am unaware on how to do this for gene names/IDs). > > Sounds like an interesting (if not uncommon) request.... You should be > able to achieve this using the 'go-database', which you can find under > here; > > http://www.geneontology.org/ The database page is here: http://www.geneontology.org/GO.database.shtml > Seems that you need to traverse the hierarchy, querying a specific > mapping as you go (performing iterative SQL queries via Perl should > allow you to do this). Actually, no iterative queries or programming is required as the closure of the relations are pre-computed in the database - see the explanation on the page above. There are some example queries here: http://wiki.geneontology.org/index.php/Example_Queries and a link to a web form for executing SQL queries & getting back results as tab-delimited files or HTML Of course, if you want to do the closure of the relations in the graph programmatically, there are APIs for doing so. Note also that export of tab delimited files from query results will be available in the next release of AmiGO - this will be the most likely route from the non-SQL or perl-savvy user. > I don't know why the database dump isn't > provided in a convenient tab delimited format. Well, technically the MySQL database dump is tab-delimited. But we recommend against using this for any purpose other than building a MySQL instance. The relatively normalized schema and prevalence of surrogate IDs makes these dumps a poor choice for writing parsers against. And of course the association files are tab-delimited but these are not sufficient in and of themselves to answer the query above. > You can try asking for a more direct solution on either the "GO > Friends" mailing list or the "GO Database" mailing list, here; > > http://www.geneontology.org/GO.mailing.lists.shtml There is also the GO helpdesk, linked from the front page. > Which reminds me... (more in the next email). > > > Dan. > > -- > > Join the # bioinformatics fun! > > irc://freenode.net/#bioinformatics or > > http://www.acm.jhu.edu/cgi-irc/irc.cgi?chan=%23bioinformatics > > From s_uchida21 at yahoo.co.jp Sun Dec 2 14:01:38 2007 From: s_uchida21 at yahoo.co.jp (=?ISO-2022-JP?B?GyRCRmJFRBsoQiAbJEJMdzpIGyhC?=) Date: Mon, 3 Dec 2007 04:01:38 +0900 (JST) Subject: [BiO BB] Finding PMID related to MeSH terms Message-ID: <20071202190138.49452.qmail@web3906.mail.bbt.yahoo.co.jp> Hello. I want to obtain all PMIDs related to a certain MeSH term. For example, >From MeSH homepage http://www.ncbi.nlm.nih.gov/sites/entrez?db=mesh, search "Liver" => click the "Links" for "1: Liver Year introduced: /cytology was LIVER CYTOLOGY 1964-1965" => jump to "PubMed" site Result display: "All: 327807 Review: 17161" >From the above result, I want to obatin all 327,807 PMID. By using this PubMed website, I am only allowed to download 500 PMIDs each. Could anyone give me some suggestions on how I can download all PMIDs at once? Or better, do anyone know a FTP site where I can download all related PMIDs to MeSH terms? Thank you very much for your help in advance. Shizuka -------------------------------------- New Design Yahoo! JAPAN 2008/01/01 http://pr.mail.yahoo.co.jp/newdesign/ From jorgemdfaria at gmail.com Sun Dec 2 07:37:27 2007 From: jorgemdfaria at gmail.com (Jorge Faria) Date: Sun, 2 Dec 2007 12:37:27 +0000 Subject: [BiO BB] Biomedical Informatics Message-ID: Does anyone have this e-book? Biomedical Informatics-Computer Applications in Health Care and Biomedicine From sankar.achuth at gmail.com Sun Dec 2 06:52:47 2007 From: sankar.achuth at gmail.com (Dr. Achuthsankar S. Nair) Date: Sun, 2 Dec 2007 11:52:47 +0000 Subject: [BiO BB] Bioinformatica Indica :: Jan 17-19, 2008 Message-ID: <2b168b460712020352i4cad372fvf6f247a89551defc@mail.gmail.com> Dear fellow researcher Let me first of all apologise for any cross-postings.The Centre for Bioinformatics at University of Kerala, India is organising an International Symposium christened Bioinformatica Indica 08 from January 17-19, 2008. Dr Todd Taylor from Riken Yokohama Institute, Tokyo will be the keynote speaker. Computational Biology, Bioinformatics and Synthetic biology will be focused. Posters are welcome. Please see attached flyer for details or visit the site www.bioinformaticaindica.org Regards -- Dr Achuthsankar S Nair Director, Centre for Bioinformatics, University of Kerala, India www.achu.keralauniversity.edu From marchywka at hotmail.com Mon Dec 3 21:49:18 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 3 Dec 2007 21:49:18 -0500 Subject: [BiO BB] Finding PMID related to MeSH terms In-Reply-To: <20071202190138.49452.qmail@web3906.mail.bbt.yahoo.co.jp> References: <20071202190138.49452.qmail@web3906.mail.bbt.yahoo.co.jp> Message-ID: > Could anyone give me some suggestions on how I can > download all PMIDs at once? Or better, do anyone I've never encountered a limitation with eutils: ( hit these links, I pulled them out of a script I use ) SNPHELPURL="http://www.ncbi.nlm.nih.gov/projects/SNP/SNPeutils.htm" DBHELPURL="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html" #http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pccompound #http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html #http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? #http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html#SequenceDatabases SEARCHHELPURL="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html" #http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html I tried it myself, and it would have worked but I killed it: $ eutilsnew -v -out junk "liver[mesh]" Count is 327807 --21:46:17-- http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=biot echmarchywka&email=marchywka at hotmail.com&rettype=abstract&retmode=text&retstart= 0&retmax=327807&db=Pubmed&query_key=1&WebEnv=0pNNCKO60mP4gg0SvlhFxs1uZ6fgH_IZxjO ZEs3mmUL9qzejO1IO9A_Hsr at 1EDE7B35754BF7D0_0014SID => `junk' Resolving eutils.ncbi.nlm.nih.gov... 130.14.29.110 Connecting to eutils.ncbi.nlm.nih.gov[130.14.29.110]:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] [ <=> ] 230,932 42.60K/s I could send you the script but it has a lot of idiosyncratic stuff for myself, there are good examples on their site. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Mon, 3 Dec 2007 04:01:38 +0900 > From: s_uchida21 at yahoo.co.jp > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Finding PMID related to MeSH terms > > Hello. I want to obtain all PMIDs related to a > certain MeSH term. For example, > >>From MeSH homepage > http://www.ncbi.nlm.nih.gov/sites/entrez?db=mesh, > > search "Liver" > > => click the "Links" for "1: Liver > Year introduced: /cytology was LIVER CYTOLOGY > 1964-1965" > > => jump to "PubMed" site > > Result display: "All: 327807 Review: 17161" > > >>From the above result, I want to obatin all 327,807 > PMID. By using this PubMed website, I am only > allowed to download 500 PMIDs each. > > Could anyone give me some suggestions on how I can > download all PMIDs at once? Or better, do anyone > know a FTP site where I can download all related > PMIDs to MeSH terms? > > Thank you very much for your help in advance. > > Shizuka > > From skravitz at jcvi.org Mon Dec 3 21:31:02 2007 From: skravitz at jcvi.org (Kravitz, Saul) Date: Mon, 3 Dec 2007 21:31:02 -0500 Subject: [BiO BB] Web-based BLAST Services Message-ID: We have developed a web-based implementation of BLAST as part of the CAMERA project (http://calit2.camera.net). Although we realize that there are a number of parallel implementations of BLAST, I am interested in the capabilities of web-based deployments of BLAST. Specifically, there capacities as measured in terms of: - Maximum number of query sequences - Maximum total size of the query sequences - Maximum number or data volume of hits returned (NCBI seems to be 500) - Maximum Total Search Time (NCBI is 1 Hr) In CAMERA's case, the numbers today are: - Maximum number of query sequences -- we've tested to 250k - Maximum total size of the query sequences -- we've tested to 100Mbp - Maximum number or data volume of hits returned (we've tested to several hundred thousand) - Maximum Total Search Time (None so far) Regards, Saul Kravitz J. Craig Venter Institute From wilfred at sdsc.edu Tue Dec 4 16:54:54 2007 From: wilfred at sdsc.edu (Wilfred Li) Date: Tue, 4 Dec 2007 13:54:54 -0800 Subject: [BiO BB] Web-based BLAST Services In-Reply-To: References: Message-ID: <452F37AE49199D49B1702D7D45038C4DC935B0@et.ad.sdsc.edu> The URL is http://camera.calit2.net. :) Regards, Wilfred -----Original Message----- From: bio_bulletin-bounces at restools.sdsc.edu [mailto:bio_bulletin- bounces at restools.sdsc.edu] On Behalf Of Kravitz, Saul Sent: Tuesday, December 04, 2007 10:31 AM To: bbb at bioinformatics.org Subject: [BiO BB] Web-based BLAST Services We have developed a web-based implementation of BLAST as part of the CAMERA project (http://calit2.camera.net). Although we realize that there are a number of parallel implementations of BLAST, I am interested in the capabilities of web-based deployments of BLAST. Specifically, there capacities as measured in terms of: - Maximum number of query sequences - Maximum total size of the query sequences - Maximum number or data volume of hits returned (NCBI seems to be 500) - Maximum Total Search Time (NCBI is 1 Hr) In CAMERA's case, the numbers today are: - Maximum number of query sequences -- we've tested to 250k - Maximum total size of the query sequences -- we've tested to 100Mbp - Maximum number or data volume of hits returned (we've tested to several hundred thousand) - Maximum Total Search Time (None so far) Regards, Saul Kravitz J. Craig Venter Institute From skravitz at jcvi.org Tue Dec 4 14:50:34 2007 From: skravitz at jcvi.org (Kravitz, Saul) Date: Tue, 4 Dec 2007 14:50:34 -0500 Subject: [BiO BB] Web-based BLAST Services (addendum) In-Reply-To: References: Message-ID: Oops...got the URL for our project wrong... should be http://camera.calit2.net. We welcome registrations from the bioinformatics.org community. Also, I inquired of NCBI regarding their capabilities and got the following response from Wayne Matten at the NCBI Service Desk: This is impossible to say due to the variability in queries, databases and the output generated. Our only set limit is on cpu time (about 1 hour cumulative, over several machines). In other words, you can only determine the practical limits of your searches by testing them. -Saul ________________________________ From: Kravitz, Saul Sent: Monday, December 03, 2007 9:31 PM To: bbb at bioinformatics.org Subject: Web-based BLAST Services We have developed a web-based implementation of BLAST as part of the CAMERA project (http://calit2.camera.net). Although we realize that there are a number of parallel implementations of BLAST, I am interested in the capabilities of web-based deployments of BLAST. Specifically, there capacities as measured in terms of: - Maximum number of query sequences - Maximum total size of the query sequences - Maximum number or data volume of hits returned (NCBI seems to be 500) - Maximum Total Search Time (NCBI is 1 Hr) In CAMERA's case, the numbers today are: - Maximum number of query sequences -- we've tested to 250k - Maximum total size of the query sequences -- we've tested to 100Mbp - Maximum number or data volume of hits returned (we've tested to several hundred thousand) - Maximum Total Search Time (None so far) Regards, Saul Kravitz J. Craig Venter Institute From sowmiya_raj at rediffmail.com Wed Dec 5 00:08:04 2007 From: sowmiya_raj at rediffmail.com (Sowmiya Raj) Date: 5 Dec 2007 05:08:04 -0000 Subject: [BiO BB] blast graphical result & gapped alignment Message-ID: <20071205050804.9480.qmail@f5mail-237-208.rediffmail.com> hi all, I am developing a webserver using the standalone BLAST program. I am getting the results. I want to include the graphical results in the text result page(html). How do i go about it? Should i use any GD modules from PERL? And also, i am able to get only the ungapped results, but not the gapped results. though i have included the command -g T -G 13 -E 3. Please let me know how to do gapped alignment. regards somya. On Tue, 04 Dec 2007 sysadmins at bioinformatics.org wrote : >Somya, we have a mailing list that is better for that question: > > bbb at bioinformatics.org > http://bioinformatics.org/lists/bbb > >But please elaborate: what do you mean by "include the graphical results"? > >---------------- >How do i include the graphical results of blast in image format while building a web server using stand alone blast program? > From marchywka at hotmail.com Wed Dec 5 13:41:59 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 5 Dec 2007 13:41:59 -0500 Subject: [BiO BB] blast graphical result & gapped alignment In-Reply-To: <20071205050804.9480.qmail@f5mail-237-208.rediffmail.com> References: <20071205050804.9480.qmail@f5mail-237-208.rediffmail.com> Message-ID: > I am developing a webserver using the standalone BLAST program. I am getting the results. I want to include the graphical results in the text result page(html). How do i go about it? Should i use any GD modules from PERL? And also, i am able to get only the ungapped results, but not the gapped results. though i have included the command -g T -G 13 -E 3. Please let me know how to do gapped alignment. One option would be to use a servlet to generate html or use various command line utilities to generate image files that could be displayed with static or almost static html. It is probably not hard with something like cold fusion but you can get a servlet engine for free :) I haven't used the GD modules but Java provides a lot of simple drawing methods, it is probably just as fast as PERL and would integrate nicely with servlets. One of the popular genome browsers, IGB, I think is written in java- you may be able to get source code and adapt: http://www.affymetrix.com/support/developer/tools/affytools.affx If you are looking for a canned example, you may try contacting sites that do something similar or just look at their source code- you can probably figure out how they do it. The coarse graphics I've encountered for viewing sequences look like it is all generated html rather than drawn images. If you find something you like it is easier to talk about specifics. Obviously, a lot would depend on how much customization you think you will need and performance issues. I haven't checked all the available output options but I wrote some bash scripts for reformatting default blast output into "annotation format" that I use with my own tools. If you care to comment on this I would appreciate any input ( click on qseg.bmp to see the graphics stuff , I'm still putting this together please don't critique web page design :) Thanks to phluant.com for providing the server): http://www.spottext.com/marchywka/mydownloads.cfm The above was generated with C++ tools- quite fast but the bmp files are huge and don't compress well as jpg. You will probably need to view it in an image viewer rather than browser as you really will need to zoom in to see details. Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka at yahoo.com if no reply here. Thanks. _________________________________________________________________ Put your friends on the big screen with Windows Vista? + Windows Live?. http://www.microsoft.com/windows/shop/specialoffers.mspx?ocid=TXT_TAGLM_CPC_MediaCtr_bigscreen_102007 From golharam at umdnj.edu Wed Dec 5 15:27:27 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 05 Dec 2007 15:27:27 -0500 Subject: [BiO BB] blast graphical result & gapped alignment In-Reply-To: References: <20071205050804.9480.qmail@f5mail-237-208.rediffmail.com> Message-ID: <475709AF.8000109@umdnj.edu> BioPerl has an example of creating a graphic from Blast output. Mike Marchywka wrote: >> I am developing a webserver using the standalone BLAST program. I am getting the results. I want to include the graphical results in the text result page(html). How do i go about it? Should i use any GD modules from PERL? And also, i am able to get only the ungapped results, but not the gapped results. though i have included the command -g T -G 13 -E 3. Please let me know how to do gapped alignment. > > > One option would be to use a servlet to generate html > or use various command line utilities to generate image files that could be displayed with > static or almost static html. It is probably not hard with something like cold fusion but you can get a servlet engine for free :) I haven't used the GD modules but Java provides a lot of simple drawing methods, it is probably > just as fast as PERL and would integrate nicely with servlets. One of the popular genome browsers, > IGB, I think is written in java- you may be able to get source code and > adapt: > > http://www.affymetrix.com/support/developer/tools/affytools.affx > > If you are looking for a canned example, you may try contacting sites that do something > similar or just look at their source code- you can probably figure out how they do it. > The coarse graphics I've encountered for viewing sequences look like it is all generated > html rather than drawn images. > If you find something you like it is easier to talk about specifics. > Obviously, a lot would depend on how much customization you think you will need > and performance issues. > > > I haven't checked all the available output options but I wrote some bash scripts for reformatting > default blast output into "annotation format" that I use with my own tools. > If you care to comment on this I would appreciate any input ( click on qseg.bmp to > see the graphics stuff , I'm still putting this together please don't critique web page design :) > Thanks to phluant.com for providing the server): > > http://www.spottext.com/marchywka/mydownloads.cfm > > The above was generated with C++ tools- quite fast but the bmp files are huge and > don't compress well as jpg. You will probably need to view it in an image viewer rather than browser > as you really will need to zoom in to see details. > > > Thanks. > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > marchywka at hotmail.com > Note: Hotmail is blocking my mom's entire > ISP claiming it is to reduce spam but probably > to force users to use hotmail. Please DON'T > assume I am ignoring you and try > me on marchywka at yahoo.com if no reply > here. Thanks. > > > _________________________________________________________________ > Put your friends on the big screen with Windows Vista? + Windows Live?. > http://www.microsoft.com/windows/shop/specialoffers.mspx?ocid=TXT_TAGLM_CPC_MediaCtr_bigscreen_102007 > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From carlosjmviana at gmail.com Thu Dec 6 06:51:42 2007 From: carlosjmviana at gmail.com (Carlos Viana) Date: Thu, 6 Dec 2007 07:51:42 -0400 Subject: [BiO BB] blast graphical result & gapped alignment In-Reply-To: <475709AF.8000109@umdnj.edu> References: <20071205050804.9480.qmail@f5mail-237-208.rediffmail.com> <475709AF.8000109@umdnj.edu> Message-ID: You could use GBrowse for display your results. You may include graphical results using tracks for each type of results: gapped and ungapped. For details and examples: * Details http://www.gmod.org/wiki/index.php/Gbrowse#Documentation http://www.bioperl.org/wiki/Gbrowse * Examples http://www.hapmap.org/cgi-perl/gbrowse/hapmap_B35/?name=Chr20 http://flybase.net/cgi-bin/gbrowse/dmel/ Carlos Juliano. On Dec 5, 2007 4:27 PM, Ryan Golhar wrote: > BioPerl has an example of creating a graphic from Blast output. > > Mike Marchywka wrote: > >> I am developing a webserver using the standalone BLAST program. I am > getting the results. I want to include the graphical results in the text > result page(html). How do i go about it? Should i use any GD modules from > PERL? And also, i am able to get only the ungapped results, but not the > gapped results. though i have included the command -g T -G 13 -E 3. Please > let me know how to do gapped alignment. > > > > > > One option would be to use a servlet to generate html > > or use various command line utilities to generate image files that could > be displayed with > > static or almost static html. It is probably not hard with something > like cold fusion but you can get a servlet engine for free :) I haven't used > the GD modules but Java provides a lot of simple drawing methods, it is > probably > > just as fast as PERL and would integrate nicely with servlets. One of > the popular genome browsers, > > IGB, I think is written in java- you may be able to get source code and > > adapt: > > > > http://www.affymetrix.com/support/developer/tools/affytools.affx > > > > If you are looking for a canned example, you may try contacting sites > that do something > > similar or just look at their source code- you can probably figure out > how they do it. > > The coarse graphics I've encountered for viewing sequences look like it > is all generated > > html rather than drawn images. > > If you find something you like it is easier to talk about specifics. > > Obviously, a lot would depend on how much customization you think you > will need > > and performance issues. > > > > > > I haven't checked all the available output options but I wrote some bash > scripts for reformatting > > default blast output into "annotation format" that I use with my own > tools. > > If you care to comment on this I would appreciate any input ( click on > qseg.bmp to > > see the graphics stuff , I'm still putting this together please don't > critique web page design :) > > Thanks to phluant.com for providing the server): > > > > http://www.spottext.com/marchywka/mydownloads.cfm > > > > The above was generated with C++ tools- quite fast but the bmp files are > huge and > > don't compress well as jpg. You will probably need to view it in an > image viewer rather than browser > > as you really will need to zoom in to see details. > > > > > > Thanks. > > > > Mike Marchywka > > 586 Saint James Walk > > Marietta GA 30067-7165 > > 404-788-1216 (C)<- leave message > > 989-348-4796 (P)<- emergency only > > marchywka at hotmail.com > > Note: Hotmail is blocking my mom's entire > > ISP claiming it is to reduce spam but probably > > to force users to use hotmail. Please DON'T > > assume I am ignoring you and try > > me on marchywka at yahoo.com if no reply > > here. Thanks. > > > > > > _________________________________________________________________ > > Put your friends on the big screen with Windows Vista(R) + Windows Live?. > > > http://www.microsoft.com/windows/shop/specialoffers.mspx?ocid=TXT_TAGLM_CPC_MediaCtr_bigscreen_102007 > > _______________________________________________ > > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- ********************************************** * Carlos Juliano ********************************************** *********************************************** From marchywka at hotmail.com Fri Dec 7 10:30:04 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 7 Dec 2007 10:30:04 -0500 Subject: [BiO BB] blast graphical result & gapped alignment In-Reply-To: References: <20071205050804.9480.qmail@f5mail-237-208.rediffmail.com> <475709AF.8000109@umdnj.edu> Message-ID: >>> The coarse graphics I've encountered for viewing sequences look like it >> is all generated >>> html rather than drawn images. Certainly flybase is using generated html for the coarse stuff, ( I took out "<" and ">" since some program try to execute code excerpts...) area shape="rect" coords="25,0,65,20" href="?ref=2R;start=9318082;stop=9333256;nav4=1;plugin=" title="recenter" alt="recenter" area shape="rect" coords="65,0,105,20" href="?ref=2R;start=9318840;stop=9334014;nav4=1;plugin=" title="recenter" alt="recenter" Looks like hapmap is taking a similar approach but it isn't clear how it is generated. I've got a fully text output that I'm considering augmenting to generated html for annotation but I'm trying to concentrate on the automated analysis part rather than interactive graphics. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Thu, 6 Dec 2007 07:51:42 -0400 > From: carlosjmviana at gmail.com > To: sowmiya_raj at rediffmail.com > CC: bbb at bioinformatics.org > Subject: Re: [BiO BB] blast graphical result & gapped alignment > > You could use GBrowse for display your results. You may include graphical > results using tracks for each type of results: gapped and ungapped. For > details and examples: > > * Details > http://www.gmod.org/wiki/index.php/Gbrowse#Documentation > http://www.bioperl.org/wiki/Gbrowse > > * Examples > http://www.hapmap.org/cgi-perl/gbrowse/hapmap_B35/?name=Chr20 > http://flybase.net/cgi-bin/gbrowse/dmel/ > > > Carlos Juliano. > > From isbra-l at engr.uconn.edu Fri Dec 7 21:13:35 2007 From: isbra-l at engr.uconn.edu (ISBRA Symposium Announcements) Date: Fri, 7 Dec 2007 21:13:35 -0500 (EST) Subject: [BiO BB] [ISBRA-L] ODGEA08 Call For Papers In-Reply-To: References: Message-ID: CALL FOR PAPERS ==================================================================== 1st International Workshop on Optimal Data Mining in Gene Expression Analysis (ODGEA08) http://giscompute.gis.a-star.edu.sg/~karu/ODGEA08/CFP.html in conjunction with International Symposium on Bioinformatics Research and Applications (ISBRA08) http://www.cs.gsu.edu/isbra08/ May 6-9, 2008, Atlanta, GA, USA ==================================================================== The rapid development of several high-throughput gene expression monitoring technologies in the past decade has facilitated the generation of a huge amount of gene expression data. The data could either be rich or poor in the number of samples in a wide variety of experimental design setups. Aforementioned factors led to a need to develop suitable statistical procedures for optimal analysis, visualization and interpretation of the data. We are soliciting original research papers (including significant works in progress) involving gene expression analysis, including the following: A. Novel supervised and unsupervised analysis and visualization methodologies B. Novel experimental designs, problems and suitable procedures to solve them C. Optimal feature selection for tumor classification and patient-outcome prediction D. Integrative analysis of gene expression data obtained from different platforms and laboratories E. Interpretation of gene expression data with other datasets such as ChIP-chip data and proteomics data. F. Significance assessment of predictions SUBMISSION and PUBLICATION The workshop proceedings will be published along with the ISBRA proceedings in Springer-Verlag's Lecture Notes in Bioinformatics series. Papers must be submitted electronically by following the instructions at: http://www.cs.gsu.edu/isbra08/papers.html Submissions must be formatted using the Springer LNCS style and must not exceed 12 pages in length. Simultaneous submission to journals or other conferences with published proceedings is not allowed. Further, it is anticipated that a special issue of a major bioinformatics journal will be devoted to extended versions of best conference and workshop papers. IMPORTANT DATES 02 Jan 2008 Submission of papers 25 Jan 2008 Notification 15 Feb 2008 Camera Ready Papers 09 May 2008 Workshop Presentation WORKSHOP ORGANIZERS General Chair: Lonnie R. Welch, Stuckey Professor 322A Stocker Center School of Electrical Engineering and Computer Science Ohio University Athens, OH 45701-2979 welch at ohio.edu Program Chairs: R. Krishna Murthy Karuturi Sr Research Scientist Computational & Mathematical Biology Genome Institute of Singapore A*STAR (Agency for Science, Technology and Research) #02-01, Genome, 60 Biopolis ST Republic of Singapore 138672 karuturikm at gis.a-star.edu.sg Qihua Tan, Associate Professor Dept of Biochemistry, Pharmacology and Genetics Odense University Hospital Sdr. Boulevard 29 DK-5000, Odense C Denmark Qihua.Tan at ouh.regionsyddanmark.dk Jahangheer Shareef Shaik Computer Vision, Pattern and Image Analysis Lab University of Memphis Memphis, TN, USA jahangeer.shaik at gmail.com _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From wongls at comp.nus.edu.sg Thu Dec 13 02:24:06 2007 From: wongls at comp.nus.edu.sg (Limsoon Wong) Date: Thu, 13 Dec 2007 15:24:06 +0800 Subject: [BiO BB] Call for Posters - RECOMB2008 Message-ID: <018601c83d59$250b9980$76b81aac@comp.nus.edu.sg> Call for Posters for RECOMB2008 http://www.comp.nus.edu.sg/~recomb08/ The 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB2008) will be held 30th March - 2nd April 2008 at the University Cultural Centre, National University of Singapore, Singapore. RECOMB 2008 will provide a general forum for disseminating the latest research in bioinformatics and computational biology. The multidisciplinary conference brings together academic and industrial scientists from molecular biology, genetics, medicine, computer science, mathematics, and statistics. Poster abstract submission for RECOMB 2008 is now open. Poster abstracts are limited to 2 pages, including title, figures, tables, text, and bibliography. Please see below for Abstract Templates. Please conform to the template. All abstracts should be submitted at the site http://www.easychair.org/conferences/?conf=recomb2008_poster Accepted poster abstracts will be compiled into "The 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB2008): Poster Book". Additionally, a number of notable abstracts will be invited for submission to a reputable journal. Important Dates Poster submission deadline: 14th January 2008. Poster decision: 4th February 2008. Poster Abstract Templates LaTeX: http://www.comp.nus.edu.sg/~wongls/psZ/recomb08/Poster_Template2008.tex Word: http://www.comp.nus.edu.sg/~wongls/psZ/recomb08/Poster_Template2007.doc A sample PDF file can be obtained at http://www.comp.nus.edu.sg/~wongls/psZ/recomb08/Poster_Template2008.pdf Professor Limsoon WONG:: National University of Singapore :: School of Computing, COM1 #3-34, 13 Law Link, Singapore 117590:: 65-6516 2902(DID) :: 65-6779 4580 (Fax) :: dcswls at nus.edu.sg (E) :: www.comp.nus.edu.sg/~wongls (W) :: Company Registration No: 200604346E From codeshepherd at gmail.com Mon Dec 17 09:32:55 2007 From: codeshepherd at gmail.com (=?ISO-8859-1?Q?Dee=FEan_Chakravarthy?=) Date: Mon, 17 Dec 2007 22:32:55 +0800 Subject: [BiO BB] hi help me pls In-Reply-To: <9c9e3ba10711200148m3d1b2368v2f698dcf45cb38e7@mail.gmail.com> References: <6dd7f9b90711192209x3a0291b6s75b326cad2345fdd@mail.gmail.com> <9c9e3ba10711200148m3d1b2368v2f698dcf45cb38e7@mail.gmail.com> Message-ID: <47668897.5040308@gmail.com> jay ananth wrote: > I need one help from u... > > search for best tools for the following : > 1.Secondary Structure prediction in RNA > 2.Protein Secondary Structure Prediction. > 3.Prediction of disordered regions in proteins.. > 4.Case Std on Structure-function relationships in proteins > 5.Prediction of transmembrane regions in proteins > 6.Characterization of antigenecity in polypeptides- epitope mapping > > > > Are you looking for computational tools to do the above ? Can you be more specific ? Autodock, Gromacs are some of the tools that you can use for protein structure prediction. -- Deepan http://codeshepherd.com/ http://codeshepherd.blogspot.com/ http://sudoku-solver.net/ From lijo.skb at gmail.com Mon Dec 17 23:03:53 2007 From: lijo.skb at gmail.com (lijo skb) Date: Tue, 18 Dec 2007 09:33:53 +0530 Subject: [BiO BB] hi help me pls In-Reply-To: <47668897.5040308@gmail.com> References: <6dd7f9b90711192209x3a0291b6s75b326cad2345fdd@mail.gmail.com> <9c9e3ba10711200148m3d1b2368v2f698dcf45cb38e7@mail.gmail.com> <47668897.5040308@gmail.com> Message-ID: Hi Deepan, Is it possible to predict the stucture of a new sequence with gromacs? Lijo On Dec 17, 2007 8:02 PM, Dee?an Chakravarthy wrote: > jay ananth wrote: > > I need one help from u... > > > > search for best tools for the following : > > 1.Secondary Structure prediction in RNA > > 2.Protein Secondary Structure Prediction. > > 3.Prediction of disordered regions in proteins.. > > 4.Case Std on Structure-function relationships in proteins > > 5.Prediction of transmembrane regions in proteins > > 6.Characterization of antigenecity in polypeptides- epitope mapping > > > > > > > > > Are you looking for computational tools to do the above ? Can you be > more specific ? Autodock, Gromacs are some of the tools that you can > use for protein structure prediction. > > -- > Deepan > http://codeshepherd.com/ > http://codeshepherd.blogspot.com/ > http://sudoku-solver.net/ > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Lijo From marchywka at hotmail.com Tue Dec 18 18:37:15 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 18 Dec 2007 18:37:15 -0500 Subject: [BiO BB] hi help me pls In-Reply-To: References: <6dd7f9b90711192209x3a0291b6s75b326cad2345fdd@mail.gmail.com> <9c9e3ba10711200148m3d1b2368v2f698dcf45cb38e7@mail.gmail.com> <47668897.5040308@gmail.com> Message-ID: >>> 6.Characterization of antigenecity in polypeptides- epitope mapping This site is fairly new, not sure how it compares to anything, http://tools.immuneepitope.org/main/jsp/menu.jsp Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Tue, 18 Dec 2007 09:33:53 +0530 > From: lijo.skb at gmail.com > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] hi help me pls > > _________________________________________________________________ Don't get caught with egg on your face. Play Chicktionary! http://club.live.com/chicktionary.aspx?icid=chick_wlhmtextlink1_dec From skhadar at gmail.com Wed Dec 19 00:56:20 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 19 Dec 2007 12:26:20 +0630 Subject: [BiO BB] hi help me pls In-Reply-To: References: <6dd7f9b90711192209x3a0291b6s75b326cad2345fdd@mail.gmail.com> <9c9e3ba10711200148m3d1b2368v2f698dcf45cb38e7@mail.gmail.com> <47668897.5040308@gmail.com> Message-ID: Hi Deepan, Autodock and Gromacs are not for structure prediction. Autodock -> Docking Gromacs -> Molecular Dynamics For Secondory structure prediction - use PSIPRED, JPRED etc. For Teritiary structure prediction - Use either abinito base methods like Rosetta or Honology based methods like MODELLER. Lijo AutoDoc/Gromacs can do any strucure prediction. Use Rosetta for abinito structure prediction after the structure is obtained you may use Gromacs for simulation. Cheers, K Shameer NCBS-TIFR Banglaore On Dec 19, 2007 6:07 AM, Mike Marchywka wrote: > > >>> 6.Characterization of antigenecity in polypeptides- epitope mapping > > This site is fairly new, not sure how it compares to anything, > > http://tools.immuneepitope.org/main/jsp/menu.jsp > > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > marchywka at hotmail.com > Note: Hotmail is blocking my mom's entire > ISP claiming it is to reduce spam but probably > to force users to use hotmail. Please DON'T > assume I am ignoring you and try > me on marchywka at yahoo.com if no reply > here. Thanks. > > > Date: Tue, 18 Dec 2007 09:33:53 +0530 > > From: lijo.skb at gmail.com > > To: bio_bulletin_board at bioinformatics.org > > Subject: Re: [BiO BB] hi help me pls > > > > > _________________________________________________________________ > Don't get caught with egg on your face. Play Chicktionary! > http://club.live.com/chicktionary.aspx?icid=chick_wlhmtextlink1_dec > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- K Shameer ======================================== I am attending FOSS.in, Are you ? http://foss.in/2007/info/Home From franconi at inf.unibz.it Thu Dec 20 13:34:05 2007 From: franconi at inf.unibz.it (Enrico Franconi) Date: Thu, 20 Dec 2007 19:34:05 +0100 Subject: [BiO BB] European Master in Computational Logic - scholarships for non-European and European students Message-ID: *** EUROPEAN MASTERS PROGRAM IN COMPUTATIONAL LOGIC *** http://www.computational-logic.eu The Faculty of Computer Science at the Free University of Bozen- Bolzano (FUB), in Italy (at the heart of the Dolomites mountains in South-Tyrol), is offering the European Masters Program in Computational Logic as part of its Master of Science in Computer Science offer (Laurea Specialistica). The European Masters Program in Computational Logic is an international distributed Master of Science course, in cooperation with the computer science departments in the following universities: * Free University of Bozen-Bolzano, Italy * Technische Universitaet Dresden, Germany * Universidade Nova de Lisboa, Portugal * Technische Universitaet Wien, Austria * Universidad Politecnica de Madrid, Spain This program, completely in English, involves studying one year at the Free University of Bozen-Bolzano, and completing the second year with a stay in one of the partner universities. After this, the student will obtain, together with the European degree, two Master of Science degrees: the Laurea Specialistica degree from the Free University of Bozen-Bolzano, with legal value in Italy, and the respective Master of Science degree from the visited university, with legal value in its country. APPLICATION DEADLINES: - *** 10 FEBRUARY 2008* ** : first deadline for all European and non- European students, and final deadline for non-European students requesting an Erasmus Mundus scholarship (notification of acceptance: 10 March 2008) - 31 May 2008: deadline for all European and non-European students (notification of acceptance: 15 June 2008) - 24 August 2008: last deadline only for European students starting at the Free University of Bozen-Bolzano, Italy (notification of acceptance: 10 September 2008) SCHOLARSHIPS & MONEY SUPPORT: In 2008 the European Masters Program in Computational Logic will offer several new Erasmus Mundus scholarships for non-European citizens (in 2004, 2005, 2006, and 2007 more than 70 Erasmus Mundus scholarships were given). Each scholarship for each student amounts to 21,000 EUR per academic year; this includes 10 monthly grants of 1,600 EUR and a fixed amount of 5,000 EUR for fees, travel expenses, relocation costs, etc. The 10th of February 2008 is the final deadline for requesting an Erasmus Mundus scholarship for non-European students. European citizens can apply to scholarships which are granted purely on the basis of the yearly income of the applicant and of her/his parents or husband/wife. Scholarships may amount up to more than 6,000 EUR per academic year, including support on the accommodation and total reimbursement of the enrolment fees. These scholarships are also available to non-European citizens with residence in Italy. European students will also get a LLP Socrates Erasmus scholarship for the second year of study abroad, which is up to 250 EUR per month. NEW! Every year 10 students with European citizenship can visit Australia (Canberra, Sidney, Melbourne or Brisbane) up to 3 months to work on a research project, sponsored by the European Master. The study period in Australia is part of the study programme and it is fully recognised by the European Master's Program in Computational Logic. The guaranteed scholarship is of 3,100 EUR and it covers the travel and living expenses in Australia. The KRDB Research Centre offers the annual "IBM & KRDB" awards for the best thesis on a Computational Logic related topic, which is generously sponsored by the IBM Center for Advanced Studies; each winner will receive 500 EUR from IBM. In addition to that, the Italian site in Rome of the IBM Center for Advanced Studies supports scholarships of up to 2,400 EUR to work on a research project or on the thesis at their labs in Rome. Check the web page for detailed info on other available scholarships: http://www.computational-logic.eu THE STUDY PROGRAMME: The European Masters Program in Computational Logic is designed to meet the demands of industry and research in this rapidly growing area. Based on a solid foundation in mathematical logic, theoretical computer science, artificial intelligence and declarative programming students will acquire in-depth knowledge necessary to specify, implement and run complex systems as well as to prove properties of these systems. In particular, the focus of instruction will be in deduction systems, knowledge representation and reasoning, artificial intelligence, formal specification and verification, syntax directed semantics, logic and automata theory, logic and computability. This basic knowledge is then applied to areas like logic and natural language processing, logic and the semantic web, bioinformatics, information systems and database technology, software and hardware verification. Students will acquire practical experience and will become familiar in the use of tools within these applications. In addition, students will be prepared for a future PhD, they will come in contact with the international research community and will be integrated into ongoing research projects. They will develop competence in foreign languages and international relationships, thereby improving their social skills. Applicants should have a Bachelor degree (Laurea triennale) in Computer Science, Computer Engineering, or other relevant disciplines; special cases will be considered. The programme is part of the Master in Computer Science (Laurea Specialistica in Informatica) and it has various strengths that make it unique amongst Italian and European universities: * Curriculum taught entirely in English: The programme is open to the world and prepares the students to move on the international scene. * Possibility of a strongly research-oriented curriculum. * Possibility for project-based routes to obtain the degree and extensive lab facilities. * Other specialisations with streams in the hottest Computer Science areas, such as Web Technologies, Information and Knowledge Management, Databases and Software Engineering. * International student community. * Direct interaction with the local and international industry and research centres, with the possibility of practical and research internships that can lead to future employment. * Excellent scholarship opportunities and student accommodations. The European Masters Program in Computational Logic is sponsored scientifically by the European Network of Excellence on Computational Logic (CoLogNET), the European Association of Logic, Language and Information (FoLLI), the European Coordinating Committee for Artificial Intelligence (ECCAI), the Italian Association for Artificial Intelligence (AI*IA), the Italian Association for Informatics (AICA, member of the Council of European Professional Informatics Societies), the Italian Association for Logic and its Applications (AILA), and the Portuguese Association for Artificial Intelligence (APPIA). THE FREE UNIVERSITY OF BOZEN-BOLZANO: The Free University of Bozen-Bolzano, founded in 1997, boasts modern premises in the centre of Bozen-Bolzano. The environment is multilingual, South Tyrol being a region where three languages are spoken: German, Italian and Ladin. Studying in a multilingual area has shown that our students acquire the cutting edge needed in the international business world. Many of our teaching staff hails from abroad. Normal lectures are complemented with seminars, work placements and laboratory work, which give our students a vocational as well as theoretical training, preparing them for their subsequent professional careers. Studying at the Free University of Bozen-Bolzano means, first and foremost, being guided all the way through the student's educational career. Bozen-Bolzano, due to its enviable geographical position in the centre of the Dolomites, also offers our students a multitude of opportunities for spending their free-time. The city unites the traditional with the modern. Young people and fashionable shops throng the city centre where ancient mercantile buildings are an attractive backdrop to a city that is in continual growth. To the south there is the industrial and manufacturing area with prosperous small and medium-sized businesses active in every economic sector. Back in the 17th century Bozen-Bolzano was already a flourishing mercantile city that, thanks to its particular geographic position, functioned as a kind of bridge between northern and southern Europe. As a multilingual town and a cultural centre Bozen-Bolzano still has a lot to offer today. Its plethora of theatres, concerts with special programmes, cinemas and museums, combined with a series of trendy night spots that create local colour make Bozen-Bolzano a city that is beginning to cater for its increasingly demanding student population. And if you fancy a very special experience, go and visit the city's favourite and most famous resident - "Oetzi", the Ice Man of Similaun, housed in his very own refrigerated room in the recently opened archaeological museum. Bozen-Bolzano and its surroundings are an El Dorado for sports lovers: jogging on the grass alongside the River Talfer-Talvera, walks to Jenesien-S.Genesio and on the nearby Schlern-Sciliar plateau, excursions and mountain climbing in the Dolomites, swimming in the numerous nearby lakes and, last but not least, skiing and snowboarding in the surrounding ski areas. FURTHER INFORMATION: Prof. Enrico Franconi or Dr. Sergio Tessaris at info at fub.computational-logic.eu European Masters Program in Computational Logic Faculty of Computer Science Free University of Bozen-Bolzano Piazza Domenicani, 3 I-39100 Bozen-Bolzano BZ, Italy Phone: +39 0471 016 000 Fax: +39 0471 016 009 Email: info at fub.computational-logic.eu Web site: http://www.computational-logic.eu From jeff at bioinformatics.org Fri Dec 21 14:47:52 2007 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 21 Dec 2007 14:47:52 -0500 Subject: [BiO BB] List configuration Message-ID: <476C1868.8060101@bioinformatics.org> Greetings, FYI, the Mailman mailing list system that we use no longer accepts underscore characters in the mailing list name and was printing "bio_bulletin_board-bounces at bioinformatics.org" as "bio_bulletin-bounces at board" in outgoing messages. This was of course causing messages to be bounced back, leading to many subscribers being automatically unsubscribed. If you're a subscriber, you just received a message providing you with new subscription information. That message is legitimate. As mentioned in there, please note that you have a new password to modify your settings. And if you previously altered your settings to receive messages in digest mode or made any other alterations, they have been reset and will need to be changed again. We apologize for this inconvenience. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From idoerg at gmail.com Fri Dec 21 20:00:02 2007 From: idoerg at gmail.com (Iddo Friedberg) Date: Fri, 21 Dec 2007 17:00:02 -0800 Subject: [BiO BB] all vs. all COGs? Message-ID: Hi, Is there an all-vs-all comparison of COGs out there? I am basically looking for a distance mapping based on profile alignments between COG families. Has this been done? thanks, Iddo -- I. Friedberg "The only problem with troubleshooting is that sometimes trouble shoots back." From marty.gollery at gmail.com Mon Dec 24 16:34:27 2007 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 24 Dec 2007 13:34:27 -0800 Subject: [BiO BB] all vs. all COGs? In-Reply-To: References: Message-ID: I haven't seen anyone do this, Iddo, but I have an idea of how this could be done. I have the COGs built into HMMs, and you could use these together with an HMM-HMM comparison tool to get the distance mappings. Cheers, Marty On Dec 21, 2007 5:00 PM, Iddo Friedberg wrote: > Hi, > > Is there an all-vs-all comparison of COGs out there? I am basically looking > for a distance mapping based on profile alignments between COG families. Has > this been done? > > thanks, > > Iddo > > > > -- > > I. Friedberg > > "The only problem with troubleshooting is that > sometimes trouble shoots back." > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif 775-833-9113 880 Northwood Blvd. Suite 7 Incline Village, NV 89451 From marchywka at hotmail.com Mon Dec 24 12:22:51 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 24 Dec 2007 12:22:51 -0500 Subject: [BiO BB] all vs. all COGs? In-Reply-To: References: Message-ID: If you really get stuck you can check for algorithm ideas here: http://www.google.com/search?hl=en&q=biological+alignment+site%3Aciteseer.ist.psu.edu I'm in the process of writing my own alignment stuff based on exact string matches and just trying it out on some real test cases. If you can cite background on your particular objectives and any known tools and their limitations for your usage that may help many readers here. If you can identify something particularly relevant, contacting authors can be helpful. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Fri, 21 Dec 2007 17:00:02 -0800 > From: idoerg at gmail.com > To: BBB at bioinformatics.org > Subject: [BiO BB] all vs. all COGs? > > Hi, > > Is there an all-vs-all comparison of COGs out there? I am basically looking > for a distance mapping based on profile alignments between COG families. Has > this been done? > > thanks, > > Iddo > > > > -- > > I. Friedberg > > "The only problem with troubleshooting is that > sometimes trouble shoots back." > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Share life as it happens with the new Windows Live. http://www.windowslive.com/share.html?ocid=TXT_TAGHM_Wave2_sharelife_122007 From marchywka at hotmail.com Thu Dec 27 17:51:42 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 27 Dec 2007 17:51:42 -0500 Subject: [BiO BB] RNA 3D structure codes/ splicing prediction In-Reply-To: References: Message-ID: Hi, I was working on a framework for generalized splicing and editing analysis while I can across this paper, http://citeseer.ist.psu.edu/patterson02premrna.html Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction (2002) (Make Corrections) (3 citations) Donald J. Patterson, Ken Yasuhara, Walter L. Ruzzo Proceedings of the Pacific Symposium on Biocomputing which seemed intuitively appealing but I didn't immediately find a lot of more recent work. I guess I have three questions, 1) Is splicing still a bit of an open area or has it been "solved?" 2) Is anyone familiar with this or related work? 3) Any comments on code or papers for predicting RNA shape from sequence? The author of this paper conclude, "While specific structural signatures were not detected, general trends toward helix formation in the region of the splice site suggest the possibility of greater exploitation of structural cues by gene finding algorithms. Similar structural biases were observed at the donor splice site in the same data set, but not with sufficient strength that statistical significance could be ascribed to them. Future research is warranted toward the development of models that capture structural features at the donor splice site, as well as improving upon the acceptor site models we have presented and their biological interpretation." and I thought there may be some easy ways today( paper is from 2002) to explore this idea ( If I had a model for the cavity into which the RNA had to fit this may not be too difficult to figure out). Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka at yahoo.com if no reply here. Thanks. _________________________________________________________________ Share life as it happens with the new Windows Live. http://www.windowslive.com/share.html?ocid=TXT_TAGHM_Wave2_sharelife_122007 From DGURGUL at PARTNERS.ORG Fri Dec 28 08:22:20 2007 From: DGURGUL at PARTNERS.ORG (Gurgul, Dennis J.) Date: Fri, 28 Dec 2007 08:22:20 -0500 Subject: [BiO BB] anyone familiar with flybase or scaffolding nomenclature? In-Reply-To: References: <473091E0.8020400@bioinformatics.org> Message-ID: Received the attached from a friend who was involved in the development of flybase. Hope it helps. Dennis Dennis J. Gurgul Research Computing Partners Health Care 617.724.3169 http://www.partners.org/rescomputing >https://research.partners.org/wiki/index.php/HPC_Clusters -----Original Message----- From: bio_bulletin-bounces at board [mailto:bio_bulletin-bounces at board] On Behalf Of Mike Marchywka Sent: Thursday, November 08, 2007 8:19 AM To: bbb at bioinformatics.org Subject: [BiO BB] anyone familiar with flybase or scaffolding nomenclature? Hi, I read this http://www.nih.gov/news/pr/nov2007/nhgri-07.htm and thought it may be interesting to go get 12 assembled small genomes to search for various polymoprhisms and test some code. I downloaded the fasta files from flybase and hunted around their site for a while but I couldn't figure out what the scaffold names mean or if there is a set of assembled genomes somewhere. Anyone have a link to relevant tutorial info? For that matter, can anyone suggest another set of closely related organisms ( breeds within species or cultivars among plants, I'm quite open to ideas) with small genomes for testing? Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka at yahoo.com if no reply here. Thanks. _________________________________________________________________ You IM, we give. ?Make every IM count for the cause of your choice. Join Now.? http://im.live.com/messenger/im/home/?source=TAGHM The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. 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