From goodb at interchange.ubc.ca Fri Sep 12 17:25:16 2008 From: goodb at interchange.ubc.ca (Benjamin Good) Date: Fri, 12 Sep 2008 14:25:16 -0700 Subject: [MOBY-l] a request: In preparation for the Moby Annotation Jamboree... In-Reply-To: <48AD7BAE.7060903@cnio.es> References: <48AD7BAE.7060903@cnio.es> Message-ID: <023BB0FF-3D50-4971-8876-B9621DCA2393@interchange.ubc.ca> Hello everyone, For those of you that are interested in participating in the service annotation jamboree, could you please do the following: 1) Make sure any service (at this stage, we are working on individual services, not workflows), that you would like to see annotated appears in the Canada moby central registry. If this is a problem, please contact me. 2) Email me a list of services that you are specifically interested in - the URIs for the services name would be ideal. I don't know how many people will participate so I want to develop a focused list of high-priority services to start things off with. Eventually we hope all of the services in the registry will be described. 3) Send me a list of email addresses for people that you think would be interested in participating (or that you can force somehow ;). We are testing the annotation interface/code now (written by Paul Lu). Assuming it passes the tests, we should be ready to get started by the end of next week. thanks very much -Ben From goodb at interchange.ubc.ca Mon Sep 15 12:00:43 2008 From: goodb at interchange.ubc.ca (Benjamin Good) Date: Mon, 15 Sep 2008 09:00:43 -0700 Subject: [MOBY-l] a request: In preparation for the Moby Annotation Jamboree... In-Reply-To: <48CE1E56.9050103@mpimp-golm.mpg.de> References: <48AD7BAE.7060903@cnio.es> <023BB0FF-3D50-4971-8876-B9621DCA2393@interchange.ubc.ca> <48CE1E56.9050103@mpimp-golm.mpg.de> Message-ID: Hi Bjoern, Participation is very simple. All you will need to do is 1) log in into the website we are still constructing with an OpenID (http://openid.net/get/ - we have tested with myvidoop and yahoo id providers) 2) answer a few questions about your experience with biomoby web services 3) you will then be presented with a service and some information about it and then will be asked to add descriptive annotations to it using one of two kinds of tagging system. When you finish one service, another one will be presented and you be able to continue for as long as you wish. Anyone could do this and even 10 minutes of time would help - though biologists and bioinformaticians willing to tag for hours would be ideal. I sent the previous message mostly for service providers who might wish to ensure that their services are in the group to be annotated. thanks for your interest, please do let me know if you have any more questions -Ben On Sep 15, 2008, at 1:35 AM, Bjoern Usadel wrote: > Dear Ben, > > As I wasn't following this, and before I sign away somebody's > firstborn, what would one have to do? > > Annotate biology, inputs outputs, testing? > > Best Wishes, > Bj?rn > > Benjamin Good wrote: >> Hello everyone, >> For those of you that are interested in participating in the service >> annotation jamboree, could you please do the following: >> 1) Make sure any service (at this stage, we are working on individual >> services, not workflows), that you would like to see annotated >> appears >> in the Canada moby central registry. If this is a problem, please >> contact me. >> 2) Email me a list of services that you are specifically interested >> in >> - the URIs for the services name would be ideal. I don't know how >> many people will participate so I want to develop a focused list of >> high-priority services to start things off with. Eventually we hope >> all of the services in the registry will be described. >> 3) Send me a list of email addresses for people that you think would >> be interested in participating (or that you can force somehow ;). >> We are testing the annotation interface/code now (written by Paul >> Lu). Assuming it passes the tests, we should be ready to get started >> by the end of next week. >> thanks very much >> -Ben >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l >> This email was Anti Virus checked by the MPIMP-Golm Astaro Security >> Gateway. >> . > > -- > ---------------------------------------------- > Bj?rn Usadel, PhD > Max Planck Institute of Molecular Plant Physiology > AG Integrative Carbon Biology > Am Muehlenberg 1 > 14476 Potsdam-Golm > Tel.: +49 331 5678153 > email usadel at mpimp-golm.mpg.de > ---------------------------------------------- > > This email was Anti Virus checked by the MPIMP-Golm Astaro Security > Gateway. > From paolo.romano at istge.it Tue Sep 16 11:53:15 2008 From: paolo.romano at istge.it (Paolo Romano) Date: Tue, 16 Sep 2008 17:53:15 +0200 Subject: [MOBY-l] CFP: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) Message-ID: <200809161608.m8GG8gC9044506@ibm43p.biotech.ist.unige.it> Apologies, if you're receiving multiple copies. ---------------------------------------------------------------- International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 28th November 2008, Edinburgh, UK http://www.swat4ls.org/ CALL FOR PAPERS Overview -------- The workshop is organized in sessions and open discussions. Invited speakers will present state-of-the-art, provocative lectures on the workshop's main topic, while a number of submissions will be accepted as oral presentations and posters on all workshop's topics. Workshop Description -------------------- Semantic Web technologies, tools and applications are starting to emerge in Life Sciences. In recent years, systems have been introduced and an increasing interest among researchers is arising. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences. Keynote Speakers ------------------------ + Semantic web technology in translational cancer research, Michael Krauthammer, Department of Pathology, Yale University School of Medicine, USA + Using Ontologies to bring Web Services on to the Semantic Web Mark Wilkinson, Dept. of Medical Genetics, University of British Columbia, Canada Workshop Venue and Format ------------------------ The workshop will take place in Edinburgh, Scotland, on 28 November 2008, and is hosted by the e-Science Institute of the UK's National e-Science Centre (NeSC). SWAT4LS will be a one-day workshop and will consist of two invited talks, regular paper and poster presentations. The workshop will conclude with a panel discussion on the strength and weaknesses of the Semantic Web for the Life Sciences. Deadlines --------- * Submission deadline (both papers and posters): 30 September 2008 * Notification of acceptance: 20 October 2008 * Camera-ready submission: 3 November 2008 (Authors who are interested in submitting a paper/poster to the workshop, but may require a short extension to the deadline, should get in touch with the organisers.) Topics of Interest ------------------ Topics of interest include, but are not limited to: * Standards, Technologies, Tools for the Semantic Web o Semantic Web standards (RDF, OWL, ...) o RDF/OWL, SKOS, .... and their applicability to bioinformatics o RDF Schemas and Query systems o Biomedical Ontologies and related tools o Formal approaches to large biomedical controlled terminologies and vocabularies * Systems for a Semantic Web for Bioinformatics o Bio-ontologies, RDF stores, Semantic Web Services o RDF repositories and query systems for life sciences o Semantically aware biomedical Web Services o Semantic Biological Data Integration Systems * Existing and perspective applications of the Semantic Web for Bioinformatics o Semantic browsers, Semantic collaborative research o Case studies, use cases, and scenarios o Semantic Web applications in life sciences Type of contributions ---------------------- The following possible original contributions are sought: * Oral communications (regular papers) * Posters * Software demos All accepted oral communications and posters will be published with the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). Furthermore, a selection of papers will be published in a special issue of the BMC Bioinformatics journal devoted to the SWAT4LS workshop. To this end, a special Call will be launched shortly after the workshop, for extended and revised versions of contributions submitted to the workshop and accepted either as oral communication or poster. Workshop Chairs ---------------- + Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, United Kingdom + Adrian Paschke, Biotechnology Centre, TU Dresden, Dresden, Germany + Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy + Andrea Splendiani, Medical Informatics Department, University of Rennes 1, Rennes, France ===================================================================== In Co-operation with: - National Cancer Research Institute, Genova, Italy - Biotechnology Centre, TU Dresden, Dresden, Germany - School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, United Kingdom - Universit? de Rennes 1, Rennes, France - e-Science Institute, Edinburgh, Scotland, United Kingdom - SeaLife Project, European Commission Information Society and Media - Laboratory for Interdisciplinary Technologies in Bioinformatics (LITBIO), Italy ===================================================================== For any information, refer to info at swat4ls.org . 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 From goodb at interchange.ubc.ca Tue Sep 16 20:21:14 2008 From: goodb at interchange.ubc.ca (Benjamin Good) Date: Tue, 16 Sep 2008 17:21:14 -0700 Subject: [MOBY-l] [MOBY-dev] building jMoby on Mac - help needed In-Reply-To: References: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com> Message-ID: Hi Martin, I just hit this error you describe here. I don't know how to correct the project.pom (never used Maven before) but I can get it to work on my mac by changing the ant file as follows: If you like, I can test out other solutions for you if you or Eddie come up with them. cheers -Ben On May 6, 2008, at 9:12 AM, Mark Wilkinson wrote: > > > ------- Forwarded message ------- > From: "Martin Senger" > To: "Core developer announcements" > Cc: "Skofic, Milko (Bioversity)" > Subject: [MOBY-dev] building jMoby on Mac - help needed > Date: Tue, 06 May 2008 02:07:20 -0700 > > I am looking for Mac-ists who can help with the building/compiling > jMoby on > Mac OS X. > > The problem (as identified already during the last Biohackathon in > Tokyo) is > the tools.jar library. On Mac, there is no such file because its > contents is > part of the default library classes.jar. On other platforms we have > to add > the tools.jar separately. That's why there is a "mac profile" in the > xmls/project.pom. But it does not work... (I wonder if it was > working in the > past, at all; was it?). > > The problematic (the one causing an error under Mac OS X) are the > lines (in > build.xml): > > > > > > I really do not understand how the profile tag in xmls/project.pom > works, or > should work, to make the lines above working. Any help around? > > Many thanks, > Martin > > > > -- > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From jeedward at yahoo.com Sun Sep 21 13:10:25 2008 From: jeedward at yahoo.com (Ed) Date: Sun, 21 Sep 2008 10:10:25 -0700 (PDT) Subject: [MOBY-l] IICAI-09 Call for papers Message-ID: <275220.74134.qm@web45902.mail.sp1.yahoo.com> Dear Colleagues ? ? The 4th Indian International Conference on Artificial Intelligence (IICAI-09) will be held in Tumkur (near Bangalore), India during December 16-18 2009. The conference consists of paper presentations, special workshops, sessions, invited talks and local tours, etc.? and it is one of the biggest AI events in the world. We invite draft paper submissions. Please see the website: www.iiconference.org ?for more details of the conference. ? Sincerely ? ? Edward Publicity Committee