From jw12 at sanger.ac.uk Tue Jun 1 04:42:49 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 1 Jun 2010 09:42:49 +0100 Subject: [Biojava-l] Summer Coding Project In-Reply-To: References: Message-ID: <61BC043F-7939-4231-9A11-E1C1B8D24275@sanger.ac.uk> Hi Jonathan If you want any help or advise on this - then don't hesitate to ask me. Cheers Jonathan. On 29 May 2010, at 20:37, jdlkem wrote: > Hello, > > My name is Jonathan, and I'm a rising junior at Harvard University. My > interests lie primarily in all of the the sciences, with a slight > emphasis > on chemistry and computer science. > > This summer I am working on a project with the support of the > Molgenis team > to extend XGAP (http://xgap.org/) as a DAS service. I will be > blogging my > progress at http://blog.jdl-kem.com/. > > Best, > > -Jonathan > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jnarayan81 at gmail.com Thu Jun 3 07:21:06 2010 From: jnarayan81 at gmail.com (jitendra narayan) Date: Thu, 3 Jun 2010 16:51:06 +0530 Subject: [Biojava-l] need help for surface protein identification Message-ID: dear all can you please guide me how to find surface protein using biojava. -- Jitendra Narayan Bioinformatist www.bioinformaticsonline.com From kurka at mikro.biologie.tu-muenchen.de Fri Jun 4 09:47:00 2010 From: kurka at mikro.biologie.tu-muenchen.de (Hedwig Kurka) Date: Fri, 04 Jun 2010 15:47:00 +0200 Subject: [Biojava-l] org.xml.sax.SAXException when parsing Blast-file Message-ID: <4C0903D4.8000603@mikro.biologie.tu-muenchen.de> Hi everyone, I have a problem, when parsing a BLAST-file. The error is: org.xml.sax.SAXException: Could not recognise the format of this file as one supported by the framework. The error occurs in that line: parser.parse(new InputSource(is)); and the input-file is a "normal" Blast-file (not in xml-format). The code is taken from the Biojava-tutorial. I use the BlastLikeSAXParser. I don't understand, what's wrong because the program runs without any error, when I use it alone, but the error occurs, when I integrate the code in my other program, where I implemented e.g. a GUI. Thanks, Hedwig From asidhu at biomap.org Fri Jun 4 11:35:51 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Fri, 4 Jun 2010 23:35:51 +0800 Subject: [Biojava-l] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 (IEEE CBMS 2010) Message-ID: IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Phoebe Chen, La Trobe University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From asidhu at biomap.org Fri Jun 4 11:37:27 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Fri, 4 Jun 2010 23:37:27 +0800 Subject: [Biojava-l] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 (IEEE CBMS 2010) Message-ID: IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Phoebe Chen, La Trobe University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From buiduyminh at gmail.com Tue Jun 15 14:32:49 2010 From: buiduyminh at gmail.com (Minh Bui) Date: Tue, 15 Jun 2010 14:32:49 -0400 Subject: [Biojava-l] BLAST?? Message-ID: Hi everyone, I am currently working on BLAST project for my research. My job is to integrate BLAST to my website (server WINDOW and MAC). I dont know if anyone here already have web-based BLAST install on their computer (like NCBI BLAST). If so, could you show me how to install web-BLAST on my local computer which is running window 7 and mac? Thank you so much and sorry for my English. Its my second language. From kstillou at gmail.com Thu Jun 17 19:38:35 2010 From: kstillou at gmail.com (Katerina Stillou) Date: Fri, 18 Jun 2010 02:38:35 +0300 Subject: [Biojava-l] DNA sequence alignment - class AlignmentPair Message-ID: Hello, I would like to ask a question concerning the class AlignmentPair. My goal is to align two DNA sequences in order to find their percent identity. I know that the latest version of the alignment module found in SVN offers this function. So, I downloaded the latest snapshot of the alignment module found in http://www.biojava.org/download/maven/ , specifically I used the file alignment-3.0-SNAPSHOT.jar . The code in my program is the following: FiniteAlphabet alphabet = (FiniteAlphabet) AlphabetManager.alphabetForName("DNA"); short match = 1; short replace = 0; File simple=new File("genome/NUC.4.4.txt"); SubstitutionMatrix matrix = new SubstitutionMatrix(alphabet, simple); Sequence query = DNATools.createDNASequence(seq1, "query"); Sequence target = DNATools.createDNASequence(seq2, "target"); NeedlemanWunsch nw = new NeedlemanWunsch( (short) 0, // match (short) 3, // replace (short) 2, // insert (short) 2, // delete (short) 1, // gapExtend matrix // SubstitutionMatrix ); AlignmentPair aligner = nw.pairwiseAlignment( query, // first sequence target // second one ); System.out.println("Align Results: "+aligner.getPercentIdentitySubject()); First, I want to ask if there is any problem with my code because I get the this error when I build it: cannot access org.biojava.bio.alignment.SimpleAlignment class file for org.biojava.bio.alignment.SimpleAlignment not found System.out.println("Align Results: "+aligner.getPercentIdentitySubject()); It seems to me that the problem is in the class AlignmentPair. I have also downloaded all the source files from SVN and noticed that the class AlignmentPair is supposed to extend the class SimpleAlignment which doesn't exist in the alignment module from SVN. Is this actually where the problem lies or am I doing something wrong? I would really appreciate any help! Thanks in advance, Katerina From andreas.draeger at uni-tuebingen.de Fri Jun 18 02:47:50 2010 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Fri, 18 Jun 2010 08:47:50 +0200 Subject: [Biojava-l] DNA sequence alignment - class AlignmentPair In-Reply-To: References: Message-ID: <4C1B1696.9040608@uni-tuebingen.de> Hi Katerina, > First, I want to ask if there is any problem with my code because I get the > this error when I build it: > > cannot access org.biojava.bio.alignment.SimpleAlignment > class file for org.biojava.bio.alignment.SimpleAlignment not found > System.out.println("Align Results: "+aligner.getPercentIdentitySubject()); > > It seems to me that the problem is in the class AlignmentPair. I have also > downloaded all the source files from SVN and noticed that the class > AlignmentPair is supposed to extend the class SimpleAlignment which doesn't > exist in the alignment module from SVN. Is this actually where the problem > lies or am I doing something wrong? Your code example looks perfect to me! Actually, I don't think that your version of the class AlignmentPair is broken. It seems to me that you require additional parts of BioJava. The class SimpleAlignment is missing. Did you check the content of the jar file you downloaded? I bet this class is not in there. Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Sand 1 72076 T?bingen Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From andreas at sdsc.edu Tue Jun 29 19:00:25 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 29 Jun 2010 16:00:25 -0700 Subject: [Biojava-l] BioJava 3 current status Message-ID: Hi, The mailing lists have been a bit quiet lately, but there was a lot of communication off-list and many SVN commit. As such here a quick update on the current status of BioJava 3 and the Google summer of code projects: The two GSoC projects are well under way and on track. If you are interested in following what is going on, check out the project pages for Posttranslational Modification: http://biojava.org/wiki/GSoC:PTM Multiple Sequence Alignment: http://biojava.org/wiki/GSoC:MSA About BioJava 3: This has made great progress over the last weeks and a lot of new functionality has been committed to SVN. To make this release ready there are now two new tools: * There is now a BioJava Maven repository, which is hosting SNAPSHOT builds from the current SVN. http://www.biojava.org/download/maven/ These builds are made available by the * Automated build system (using CruiseControl) which is running at: http://emmy.rcsb.org:8080/cruisecontrol/ and http://emmy.rcsb.org:8080/dashboard/ Andreas From kstillou at gmail.com Wed Jun 30 04:53:53 2010 From: kstillou at gmail.com (Katerina Stillou) Date: Wed, 30 Jun 2010 11:53:53 +0300 Subject: [Biojava-l] RichSequence.IOTools.writeFasta Namespace question Message-ID: Hello, I would like to ask a question and hopefully it won't be too silly. I've been trying to write a single DNA sequence in FASTA format but I am having a problem. First of all, I'm using the following code: Sequence dna; try { dna = DNATools.createDNASequence("tgtgcac","dna_1"); RichSequence.IOTools.writeFasta(System.out, dna, null); } The output is like this: >lcl|dna_1.0| tgtgcac The problem here is that that I don't want to use Namespace. In fact I want the symbol > to be followed by "dna_1". Is there a way to achieve this? Thanks in advance, Katerina From jw12 at sanger.ac.uk Tue Jun 1 08:42:49 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 1 Jun 2010 09:42:49 +0100 Subject: [Biojava-l] Summer Coding Project In-Reply-To: References: Message-ID: <61BC043F-7939-4231-9A11-E1C1B8D24275@sanger.ac.uk> Hi Jonathan If you want any help or advise on this - then don't hesitate to ask me. Cheers Jonathan. On 29 May 2010, at 20:37, jdlkem wrote: > Hello, > > My name is Jonathan, and I'm a rising junior at Harvard University. My > interests lie primarily in all of the the sciences, with a slight > emphasis > on chemistry and computer science. > > This summer I am working on a project with the support of the > Molgenis team > to extend XGAP (http://xgap.org/) as a DAS service. I will be > blogging my > progress at http://blog.jdl-kem.com/. > > Best, > > -Jonathan > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From jnarayan81 at gmail.com Thu Jun 3 11:21:06 2010 From: jnarayan81 at gmail.com (jitendra narayan) Date: Thu, 3 Jun 2010 16:51:06 +0530 Subject: [Biojava-l] need help for surface protein identification Message-ID: dear all can you please guide me how to find surface protein using biojava. -- Jitendra Narayan Bioinformatist www.bioinformaticsonline.com From kurka at mikro.biologie.tu-muenchen.de Fri Jun 4 13:47:00 2010 From: kurka at mikro.biologie.tu-muenchen.de (Hedwig Kurka) Date: Fri, 04 Jun 2010 15:47:00 +0200 Subject: [Biojava-l] org.xml.sax.SAXException when parsing Blast-file Message-ID: <4C0903D4.8000603@mikro.biologie.tu-muenchen.de> Hi everyone, I have a problem, when parsing a BLAST-file. The error is: org.xml.sax.SAXException: Could not recognise the format of this file as one supported by the framework. The error occurs in that line: parser.parse(new InputSource(is)); and the input-file is a "normal" Blast-file (not in xml-format). The code is taken from the Biojava-tutorial. I use the BlastLikeSAXParser. I don't understand, what's wrong because the program runs without any error, when I use it alone, but the error occurs, when I integrate the code in my other program, where I implemented e.g. a GUI. Thanks, Hedwig From asidhu at biomap.org Fri Jun 4 15:35:51 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Fri, 4 Jun 2010 23:35:51 +0800 Subject: [Biojava-l] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 (IEEE CBMS 2010) Message-ID: IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Phoebe Chen, La Trobe University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From asidhu at biomap.org Fri Jun 4 15:37:27 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Fri, 4 Jun 2010 23:37:27 +0800 Subject: [Biojava-l] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 (IEEE CBMS 2010) Message-ID: IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Phoebe Chen, La Trobe University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From buiduyminh at gmail.com Tue Jun 15 18:32:49 2010 From: buiduyminh at gmail.com (Minh Bui) Date: Tue, 15 Jun 2010 14:32:49 -0400 Subject: [Biojava-l] BLAST?? Message-ID: Hi everyone, I am currently working on BLAST project for my research. My job is to integrate BLAST to my website (server WINDOW and MAC). I dont know if anyone here already have web-based BLAST install on their computer (like NCBI BLAST). If so, could you show me how to install web-BLAST on my local computer which is running window 7 and mac? Thank you so much and sorry for my English. Its my second language. From kstillou at gmail.com Thu Jun 17 23:38:35 2010 From: kstillou at gmail.com (Katerina Stillou) Date: Fri, 18 Jun 2010 02:38:35 +0300 Subject: [Biojava-l] DNA sequence alignment - class AlignmentPair Message-ID: Hello, I would like to ask a question concerning the class AlignmentPair. My goal is to align two DNA sequences in order to find their percent identity. I know that the latest version of the alignment module found in SVN offers this function. So, I downloaded the latest snapshot of the alignment module found in http://www.biojava.org/download/maven/ , specifically I used the file alignment-3.0-SNAPSHOT.jar . The code in my program is the following: FiniteAlphabet alphabet = (FiniteAlphabet) AlphabetManager.alphabetForName("DNA"); short match = 1; short replace = 0; File simple=new File("genome/NUC.4.4.txt"); SubstitutionMatrix matrix = new SubstitutionMatrix(alphabet, simple); Sequence query = DNATools.createDNASequence(seq1, "query"); Sequence target = DNATools.createDNASequence(seq2, "target"); NeedlemanWunsch nw = new NeedlemanWunsch( (short) 0, // match (short) 3, // replace (short) 2, // insert (short) 2, // delete (short) 1, // gapExtend matrix // SubstitutionMatrix ); AlignmentPair aligner = nw.pairwiseAlignment( query, // first sequence target // second one ); System.out.println("Align Results: "+aligner.getPercentIdentitySubject()); First, I want to ask if there is any problem with my code because I get the this error when I build it: cannot access org.biojava.bio.alignment.SimpleAlignment class file for org.biojava.bio.alignment.SimpleAlignment not found System.out.println("Align Results: "+aligner.getPercentIdentitySubject()); It seems to me that the problem is in the class AlignmentPair. I have also downloaded all the source files from SVN and noticed that the class AlignmentPair is supposed to extend the class SimpleAlignment which doesn't exist in the alignment module from SVN. Is this actually where the problem lies or am I doing something wrong? I would really appreciate any help! Thanks in advance, Katerina From andreas.draeger at uni-tuebingen.de Fri Jun 18 06:47:50 2010 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Fri, 18 Jun 2010 08:47:50 +0200 Subject: [Biojava-l] DNA sequence alignment - class AlignmentPair In-Reply-To: References: Message-ID: <4C1B1696.9040608@uni-tuebingen.de> Hi Katerina, > First, I want to ask if there is any problem with my code because I get the > this error when I build it: > > cannot access org.biojava.bio.alignment.SimpleAlignment > class file for org.biojava.bio.alignment.SimpleAlignment not found > System.out.println("Align Results: "+aligner.getPercentIdentitySubject()); > > It seems to me that the problem is in the class AlignmentPair. I have also > downloaded all the source files from SVN and noticed that the class > AlignmentPair is supposed to extend the class SimpleAlignment which doesn't > exist in the alignment module from SVN. Is this actually where the problem > lies or am I doing something wrong? Your code example looks perfect to me! Actually, I don't think that your version of the class AlignmentPair is broken. It seems to me that you require additional parts of BioJava. The class SimpleAlignment is missing. Did you check the content of the jar file you downloaded? I bet this class is not in there. Cheers Andreas -- Dipl.-Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Sand 1 72076 T?bingen Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From andreas at sdsc.edu Tue Jun 29 23:00:25 2010 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 29 Jun 2010 16:00:25 -0700 Subject: [Biojava-l] BioJava 3 current status Message-ID: Hi, The mailing lists have been a bit quiet lately, but there was a lot of communication off-list and many SVN commit. As such here a quick update on the current status of BioJava 3 and the Google summer of code projects: The two GSoC projects are well under way and on track. If you are interested in following what is going on, check out the project pages for Posttranslational Modification: http://biojava.org/wiki/GSoC:PTM Multiple Sequence Alignment: http://biojava.org/wiki/GSoC:MSA About BioJava 3: This has made great progress over the last weeks and a lot of new functionality has been committed to SVN. To make this release ready there are now two new tools: * There is now a BioJava Maven repository, which is hosting SNAPSHOT builds from the current SVN. http://www.biojava.org/download/maven/ These builds are made available by the * Automated build system (using CruiseControl) which is running at: http://emmy.rcsb.org:8080/cruisecontrol/ and http://emmy.rcsb.org:8080/dashboard/ Andreas From kstillou at gmail.com Wed Jun 30 08:53:53 2010 From: kstillou at gmail.com (Katerina Stillou) Date: Wed, 30 Jun 2010 11:53:53 +0300 Subject: [Biojava-l] RichSequence.IOTools.writeFasta Namespace question Message-ID: Hello, I would like to ask a question and hopefully it won't be too silly. I've been trying to write a single DNA sequence in FASTA format but I am having a problem. First of all, I'm using the following code: Sequence dna; try { dna = DNATools.createDNASequence("tgtgcac","dna_1"); RichSequence.IOTools.writeFasta(System.out, dna, null); } The output is like this: >lcl|dna_1.0| tgtgcac The problem here is that that I don't want to use Namespace. In fact I want the symbol > to be followed by "dna_1". Is there a way to achieve this? Thanks in advance, Katerina