From paolo.romano at istge.it Fri Apr 3 11:43:19 2009 From: paolo.romano at istge.it (Paolo Romano) Date: Fri, 03 Apr 2009 17:43:19 +0200 Subject: [MOBY-l] CFP: NETTAB 2009 on Collaborative Bioinformatics Research and Development (open source, social networks, wikis, ...) Message-ID: <200904031543.n33FhKvi006268@clus2.istge.it> Apologies if you receive more copies. =========================== Announce and Preliminary Call for Papers NETTAB 2009 Workshop on "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development" with a Special Session on: "Methods and Tools for RNA Structure and Functional Analysis" June 10-13, 2009 Department of Computer Science, University of Catania, Italy http://www.nettab.org/2009/ Submissions deadlines: - April 28, 2009: Oral communication submission - May 15, 2009: Posters submission Submissions must be short papers of around 3 pages or 12.000 characters long. Special Issues in peer-review journals on workshop's topics planned: post-workshop ad hoc Call for papers will be issued. RATIONALE Advent of Wide Area Networks (WAN) allowed the availability of distributed information and prompted the need for searching and retrieving this data (Network Information Retrieval tools, NIR), as well the development of unprecedented communications between users (Computer Mediated Communication tools, CMC). Initially, CMC was asynchronous and based on electronic mail and newsgroups. From email systems, mailing lists and newsletter were soon derived, while newsgroups generated, shortly after, electronic fora. Synchronous communication were introduced through the advent of chat services. On this line, current multimedia teleconference systems were then set up. Virtual reality was first introduced for educational purposes by means of MUD (Multi-users Domain) systems, and especially by means of MOO (MUD Object-oriented). This line produced current virtual reality environment, like the emerging Second Life system. Life Sciences researchers largely took profit from CMC tools. The bionet newsgroups hierarchy remains one of the most famous and useful CMC system supporting life science research. Many mailing lists that were born in that context are still used. The development of open source software was largely made possible by the possibility of exchanging, in an effective way, knowledge, practices and skills among researchers. Web sites of communities of scientists were set up and often constituted the base for a real collaborative development and research. The most recent developments of collaborative development tools are impressive. Researchers can now collaboratively develop software (open source systems), discuss and compare development strategies (social networks), write documents (google docs, wiki systems), build knowledge bases. So, it may now be the time for presenting current technologies, tools and applications for collaborative work and for discussing perspectives of their utilization in support of Bioinformatics. For these reasons, NETTAB 2009 will be devoted to "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development". Moreover, there will be a special session on "Methods and Tools for RNA Structure and Functional Analysis". The transcription of almost all genomes generates a great number of coding and non-coding RNAs (ncRNAs). Although RNA is central to the synthesis of proteins, it is not only a messenger of genetic information: many cellular functions depend on ncRNAs, which exert their functions by their sequence and structure. In particular, small silencing RNAs (miRNAs, siRNAs and piRNAs) play a crucial role in many physiological processes and their aberrant expression is a common feature of human diseases including cancer. Models and tools able to increase our understanding of RNAs functions and their involvement in diseases may lead to the design of new RNA-based therapeutics. The RNA community is also taking advantage of collaborative research tools such as Wikis and other virtual environments. The RNA WikiProject contains now over 600 articles describing families of noncoding RNAs based on the Rfam database, and invite the community to update, edit, and correct those articles. Therefore, the NETTAB 2009 special session will focus on collaborative research project, computational methods and tools for the analysis of RNA structures and functions, with a special emphasis on ncRNAs. KEYNOTE SPEAKER # Alex Bateman Wellcome Trust Sanger Institute Hinxton, Cambridge, UK # Tim Clark Director of Informatics, MassGeneral Institute for Neurodegenerative Disease Neurology Research Department, Massachusetts General Hospital, Boston, USA # Duncan Hull School of Chemistry, University of Manchester, Manchester, UK # Michael Levitt Stanford University, USA # Debora Marks Systems Biology Department, Harvard Medical School Boston, USA TOPICS - Collaborative Web sites (bioinformatics.org, biojava, bioperl, ) - Communities of Practices (CoPs) Scientific practices in scientific communities Automatic detection / gathering / modelling of scientific practices Implementations of CoPs - Social networking (myExperiment, Annotea, myScience) Social Bookmarking Semantic Document Markup Relationships mining from literature - Open Source development Sharing of data models, libraries, interfaces - Social software for collaborative documentation development Wikis, blogs, google docs Knowledge Wikis Social-software-mediated collaborative scientific research Social-software-mediated collaborative tools' development Knowledge base collaborative development Ontologies collaborative development - Education and training tools E-learning Virtual environments Methods and Tools for RNA Structure and Functional Analysis - RNA structure prediction - Collaborative studies of RNAs - ncRNAs functional analysis and classification - miRNAs and networks - Genome-wide functional studies - Identification of ncRNAs - Databases of ncRNAs and miRNA targets - miRNA targets prediction - Synthetic miRNA and siRNA design - Gene expression analysis - Analysis of viral RNAs - RNAi therapeutics - Identification of ncRNAs biomarkers - RNA-protein interaction prediction DEADLINES Submissions for both oral communications and posters must be short papers of around THREE A4 pages or 12.000 characters long. - April 28, 2009: Oral communication submission Acceptation communication: May 12, 2009 - May 15, 2009: Posters submission - May 17, 2009: Early registration - June 10-13, 2009: Tutorials and Workshop Calls for SPECIAL ISSUES We plan to launch Calls for Special Issues on the themes of the workshop in peer-review journals with associated Impact factor around July for submission in September 2009. Best regards. Paolo Romano on behalf of NETTAB 2009 Chairs Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 AIUTACI AD AIUTARE: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it From mgerlich at ipb-halle.de Mon Apr 6 08:31:26 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Mon, 06 Apr 2009 14:31:26 +0200 Subject: [MOBY-l] Collection of Biomoby inputs Message-ID: <49D9F61E.9050200@ipb-halle.de> Hi all, I'd like to know how I can find out if the input of a Biomoby service is a collection or not? I didn't find appropriate functions in MobyService or MobyDataType Objects. Anyone knows where to look? Regards, Michael -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From markw at illuminae.com Mon Apr 6 09:19:34 2009 From: markw at illuminae.com (Mark) Date: Mon, 06 Apr 2009 06:19:34 -0700 Subject: [MOBY-l] Collection of Biomoby inputs In-Reply-To: <49D9F61E.9050200@ipb-halle.de> References: <49D9F61E.9050200@ipb-halle.de> Message-ID: If you're just browsing around, use the encyclopaedia: http://moby.ucalgary.ca/cgi-bin/list.services.cgi otherwise you'll have to use the API. Cheers! M On Mon, 06 Apr 2009 05:31:26 -0700, Michael Gerlich wrote: > Hi all, > > I'd like to know how I can find out if the input of a Biomoby service is > a collection or not? > I didn't find appropriate functions in MobyService or MobyDataType > Objects. > > Anyone knows where to look? > > Regards, > Michael > From edward.kawas at gmail.com Mon Apr 6 09:40:06 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 6 Apr 2009 06:40:06 -0700 Subject: [MOBY-l] Collection of Biomoby inputs In-Reply-To: <49D9F61E.9050200@ipb-halle.de> References: <49D9F61E.9050200@ipb-halle.de> Message-ID: <49da0642.08b38c0a.643b.19b3@mx.google.com> Hi Michael, To find out whether an input is a collection or not, you need to do first get the primary inputs: MobyPrimaryData inputs = service.getPrimaryInputs(); Then while you iterate over them, you need to check if they are either MobyPrimaryDataSet or MobyPrimaryDataSimple: for (MobyPrimaryData input : inputs) { if (input instanceof MobyPrimaryDataSimple) { // not a collection } else if (input instanceof MobyPrimaryDataSet) { // collection } } Hope this helps! Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: April-06-09 5:31 AM To: moby-l at biomoby.org Subject: [MOBY-l] Collection of Biomoby inputs Hi all, I'd like to know how I can find out if the input of a Biomoby service is a collection or not? I didn't find appropriate functions in MobyService or MobyDataType Objects. Anyone knows where to look? Regards, Michael -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From phillip.lord at newcastle.ac.uk Tue Apr 7 13:13:14 2009 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Tue, 07 Apr 2009 18:13:14 +0100 Subject: [MOBY-l] CFP: Bio-Ontologies Message-ID: <878wmcwfo5.fsf@newcastle.ac.uk> ***DEADLINE FRIDAY FOR SUBMISSIONS*** ** Call for Papers Submissions are now invited Bio-Ontologies 2009: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2009. *** Key Dates - Submissions Due: April 10th (Friday) - Notifications: May 1st (Friday) - Final Version Due: May 8th (Friday) - Workshop: June 28th (Sunday) *** Introduction Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organisation, presentation and dissemination of knowledge in biology. It has existed as a SIG at ISMB (http://www.iscb.org/ismbeccb2009) for 11 years now, making it one of the longest running. We are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. We invite submissions on a wide range of topics including, but not limited to: - Semantic and/or Scientific Wikis. - Multimedia Blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for Drug Discovery - Research in Ontology Languages and its Effect on Bio-Ontologies ** Programme This year's keynote speaker will by Barend Mons (http://en.wikipedia.org/wiki/Barend_Mons). This year's panel will be - Barend Mons - Andrew Su - Dawn Field *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2009). *** Instructions to Authors We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccessful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Susie Stephens, Eli Lilly Larisa Soldatova, University of Wales, Aberystwyth *** Programme Committee The programme committee, organised alphabetically is: Michael Bada, University of Colorado Denver Olivier Bodenreider, National Library Medicine Kei Cheung, Yale Center for Medical Informatics Paolo Ciccarese, Harvard Sudeshna Das, Harvard Michel Dumontier, Carleton University Wacek Kusnierczyk, Norwegian University of Science and Technology Cliff Joslyn, Pacific Northwest National Laboratory Midori Harris, European Bioinformatics Institute James Malone, European Bioinformatics Institute Robin McEntire, Independent Consultant Parsa Mirhaji, University of Texas David Newman, ECS, University of Southampton Chimezie Ogbuji, The Cleveland Clinic Foundation Alexandre Passant, DERI Alan Ruttenberg, Science Commons Phillippe Rocca-Serra, European Bioinformatics Institute Matthias Samwald, DERI Robert Stevens, University of Manchester Yimin Wang, Eli Lilly Mark Wilkinson, Medical Genetics, U. of British Columbia Jenna Zhou, Eli Lilly and the conference organisers. *** Templates Submission templates are available from the website (http://bio-ontologies.org.uk). From jeedward at yahoo.com Sat Apr 18 12:50:33 2009 From: jeedward at yahoo.com (John Edward) Date: Sat, 18 Apr 2009 09:50:33 -0700 (PDT) Subject: [MOBY-l] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <232298.24713.qm@web45915.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee From paolo.romano at istge.it Tue Apr 28 09:20:02 2009 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 28 Apr 2009 15:20:02 +0200 Subject: [MOBY-l] NETTAB 2009: Deadline postponed to May 4, 2009, for Oral communications Message-ID: <200904281334.n3SDYD54043156@ibm43p.biotech.ist.unige.it> Due to many requests for a new deadline for submission of contributions for oral communications, the related deadline has been postponed to: Monday May 4, 2009, at 12.00 (noon), EST (GMT+1). ===== Last Call for Oral communications NETTAB 2009 Workshop on "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development" with a Special Session on: "Methods and Tools for RNA Structure and Functional Analysis" June 10-13, 2009 Department of Computer Science, University of Catania, Italy http://www.nettab.org/2009/ Deadline approaching: May 4, 2009: Oral communication submission Contributions must be short papers of around THREE A4 pages or 12.000 characters long. Submit through the EasyChair system at: http://www.easychair.org/conferences/?conf=nettab2009 . See web site for details. Motivation The most recent developments of collaborative development tools are impressive. Researchers can now collaboratively develop software (open source systems), discuss and compare development strategies (social networks), write documents (google docs, wiki systems), build knowledge bases. So, it may now be the time for presenting current technologies, tools and applications for collaborative work and for discussing perspectives of their utilization in support of Bioinformatics. For these reasons, NETTAB 2009 will be devoted to "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development". The RNA community is also taking advantage of collaborative research tools such as Wikis and other virtual environments. The RNA WikiProject contains now over 600 articles describing families of noncoding RNAs based on the Rfam database, and invite the community to update, edit, and correct those articles. Therefore, the NETTAB 2009 special session will focus on collaborative research project, computational methods and tools for the analysis of RNA structures and functions, with a special emphasis on ncRNAs. Invited Speakers (more to be announced) # Alex Bateman Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK # Doron Betel MSKCC - Computational Biology Center New York, USA # Tim Clark Director of Informatics, MassGeneral Institute for Neurodegenerative Disease Neurology Research Department, Massachusetts General Hospital, Boston, USA # Duncan Hull School of Chemistry, University of Manchester, Manchester, UK # Gabriel Valiente Technical University of Catalonia, Department of Software, Barcelona, Spain # Debora Marks Systems Biology Department, Harvard Medical School, Boston, USA # Gabriel Valiente Technical University of Catalonia, Department of Software, Barcelona, Spain Topics - Collaborative Web sites (bioinformatics.org, biojava, bioperl, ) - Communities of Practices (CoPs) Scientific practices in scientific communities Automatic detection / gathering / modelling of scientific practices Implementations of CoPs - Social networking (myExperiment, Annotea, myScience) Social Bookmarking Semantic Document Markup Relationships mining from literature - Open Source development Sharing of data models, libraries, interfaces - Social software for collaborative documentation development Wikis, blogs, google docs Knowledge Wikis Social-software-mediated collaborative scientific research Social-software-mediated collaborative tools' development Knowledge base collaborative development Ontologies collaborative development - Education and training tools E-learning Virtual environments Methods and Tools for RNA Structure and Functional Analysis - RNA structure prediction - Collaborative studies of RNAs - ncRNAs functional analysis and classification - miRNAs and networks - Genome-wide functional studies - Identification of ncRNAs - Databases of ncRNAs and miRNA targets - miRNA targets prediction - Synthetic miRNA and siRNA design - Gene expression analysis - Analysis of viral RNAs - RNAi therapeutics - Identification of ncRNAs biomarkers - RNA-protein interaction prediction Deadlines Contributions for both oral communications and posters must be short papers of around THREE A4 pages or 12.000 characters long. They must be submitted through the EasyChair system at: http://www.easychair.org/conferences/?conf=nettab2009 . - May 4, 2009: Oral communication submission - May 15, 2009: Posters submission - May 17, 2009: Early registration - June 10-13, 2009: Tutorials and Workshop Calls for SPECIAL ISSUES We plan to launch Calls for Special Issues on the themes of the workshop in peer-review journals with associated Impact factor around July for submission in September 2009. Best regards. Paolo Romano on behalf of NETTAB 2009 Chairs NETTAB '09 - Ninth International Workshop on Network Tools and Applications in Biology 10-13 June 2009, Catania, Italy http://www.nettab.org/2009/ Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) From yangkuan81 at gmail.com Thu Apr 30 17:06:28 2009 From: yangkuan81 at gmail.com (Kuan Yang) Date: Thu, 30 Apr 2009 17:06:28 -0400 Subject: [MOBY-l] how to query moby for information Message-ID: Dear all, I am new to using BioMoby so what I am asking might be naive, however, I really could not find any information on how to do it. Let's consider this example, If I have a piece of information, say GI, I want all information I can get about this GI from BioMoby, namely all the services that can take it as input. I tried to use featureclient in the jMoby package but it looks like it has some filtering so it will only query some predefined services. After I remove the filtering, I will get a Lot of errors. Some of the error messages are saying, I need to provide more input/parameters. So my question is, how do I know what other required inputs are, in terms of datatypes and namespaces? Is there some description/document on each service? Thanks Kuan From edward.kawas at gmail.com Thu Apr 30 17:14:37 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Apr 2009 14:14:37 -0700 Subject: [MOBY-l] how to query moby for information In-Reply-To: References: Message-ID: <49fa14c6.14b48c0a.4dc4.fffffbae@mx.google.com> I think that the best place for you to start is to view the gbrowse_moby client http://moby.ucalgary.ca/gbrowse_moby Once you have tried this example, the best place to look for more information is the biomoby.org homepage (http://biomoby.org). Also, since you mentioned jmoby, you should probably look at the jmoby documentation (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/index.html ) If you any more questions, please don't hesitate to ask the list! Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Kuan Yang Sent: April-30-09 2:06 PM To: moby-l at lists.open-bio.org Subject: [MOBY-l] how to query moby for information Dear all, I am new to using BioMoby so what I am asking might be naive, however, I really could not find any information on how to do it. Let's consider this example, If I have a piece of information, say GI, I want all information I can get about this GI from BioMoby, namely all the services that can take it as input. I tried to use featureclient in the jMoby package but it looks like it has some filtering so it will only query some predefined services. After I remove the filtering, I will get a Lot of errors. Some of the error messages are saying, I need to provide more input/parameters. So my question is, how do I know what other required inputs are, in terms of datatypes and namespaces? Is there some description/document on each service? Thanks Kuan _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From dxha at vt.edu Thu Apr 30 22:56:15 2009 From: dxha at vt.edu (Ha X. Dang) Date: Thu, 30 Apr 2009 22:56:15 -0400 Subject: [MOBY-l] Problem with SAWSDLServlet In-Reply-To: <49fa14c6.14b48c0a.4dc4.fffffbae@mx.google.com> References: <49fa14c6.14b48c0a.4dc4.fffffbae@mx.google.com> Message-ID: <1241146575.6234.10.camel@hadaxu-linux> Hi, I couldn't get SAWSDLServlet to work. I just followed the instruction at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/sawsdlServlet.html It seems to me that bioxml.info is not available for LSID. Does anyone ever made it work recently or know what happens? Please help. Thanks. Here is the error message: =============================== type Exception report message description The server encountered an internal error () that prevented it from fulfilling this request. exception javax.servlet.ServletException: Servlet execution threw an exception root cause java.lang.NoClassDefFoundError: org/xbill/DNS/SOARecord org.xbill.DNS.Cache.addMessage(Cache.java:670) org.xbill.DNS.Lookup.lookup(Lookup.java:399) org.xbill.DNS.Lookup.resolve(Lookup.java:424) org.xbill.DNS.Lookup.run(Lookup.java:441) org.biomoby.shared.LSIDResolver.findAuthorityWSDL(LSIDResolver.java:84) org.biomoby.shared.LSIDResolver.resolveURL(LSIDResolver.java:128) org.biomoby.shared.LSIDResolver.resolveDataURL(LSIDResolver.java:120) ca.ucalgary.services.util.WSDLConfig.getLiftingSchemaFromOperation(WSDLConfig.java:464) ca.ucalgary.services.util.WSDLConfig.getSecondaryParamRestrictionsFromService(WSDLConfig.java:352) ca.ucalgary.services.util.WSDLConfig.getSecondaryParamRestrictions(WSDLConfig.java:289) ca.ucalgary.services.util.WSDLConfig.wsdlParam2MobySecondaryParam(WSDLConfig.java:267) ca.ucalgary.services.util.WSDLConfig.parseSOAPMessageSpec(WSDLConfig.java:175) ca.ucalgary.services.util.WSDLConfig.parseSOAPMessageSpecs(WSDLConfig.java:128) ca.ucalgary.services.util.WSDLConfig.parse(WSDLConfig.java:113) ca.ucalgary.services.util.WSDLConfig.(WSDLConfig.java:92) ca.ucalgary.services.WSDLService.createServiceFromConfig(WSDLService.java:173) org.biomoby.service.MobyServlet.doGet(MobyServlet.java:92) javax.servlet.http.HttpServlet.service(HttpServlet.java:627) javax.servlet.http.HttpServlet.service(HttpServlet.java:729) note The full stack trace of the root cause is available in the Apache Tomcat/5.5.27 logs. - Ha