From harry.mangalam at uci.edu Mon Sep 1 23:09:46 2008 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Mon, 1 Sep 2008 20:09:46 -0700 Subject: [BiO BB] Phylo PostDoc position at Brown Message-ID: <200809012009.46496.harry.mangalam@uci.edu> Posting for a friend. Please respond to Casey Dunn, address below. ================================================================== Phyloinformatics Postdoc Opportunity I am currently seeking a postdoctoral researcher interested in the conceptual and practical problems of analyzing phylogenetic data from whole genomes and ESTs. This work will build on a recently published animal phylogeny (http://dx.doi.org/10.1038/nature06614) that considered 150 genes from 77 broadly sampled taxa, including 29 animals for which we collected new EST data. The primary research focus will be on homology identification (based largely on graph- theory approaches to building clusters of similar genes from pairwise similarity data) and paralogy evaluation (through phylogenetic methods). The postdoc will explore various theoretical aspects of these and related problems, and take part in the authorship of open- source software tools that will facilitate large-scale phylogenomic projects in labs without the expertise to build these tools from scratch. It is hoped that the successful candidate will take the initiative to investigate and build tools for other new challenges that are arising with the the growing use of high-throughput sequencing for phylogenetic problems. The candidate would be encouraged to get involved on the field, organismal, and wet-lab aspects of the research program if they so desire. A thorough understanding of phylogenetic theory and experience in the phylogenetic analysis of molecular data are essential. Strong unix skills, proficiency with one or more computer languages, and familiarity with relational Phyloinformatics Postdoc Opportunity I am currently seeking a postdoctoral researcher interested in the conceptual and practical problems of analyzing phylogenetic data from whole genomes and ESTs. This work will build on a recently published animal phylogeny (http://dx.doi.org/10.1038/nature06614) that considered 150 genes from 77 broadly sampled taxa, including 29 animals for which we collected new EST data. The primary research focus will be on homology identification (based largely on graph- theory approaches to building clusters of similar genes from pairwise similarity data) and paralogy evaluation (through phylogenetic methods). The postdoc will explore various theoretical aspects of these and related problems, and take part in the authorship of open- source software tools that will facilitate large-scale phylogenomic projects in labs without the expertise to build these tools from scratch. It is hoped that the successful candidate will take the initiative to investigate and build tools for other new challenges that are arising with the the growing use of high-throughput sequencing for phylogenetic problems. The candidate would be encouraged to get involved on the field, organismal, and wet-lab aspects of the research program if they so desire. A thorough understanding of phylogenetic theory and experience in the phylogenetic analysis of molecular data are essential. Strong unix skills, proficiency with one or more computer languages, and familiarity with relational databases are also required. The position will remain open until filled, with the successful candidate starting as soon as is possible for them. Please send a cover letter the reasoning for your interest in the project, a current c.v., and contact information for 3 professional references to casey_dunn at brown.edu . More information on my lab can be found at:http://www.brown.edu/Faculty/Dunn_Lab/index.php . ------------------------------------------------------------------------------- Dr. Casey Dunn http://www.brown.edu/Faculty/Dunn_Lab/index.php casey_dunn at brown.edu 80 Waterman Street office 401.863.9806 Box G-W lab 401.863.2242 Brown University siphonophores.org Providence, RI 02912 USA databases are also required. The position will remain open until filled, with the successful candidate starting as soon as is possible for them. Please send a cover letter the reasoning for your interest in the project, a current c.v., and contact information for 3 professional references to casey_dunn at brown.edu . More information on my lab can be found at:http://www.brown.edu/Faculty/Dunn_Lab/index.php . ------------------------------------------------------------------------------- Dr. Casey Dunn http://www.brown.edu/Faculty/Dunn_Lab/index.php casey_dunn at brown.edu 80 Waterman Street office 401.863.9806 Box G-W lab 401.863.2242 Brown University siphonophores.org Providence, RI 02912 USA --- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824-0084(o), 949 285-4487(c) -- "I destroy my enemies when I make them my friends" - Abraham Lincoln From dan.bolser at gmail.com Thu Sep 4 10:29:20 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 4 Sep 2008 15:29:20 +0100 Subject: [BiO BB] Parsing GenBank XML? Message-ID: <2c8757af0809040729s32d7f36fw56662014e723c14a@mail.gmail.com> Hi, Dumb / noob question I am sure but... I am parsing the results of a GenBank query obtained using esearch / efetch: http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html The XML looks like this... http://pastebin.com/f3ef02d85 the only difference being that the real document has (possibly) millions of 's. I decided to try to use XSLT to turn the XML into tabular output. This is working fine on a sample of the data. I get one row of data per Seq-entry, which is exactly what I want. For reference, my XSLT style sheet is here: http://pastebin.com/f3a512411 I am not sure how efficient that XSLT is (I never used XSLT before), however, that isn't the real problem. The real problem is that the XSLT parsers that I have tried (xsltproc and XML::XSLT) both need to slurp up the whole XML document before they output any rows of text. This is way too memory intensive, especially as the data my well grow. I figure that I can't be the first person to parse GenBank, so I was wondering what is 'out there' in terms of community consensus on how to do it... I had a quick go with XML::Simple, but I rapidly get lost in the resulting data structure, which I find leads to very messy (hard to read / write) and generally unmaintainable code. Are the various 'BioX' modules any good? i.e. do they simplify the resulting data to make it easy to get tab delimited dumps of the data? Cheers, Dan. -- http://network.nature.com/profile/dan From marchywka at hotmail.com Thu Sep 4 11:18:18 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 4 Sep 2008 11:18:18 -0400 Subject: [BiO BB] Parsing GenBank XML? In-Reply-To: <2c8757af0809040729s32d7f36fw56662014e723c14a@mail.gmail.com> References: <2c8757af0809040729s32d7f36fw56662014e723c14a@mail.gmail.com> Message-ID: You are probably looking for a SAX parser, http://en.wikipedia.org/wiki/Simple_API_for_XML I've got my own hard coded c++ that I use for my string processing rules source code, FDA AERA SGML parsing, SOAP utilities, etc, that will output all the fields in a simple format of "label value" per line, but there are SAX libraries in just about every language. Personally I finally gave up on PERL as speed, at least under cygwin, was unpredictable and degraded quickly when you ran out of physical memory. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: hotmail is getting cumbersom, try also marchywka at yahoo.com > Date: Thu, 4 Sep 2008 15:29:20 +0100 > From: dan.bolser at gmail.com > To: BBB at bioinformatics.org > Subject: [BiO BB] Parsing GenBank XML? > > Hi, > > Dumb / noob question I am sure but... I am parsing the results of a > GenBank query obtained using esearch / efetch: > > http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html > > > The XML looks like this... > > http://pastebin.com/f3ef02d85 > > the only difference being that the real document has (possibly) > millions of 's. > > I decided to try to use XSLT to turn the XML into tabular output. This > is working fine on a sample of the data. I get one row of data per > Seq-entry, which is exactly what I want. For reference, my XSLT style > sheet is here: > > http://pastebin.com/f3a512411 > > > I am not sure how efficient that XSLT is (I never used XSLT before), > however, that isn't the real problem. The real problem is that the > XSLT parsers that I have tried (xsltproc and XML::XSLT) both need to > slurp up the whole XML document before they output any rows of text. > This is way too memory intensive, especially as the data my well grow. > > I figure that I can't be the first person to parse GenBank, so I was > wondering what is 'out there' in terms of community consensus on how > to do it... > > I had a quick go with XML::Simple, but I rapidly get lost in the > resulting data structure, which I find leads to very messy (hard to > read / write) and generally unmaintainable code. > > Are the various 'BioX' modules any good? i.e. do they simplify the > resulting data to make it easy to get tab delimited dumps of the data? > > > Cheers, > > Dan. > > > -- > http://network.nature.com/profile/dan > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Stay up to date on your PC, the Web, and your mobile phone with Windows Live. http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/ From dan.bolser at gmail.com Fri Sep 5 06:24:55 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 5 Sep 2008 11:24:55 +0100 Subject: [BiO BB] Parsing GenBank XML? In-Reply-To: References: <2c8757af0809040729s32d7f36fw56662014e723c14a@mail.gmail.com> Message-ID: <2c8757af0809050324h7817d0b4tf75f8d790681bbf4@mail.gmail.com> 2008/9/4 Mike Marchywka > > > You are probably looking for a SAX parser, > > http://en.wikipedia.org/wiki/Simple_API_for_XML Hi Mike, Thanks for the link. The relevant lines seems to be: "Additionally, some kinds of XML processing simply require having access to the entire document. XSLT and XPath, for example, need to be able to access any node at any time in the parsed XML tree. While a SAX parser could be used to construct such a tree, the DOM already does so by design." So it looks like I can't combine SAX with XSLT unless I somehow trigger an XSLT parse of one 'chunk' of XML per SAX 'new-record' event... I'll try! > I've got my own hard coded c++ that I use for my string processing rules source > code, FDA AERA SGML parsing, SOAP utilities, etc, that will output all the fields > in a simple format of "label value" per line, but there are SAX libraries in just about > every language. Personally I finally gave up on PERL as speed, at least under cygwin, > was unpredictable and degraded quickly when you ran out of physical memory. > > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 415-264-8477 (w)<- use this > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > marchywka at hotmail.com > Note: If I am asking for free stuff, I normally use for hobby/non-profit > information but may use in investment forums, public and private. > Please indicate any concerns if applicable. > Note: hotmail is getting cumbersom, try also marchywka at yahoo.com > > > > > Date: Thu, 4 Sep 2008 15:29:20 +0100 > > From: dan.bolser at gmail.com > > To: BBB at bioinformatics.org > > Subject: [BiO BB] Parsing GenBank XML? > > > > Hi, > > > > Dumb / noob question I am sure but... I am parsing the results of a > > GenBank query obtained using esearch / efetch: > > > > http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html > > > > > > The XML looks like this... > > > > http://pastebin.com/f3ef02d85 > > > > the only difference being that the real document has (possibly) > > millions of 's. > > > > I decided to try to use XSLT to turn the XML into tabular output. This > > is working fine on a sample of the data. I get one row of data per > > Seq-entry, which is exactly what I want. For reference, my XSLT style > > sheet is here: > > > > http://pastebin.com/f3a512411 > > > > > > I am not sure how efficient that XSLT is (I never used XSLT before), > > however, that isn't the real problem. The real problem is that the > > XSLT parsers that I have tried (xsltproc and XML::XSLT) both need to > > slurp up the whole XML document before they output any rows of text. > > This is way too memory intensive, especially as the data my well grow. > > > > I figure that I can't be the first person to parse GenBank, so I was > > wondering what is 'out there' in terms of community consensus on how > > to do it... > > > > I had a quick go with XML::Simple, but I rapidly get lost in the > > resulting data structure, which I find leads to very messy (hard to > > read / write) and generally unmaintainable code. > > > > Are the various 'BioX' modules any good? i.e. do they simplify the > > resulting data to make it easy to get tab delimited dumps of the data? > > > > > > Cheers, > > > > Dan. > > > > > > -- > > http://network.nature.com/profile/dan > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > _________________________________________________________________ > Stay up to date on your PC, the Web, and your mobile phone with Windows Live. > http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/ > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- http://network.nature.com/profile/dan From marchywka at hotmail.com Fri Sep 5 07:28:57 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 5 Sep 2008 07:28:57 -0400 Subject: [BiO BB] Parsing GenBank XML? In-Reply-To: <2c8757af0809050324h7817d0b4tf75f8d790681bbf4@mail.gmail.com> References: <2c8757af0809040729s32d7f36fw56662014e723c14a@mail.gmail.com> <2c8757af0809050324h7817d0b4tf75f8d790681bbf4@mail.gmail.com> Message-ID: > So it looks like I can't combine SAX with XSLT unless I somehow > trigger an XSLT parse of one 'chunk' of XML per SAX 'new-record' > event... > > I'll try! > All of my eutils scripts pretty much use the text format where it is not ambiguous. If you need XML or SOAP fine but normally it doesn't add much and it can be slow to format and unformat stuff. For most situations, reasonably formatted text is just fine. > >> I've got my own hard coded c++ that I use for my string processing rules source >> code, FDA AERA SGML parsing, SOAP utilities, etc, that will output all the fields >> in a simple format of "label value" per line, but there are SAX libraries in just about >> every language. Personally I finally gave up on PERL as speed, at least under cygwin, >> was unpredictable and degraded quickly when you ran out of physical memory. >> >> >> >> Mike Marchywka >> 586 Saint James Walk >> Marietta GA 30067-7165 >> 415-264-8477 (w)<- use this >> 404-788-1216 (C)<- leave message >> 989-348-4796 (P)<- emergency only >> marchywka at hotmail.com >> Note: If I am asking for free stuff, I normally use for hobby/non-profit >> information but may use in investment forums, public and private. >> Please indicate any concerns if applicable. >> Note: hotmail is getting cumbersom, try also marchywka at yahoo.com >> >> >> >>> Date: Thu, 4 Sep 2008 15:29:20 +0100 >>> From: dan.bolser at gmail.com >>> To: BBB at bioinformatics.org >>> Subject: [BiO BB] Parsing GenBank XML? >>> >>> Hi, >>> >>> Dumb / noob question I am sure but... I am parsing the results of a >>> GenBank query obtained using esearch / efetch: >>> >>> http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html >>> >>> >>> The XML looks like this... >>> >>> http://pastebin.com/f3ef02d85 >>> >>> the only difference being that the real document has (possibly) >>> millions of 's. _________________________________________________________________ Want to do more with Windows Live? Learn ?10 hidden secrets? from Jamie. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008 From pac at lifeformulae.com Wed Sep 3 17:04:24 2008 From: pac at lifeformulae.com (Pam Culpepper) Date: Wed, 03 Sep 2008 16:04:24 -0500 Subject: [BiO BB] NCBI blastall Modifications Message-ID: <1220475864.3232.24.camel@localhost.localdomain> A. Our website -- http://www.lifeformulae.com, has been updated with the files required to modify the ncbi_c--Mar_17 version of the NCBI Toolbox blastall application to support the local BLAST alignment graphical view and extended options that include output of the BlastOutput ASN.1 data structure in binary or text. The blastall_diff.txt file is the patch file that contains the modifications to the Toolbox code. The HOW_TO.txt file provides instructions on how to apply the patch and compile the Toolbox. blastall will produce the graphical view with either the old or the new BLAST engine. You must use the blastall "-T T" (HTML option) to activate the graphical overview. For the BlastOutput format option, "-m 12" will create an ASN.1 text file, while "-m 13" will create an ASN.1 binary file. This software is provided freely to all BBB users at http://www.lifeformulae.com/pages/products_blast_fix.aspx. Thanks, Pam Culpepper From libra_tarun895 at yahoo.com Mon Sep 8 02:49:36 2008 From: libra_tarun895 at yahoo.com (Tarun Bansal) Date: Sun, 7 Sep 2008 23:49:36 -0700 (PDT) Subject: [BiO BB] Bioinformatics and Intellectual Property Rights Message-ID: <378876.97927.qm@web32908.mail.mud.yahoo.com> Hi Everyone, I was just wondering if Bioinformatics professionals really care about securing the IP rights for their inventions? With this assumptions in mind, my company 'Sagacious Research' was planning to develop certain modules on importance of IPR (specially patents) for Bioinfo professional (highlighting exceptions). Please feel free to contribute any information to the modules and indicate what would you like to see in these modules.Also, if you are already aware of certain similar modules do let me know. Further, in case you want any economical patent research done (including patent preparation, searching, etc), you can feel free to contact me at this email ID. I have an extensive experience of patent research in Bioinformatics domain and have helped many bioinfo professionals in realizing the true potential of their research. Best regards, Tarun Director, Product Development Sagacious Research From srikrishnamohan at gmail.com Wed Sep 10 04:22:01 2008 From: srikrishnamohan at gmail.com (km) Date: Wed, 10 Sep 2008 13:52:01 +0530 Subject: [BiO BB] Bioinformatics and Intellectual Property Rights In-Reply-To: <378876.97927.qm@web32908.mail.mud.yahoo.com> References: <378876.97927.qm@web32908.mail.mud.yahoo.com> Message-ID: Hi, I have some comments in general. True potential of research does not mean one has a bunch of patents (restrictive) to push others to stone age. Patent system is actually a big stumble to discovery. It is a relic/fossil of human greed and opportunism - a state where rich become even rich and poor become even poor. It is created to make products(drugs etc...) of inventions inaccessible to the poor. Moreover IPR is archaic and has not evolved. I would also like u to note that most software developed in bioinformatics is in opensource domain with a "no-no" to software patents. Please follow the link for this useless patent regime. http://www.physorg.com/news140178906.html HTH KM On Mon, Sep 8, 2008 at 12:19 PM, Tarun Bansal wrote: > Hi Everyone, > > > I was just wondering if Bioinformatics professionals really care about > securing the IP rights for their inventions? > > With this assumptions in mind, my company 'Sagacious Research' was planning > to develop certain modules on importance of IPR (specially patents) for > Bioinfo professional (highlighting exceptions). > > Please feel free to contribute any information to the modules and indicate > what would you like to see in these modules.Also, if you are already aware > of certain similar modules do let me know. > > Further, in case you want any economical patent research done (including > patent preparation, searching, etc), you can feel free to contact me at this > email ID. I have an extensive experience of patent research in > Bioinformatics domain and have helped many bioinfo professionals in > realizing the true potential of their research. > > Best regards, > Tarun > Director, Product Development > Sagacious Research > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From Robert.Austin at fiz-k.com Wed Sep 10 13:49:30 2008 From: Robert.Austin at fiz-k.com (Austin, Robert) Date: Wed, 10 Sep 2008 19:49:30 +0200 Subject: [BiO BB] Bioinformatics and Intellectual Property Rights References: <378876.97927.qm@web32908.mail.mud.yahoo.com> Message-ID: <561B608813F3E7448D792A51EF2AB03E0645BADB@EXCLUSTER.fiz-karlsruhe.de> Anyone interested in an independent in-depth academic study on this topic should study the "PATGEN Final Report" given here: http://www.sussex.ac.uk/spru/1-4-3-1-2.html Regards Rob Robert Austin FIZ Karlsruhe Inc Tel: 609 333 1466 www.stn-international.com -----Original Message----- From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] On Behalf Of km Sent: Wednesday, September 10, 2008 4:22 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Bioinformatics and Intellectual Property Rights Hi, I have some comments in general. True potential of research does not mean one has a bunch of patents (restrictive) to push others to stone age. Patent system is actually a big stumble to discovery. It is a relic/fossil of human greed and opportunism - a state where rich become even rich and poor become even poor. It is created to make products(drugs etc...) of inventions inaccessible to the poor. Moreover IPR is archaic and has not evolved. I would also like u to note that most software developed in bioinformatics is in opensource domain with a "no-no" to software patents. Please follow the link for this useless patent regime. http://www.physorg.com/news140178906.html HTH KM On Mon, Sep 8, 2008 at 12:19 PM, Tarun Bansal wrote: > Hi Everyone, > > > I was just wondering if Bioinformatics professionals really care about > securing the IP rights for their inventions? > > With this assumptions in mind, my company 'Sagacious Research' was planning > to develop certain modules on importance of IPR (specially patents) for > Bioinfo professional (highlighting exceptions). > > Please feel free to contribute any information to the modules and indicate > what would you like to see in these modules.Also, if you are already aware > of certain similar modules do let me know. > > Further, in case you want any economical patent research done (including > patent preparation, searching, etc), you can feel free to contact me at this > email ID. I have an extensive experience of patent research in > Bioinformatics domain and have helped many bioinfo professionals in > realizing the true potential of their research. > > Best regards, > Tarun > Director, Product Development > Sagacious Research > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From drjohn08318 at yahoo.com Wed Sep 10 23:09:25 2008 From: drjohn08318 at yahoo.com (drjohn08318 at yahoo.com) Date: Thu, 11 Sep 2008 03:09:25 +0000 Subject: [BiO BB] Bioinformatics and Intellectual Property Rights In-Reply-To: References: <378876.97927.qm@web32908.mail.mud.yahoo.com> Message-ID: <1613308815-1221102635-cardhu_decombobulator_blackberry.rim.net-357729603-@bxe244.bisx.prod.on.blackberry> Without knowing who you are, I can say with confidence that you have zero patents, and have never worked in industry. You are extremely naive---IP and patents fuel innovation. Only those with no creativity berate patents. JGH Sent via BlackBerry by AT&T -----Original Message----- From: km Date: Wed, 10 Sep 2008 13:52:01 To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Bioinformatics and Intellectual Property Rights Hi, I have some comments in general. True potential of research does not mean one has a bunch of patents (restrictive) to push others to stone age. Patent system is actually a big stumble to discovery. It is a relic/fossil of human greed and opportunism - a state where rich become even rich and poor become even poor. It is created to make products(drugs etc...) of inventions inaccessible to the poor. Moreover IPR is archaic and has not evolved. I would also like u to note that most software developed in bioinformatics is in opensource domain with a "no-no" to software patents. Please follow the link for this useless patent regime. http://www.physorg.com/news140178906.html HTH KM On Mon, Sep 8, 2008 at 12:19 PM, Tarun Bansal wrote: > Hi Everyone, > > > I was just wondering if Bioinformatics professionals really care about > securing the IP rights for their inventions? > > With this assumptions in mind, my company 'Sagacious Research' was planning > to develop certain modules on importance of IPR (specially patents) for > Bioinfo professional (highlighting exceptions). > > Please feel free to contribute any information to the modules and indicate > what would you like to see in these modules.Also, if you are already aware > of certain similar modules do let me know. > > Further, in case you want any economical patent research done (including > patent preparation, searching, etc), you can feel free to contact me at this > email ID. I have an extensive experience of patent research in > Bioinformatics domain and have helped many bioinfo professionals in > realizing the true potential of their research. > > Best regards, > Tarun > Director, Product Development > Sagacious Research > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From isbra-l at engr.uconn.edu Thu Sep 11 12:28:16 2008 From: isbra-l at engr.uconn.edu (ISBRA Symposium Announcements) Date: Thu, 11 Sep 2008 12:28:16 -0400 (EDT) Subject: [BiO BB] [ISBRA-L] Sumit Announcement: An Invitation to Participate In-Reply-To: References: Message-ID: Dear Colleagues and Friends: The American Medical Informatics Association (AMIA) in Partnership with The International Society for Computational Biology (ISCB) and the statistical genetics community are pleased to invite the submission of papers, abstracts, panels, and posters for the 2009 AMIA Summit on Translational Bioinformatics. The Summit will be held March 15-17, 2009, in San Francisco, California, at the Grand Hyatt San Francisco. The web page for the meeting: http://www.amia.org/meetings/stb09/ Call for Papers: Sep 01, 2008 - Sep 24, 2008 Call for Posters: Sep 01, 2008 - Sep 24, 2008 This Summit highlights the multidisciplinary nature of this research field and provides a unique opportunity to bring together the finest minds in translational bioinformatics and genetics from the academia, industry, government and non-profit sectors. It aims to forge new trans-disciplinary collaborations and identify potential avenues of research and development across all computational areas of human diseases and patient care related to genetic discoveries. We are certain that you will enjoy this occasion and be inspired. The past success of biomedical informatics in transforming clinical research and patient care is merely a glimpse to the remarkable promises it holds as genetic discoveries and bioinformatics enrich one another. I hope to see you in San Francisco in March of 2009! Dan Nicolae Track Chair, "Informatics Methods In Genetics Discoveries" Nancy Cox Senior Advisor to the Scientific Program Yves A. Lussier Scientific Program Committee Chairman Featured Sessions Featured Speaker: Review of the Year: Russ Altman Featured Tutorials: Introduction to Translational Bioinformatics: Atul Butte Applied Bioinformatics Tools: Andrea Califano and Aris Floratos Additional Tutorials to be announced Track Information - For detailed information and track descriptions go to: http://www.amia.org/meetings/stb09/Summit-CallForParticipation_Final.pdf Track Descriptions: Track 1: Informatics Methods for the Analysis of Molecular and Clinical Measurements Track Chairs: Marco Ramoni and Eitan Rubin Track 2: Computational Approaches to Finding Molecular Mechanisms and Therapies for Disease. Track Chairs: Olga Troyanskaya and Andrey Rzhetsky Track 3: Relating and Representing Phenotypes and Disease Track Chairs: Olivier Bodenreider and Maricel G. Kann Track 4: Dissecting Disease Through the Study of Organisms, Evolution, and Taxonomy Track Chair: Indra Neil Sarkar Track 5: Informatics Concepts, Tools and Techniques to Enable Integrative Translational Research Track Chair: Joel Saltz Track 6: Informatics Methods In Genetics Discoveries and Clinical Practice Track Chairs: Dan L. Nicolae and Mark Hoffman Track 7: ISCB Track Details to be announced. Scientific Program Committee - for a detailed list go to: http://www.amia.org/meetings/stb09/Summit-CallForParticipation_Final.pdf Categories of Submission: Download a copy and for format requirements at: http://www.amia.org/meetings/stb09/Summit-CallForParticipation_Final.pdf Paper Presentation: The SPC solicits papers on the latest progress on using informatics approaches to improve translational biomedical research. Abstract Presentation: NEW FOR 2009! This classical venue for clinical and biological conferences has been provided in order to allow presentation of results otherwise destined for journal publications. Posters: Poster sessions are a component of the summit designed to offer direct access to the authors in a way not possible through podium presentations. Posters are the preferred format for presenting preliminary research results or results of small scale studies. Panels: Panel topics may be on a specific aspect of theory, application, or experience pertaining to any aspect of biomedical or health informatics, or may provide interdisciplinary viewpoints that cut across traditional themes. _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From crishnakh at gmail.com Thu Sep 11 16:54:32 2008 From: crishnakh at gmail.com (BioScripts S.L.) Date: Thu, 11 Sep 2008 22:54:32 +0200 Subject: [BiO BB] BioScripts In-Reply-To: <1613308815-1221102635-cardhu_decombobulator_blackberry.rim.net-357729603-@bxe244.bisx.prod.on.blackberry> References: <378876.97927.qm@web32908.mail.mud.yahoo.com> <1613308815-1221102635-cardhu_decombobulator_blackberry.rim.net-357729603-@bxe244.bisx.prod.on.blackberry> Message-ID: <9F1F7E30-0947-4B36-9081-716AACEE343F@gmail.com> I would like to anounce http://www.bioscripts.net, principal page in some languages, please if you are interested on create new biologic o bioinformatic project related to data information, please contact me bioscripts at gmail.com or francisco at bioscripts.net THANKS! --------------------------------------- BioScripts S.L. - http://www.bioscripts.net (francisco at bioscripts.net) http://www.jobgraphy.com/buscar/es/crishnakh.html From libra_tarun895 at yahoo.com Fri Sep 12 04:17:29 2008 From: libra_tarun895 at yahoo.com (Tarun Bansal) Date: Fri, 12 Sep 2008 01:17:29 -0700 (PDT) Subject: [BiO BB] Bioinformatics and Intellectual Property Rights Message-ID: <332983.38659.qm@web32906.mail.mud.yahoo.com> Dear Krishna Mohan, I would like to advise you to please do an in-depth research before basing your opinion on just one or two articles. To let you know the concept behind patent system, it is actually designed to foster innovation rather than suppressing it. Think from a business (or rather just human) perspective that why a pharma/ bio company (or any investor) will invest millions and billions in research to design a drug for a disease, if they know that they are going to loose it to the competition in the end. You might be right in saying that its makes drugs expensive, but have you ever thought that without the patent protection system in place, these drugs would not have been discovered at the first place. Please note that no one here including Bio/pharma companies are there to do any social service. Further, if there was no patent system, most of the technological advancements would never have been published and came to public domain for further research, as greedy and opportunistic human minds would then have just kept them as a trade secret rendering future research and development impossible. This can further be visualized based on the fact that 80% of the total technical data is never published anywhere else but in patents. When you say rich becomes richer and poor becomes poorer, it clearly reflects your lack of knowledge of the patent system. The patent system is not for any special economic class but is for creative and innovative people. Rather patent system helps poor but creative and innovative people becoming rich if they are aware and proactive in protecting their innovations. Until you secure patent rights on your invention, it becomes inpossible to find a funding partner leading to tragic end of the research. However, I do agree that patent system has not evolved the way it should have been and there are many changes necessary to make it truly innovation friendly. There are still possibilities of misuing the system and authorities should work towards plugging these loop holes. This has now turned in to a nice discussion, and I would like to invite others to contribute their thoughts on this matter. Best regards, Tarun ----- Original Message ---- From: km To: General Forum at Bioinformatics.Org Sent: Wednesday, September 10, 2008 1:52:01 PM Subject: Re: [BiO BB] Bioinformatics and Intellectual Property Rights Hi, I have some comments in general. True potential of research does not mean one has a bunch of patents (restrictive) to push others to stone age. Patent system is actually a big stumble to discovery. It is a relic/fossil of human greed and opportunism - a state where rich become even rich and poor become even poor. It is created to make products(drugs etc...) of inventions inaccessible to the poor. Moreover IPR is archaic and has not evolved. I would also like u to note that most software developed in bioinformatics is in opensource domain with a "no-no" to software patents. Please follow the link for this useless patent regime. http://www.physorg.com/news140178906.html HTH KM On Mon, Sep 8, 2008 at 12:19 PM, Tarun Bansal wrote: > Hi Everyone, > > > I was just wondering if Bioinformatics professionals really care about > securing the IP rights for their inventions? > > With this assumptions in mind, my company 'Sagacious Research' was planning > to develop certain modules on importance of IPR (specially patents) for > Bioinfo professional (highlighting exceptions). > > Please feel free to contribute any information to the modules and indicate > what would you like to see in these modules.Also, if you are already aware > of certain similar modules do let me know. > > Further, in case you want any economical patent research done (including > patent preparation, searching, etc), you can feel free to contact me at this > email ID. I have an extensive experience of patent research in > Bioinformatics domain and have helped many bioinfo professionals in > realizing the true potential of their research. > > Best regards, > Tarun > Director, Product Development > Sagacious Research > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From isbra-l at engr.uconn.edu Fri Sep 12 16:14:03 2008 From: isbra-l at engr.uconn.edu (ISBRA Symposium Announcements) Date: Fri, 12 Sep 2008 16:14:03 -0400 (EDT) Subject: [BiO BB] [ISBRA-L] BICoB Call For Papers In-Reply-To: References: Message-ID: CALL FOR PAPERS 1st International Conference on Bioinformatics and Computational Biology April 8-10, 2009, New Orleans, Louisiana USA Sponsored by the International Society for Computers and Their Applications (ISCA) Computational techniques have already enabled unprecedented advances in modern biology and medicine. This continues to be a vibrant research area with broadening of computational techniques and new emerging challenges. The Bioinformatics and Computational Biology (BICoB) conference is thus established by the ISCA to promote the advancement of computing techniques and their application to life sciences. The inaugural BICoB conference will feature original unpublished research in all areas of bio-informatics and computational biology, and covering the entire spectrum of underlying computational techniques/models/paradigms. The topics of interest include (and are not limited to): o Genome analysis: Genome assembly, genome and chromosome annotation, gene finding, alternative splicing, EST analysis and comparative genomics. o Sequence analysis: Multiple sequence alignment, sequence search and clustering, function prediction, motif discovery, functional site recognition in protein, RNA and DNA sequences. o Phylogenetics: Phylogeny estimation, models of evolution, comparative biological methods, population genetics. o Structural Bioinformatics: Structure matching, prediction, analysis and comparison; methods and tools for docking; protein design o Analysis of high-throughput biological data: Microarrays (nucleic acid, protein, array CGH, genome tiling, and other arrays), EST, SAGE, MPSS, proteomics, mass spectrometry. o Genetics and population analysis: Linkage analysis, association analysis, population simulation, haplotyping, marker discovery, genotype calling. o Systems biology: Systems approaches to molecular biology, multiscale modeling, pathways,gene networks. BICoB welcomes submissions in all areas of computing with impact on life sciences including (but not limited to) algorithms, databases, languages, systems, and high performance computing. For example: o Parallel and high-performance techniques o Unifying computational techniques o Data and image mining techniques o Approximation and randomized algorithms and systems o Computational biology on emerging architectures and hardware accelerators SUBMISSION PROCEDURES: Papers will be accepted only by electronic submission (PDF only). A full paper, including title, author's name(s) and affiliation, mailing address, telephone, fax and email of the principal author, should be submitted before November 1, 2008 at the following web site: https://secure.myhostadvantage.com/V0015065FC/con-reg/default.asp?ConID=85 The submitted manuscript should closely reflect the final paper as it will appear in the Proceedings. Proceedings will be published by Springer-Verlag in its LNBI series. Papers should be formatted using Springer-Verlag format templates (http://www.springer.com/lncs). Maximum paper length for the proceedings is 12 pages. IMPORTANT DATES Full paper Submission Deadline: November 1, 2008 Notification of Acceptance: December 15, 2008 Pre-registration and Camera-ready paper due: January 10, 2009 ORGANIZERS General Chair: Sanguthevar Rajasekaran, Univ. of Connecticut Program Co-Chairs: Srinivas Aluru, Iowa State University Limsoon Wang, National University of Singapore Steering Committee: Tao Jiang, Univ. of California, Riverside Vipin Kumar, Univ. of Minnesota Ming Li, Univ. of Waterloo John Reif, Duke University Sartaj Sahni, Univ. of Florida Publicity Co-Chairs: Reda A. Ammar, Univ. of Connecticut Ian Greenshields, Univ. of Connecticut Chun-Hsi Huang, Univ. of Connecticut Program Committee: Richa Agarwala, National Institutes of Health Yutaka Akiyama, Tokyo Institute of Technology Ziv Bar-Joseph, Carnegie Mellon University Chiranjib Bhattacharyya, Indian Institute of Science Kun-Mao Chao, National Taiwan Univ. Jake Chen, Indiana Univ. Francis Y.L. Chin, Hong Kong Univ. Bhaskar Dasgupta, Univ. of Illinois, Chicago Scott J. Emrich, University of Notre Dame Oliver Eulenstein, Iowa State University Germany V. Filkov, University of California Davis Dmitrij Frishman, Technical Univ. of Munich Terry Gaasterland, UCSD Gaston Gonnet, ETH Zurich Osamu Gotoh, Kyoto University Wen-Lian Hsu, Academia Sinica Ming-Yang Kao, Northwestern University Marek Karpinski, University of Bonn George Karypis, Univ. of Minnesota Danny Krizanc, Wesleyan University Bin Ma, Univ. of Waterloo Ion Mandoiu, Univ. of Connecticut Shinichi Morishita, Univ. of Tokyo Giri Narasimhan, Florida International University Japan E. Ohlebusch, University of Ulm Yi Pan, Georgia State University Srinivasan Parthasarathy, Ohio State University Prabakaran Ponraj, Duke University Mihai Pop, University of Maryland David Posada, Campus Universitario, Vigo, Spain Ben Raphael, Brown University Knut Reinert, Freie Universitt Berlin Marie-France Sagot, INRIA Rhne-Alpes David Sankoff, Univ. of Ottawa Mona Singh, Princeton Univ. Wing-Kin Sung, National Univ. of Singapore Sing-Hoi Sze, Texas A&M University Jerzy Tiuryn, Warsaw University Ugo Vaccaro, Universit di Salerno Li-San Wang, Univ. of Pennsylvania Yufeng Wu, Univ. of Connecticut Dong Xu, Univ. of Missouri, Columbia Mohamed Zaki, RPI Alex Zelikovsky, Georgia State University _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From mahef at hotmail.com Sun Sep 14 18:58:28 2008 From: mahef at hotmail.com (Mahmoud Elhefnawi) Date: Sun, 14 Sep 2008 22:58:28 -0000 Subject: [BiO BB] BLOCKS motifs and protein protein interactions Message-ID: Dear all, I was wandering if BLOCKS database homology hits with significant e values habe been correlated before to infer protein protein interactions? i.e" if protein A interacts with protein B, and protein C has a significant match with protein B, then protein C also interacts with protein A??? Best, Mahmoud From boris.steipe at utoronto.ca Wed Sep 17 10:55:27 2008 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed, 17 Sep 2008 10:55:27 -0400 Subject: [BiO BB] BLOCKS motifs and protein protein interactions In-Reply-To: References: Message-ID: No, that inference is not generally possible. Only if the proteins are very(!) closely related. Google "interologs" for background on the limits of annotation transfer for interacting proteins. B. On 15-Sep-07, at 6:57 PM, Mahmoud Elhefnawi wrote: > Dear all, > > I was wandering if BLOCKS database homology hits with significant e > values habe been correlated before to infer protein protein > interactions? > > i.e" if protein A interacts with protein B, and protein C has a > significant match with protein B, then protein C also interacts > with protein A??? > > Best, > Mahmoud > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From sreebhapsyamal at gmail.com Mon Sep 22 00:57:55 2008 From: sreebhapsyamal at gmail.com (sreebha syamal) Date: Sun, 21 Sep 2008 21:57:55 -0700 Subject: [BiO BB] SCHEMA and FamClash Message-ID: hi all, Could anybody tell me if SCHEMA and FamClash programs are available for down loading?If so please let me know the sites. If there are any other programs usefull in protein engineering kindly let me know. Thanks -sps From isbra-l at engr.uconn.edu Wed Sep 24 14:53:59 2008 From: isbra-l at engr.uconn.edu (ISBRA Symposium Announcements) Date: Wed, 24 Sep 2008 14:53:59 -0400 (EDT) Subject: [BiO BB] [ISBRA-L] ISBRA'09 First Call for Papers In-Reply-To: References: Message-ID: 5th International Symposium on Bioinformatics Research and Applications May 13-16, 2009 Nova Southeastern University, Ft. Lauderdale, Florida, USA http://www.cs.gsu.edu/isbra09/ The International Symposium on Bioinformatics Research and Applications (ISBRA) provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Original research papers are solicited in all areas of bioinformatics and computational biology, including the development of experimental or commercial systems. Topics of interest include but are not limited to: * Biomedical databases and data integration * Biomolecular imaging * Bio-ontologies * Comparative genomics * Computational genetic epidemiology * Computational proteomics * Data mining and visualization * Gene expression analysis * Genome analysis * High-performance bio-computing * High-throughput sequencing data analysis * Molecular evolution * Molecular modeling and simulation * Pattern discovery and classification * Population genetics * Software tools and applications * Structural biology * Systems biology Accepted papers will be published in Springer-Verlag's Lecture Notes in Bioinformatics series. Extended versions of selected ISBRA papers will be invited to special issues of the IEEE/ACM Transactions on Computational Biology and Bioinformatics and the Journal of Computer Science and Technology. PAPER SUBMISSION Submissions, consisting of an extended abstract of up to 12 pages in Springer LNCS format, must be made electronically at http://www.easychair.org/conferences?conf=isbra09. Simultaneous submission to other conferences with published proceedings is not allowed. Simultaneous submission to a journal is allowed provided that authors notify the program chairs; if published in a journal before the conference date such a contribution will be allocated a 1 page abstract in ISBRA proceedings. IMPORTANT DATES Submission Deadline January 9, 2009 Notification of Acceptance February 6, 2009 Camera Version Deadline February 20, 2009 GENERAL CHAIRS Matthew He (Nova Southeastern University) Alexander Zelikovsky (Georgia State University) PROGRAM CHAIRS Ion Mandoiu (University of Connecticut) Giri Narasimhan (Florida International University) Yan-Qing Zhang (Georgia State University) _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l