From rmb32 at cornell.edu Sat Apr 3 16:09:27 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sat, 03 Apr 2010 13:09:27 -0700 Subject: [DAS] Google Summer of Code is *ON* for OBF projects! Message-ID: <4BB7A077.4070802@cornell.edu> Hi all, Reminder: GSoC student proposals must be submitted to Google by April 9th, 19:00 UTC. That's less than a week away. Students: you should ALREADY be working with mentors on the project mailing lists, they can help you get your proposal into shape. So far, we have 5 proposals submitted to our org in Google's web app. Keep them coming, and let's see some really good ones! Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Sun Apr 4 00:37:38 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sat, 03 Apr 2010 21:37:38 -0700 Subject: [DAS] Reminder: GSoC student applications due April 9, 19:00 UTC Message-ID: <4BB81792.8060001@cornell.edu> Hi all, Sending this again with a different subject line, just in case. GSoC student proposals must be submitted to Google through their web application by *April 9th, 19:00 UTC*. That's less than a week away. Students: you should ALREADY be working with mentors on the project mailing lists, they can help you get your proposal into shape. So far, we have 6 proposals submitted to our org in Google's web app. Keep them coming, and keep them good! Rob Buels OBF GSoC 2010 Administrator From andy.jenkinson at ebi.ac.uk Tue Apr 13 09:44:23 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 13 Apr 2010 14:44:23 +0100 Subject: [DAS] authentication summary Message-ID: Hi all, First of all, thank you to those of you who attended last week's DAS Workshop. I thought we had some interesting talks and, as ever, some productive and thought provoking discussions. As a follow up to the third day's discussion on authentication, I thought I would provide a quick summary: There was an initial overview about the prospect of adopting OpenID delegated authentication in DAS (which is already used by the DAS registry and some DAS clients). Specifically, the core reliance of OpenID on HTTP browser redirects makes in unsuitable for DAS server-server communications. Afterwards, two proposals emerged: firstly, that the DAS specification make a simple recommendation to use existing HTTP digest authentication, leaving DAS software to implement the components independently. Secondly, a DAS-specific delegated authentication model based around a trusted third party (probably the DAS registry) as the identity provider. Each proposal has its own advantages and disadvantages in terms of both security and implementation considerations which we now need to debate within the community before we come up with a recommendation, so I have summarised both proposals on the wiki: http://www.biodas.org/wiki/DAS1.6E#Authentication Please feel free to edit as necessary, and comment on the list. Cheers, Andy From andy.jenkinson at ebi.ac.uk Tue Apr 13 13:17:48 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 13 Apr 2010 18:17:48 +0100 Subject: [DAS] authentication summary In-Reply-To: <4BC4A076.4030901@compbio.dundee.ac.uk> References: <4BC4A076.4030901@compbio.dundee.ac.uk> Message-ID: On 13 Apr 2010, at 17:48, Jim Procter wrote: > Thanks for posting this, Andy. > > > On 13/04/2010 14:44, Andy Jenkinson wrote: >> Afterwards, two proposals emerged: firstly, that the DAS specification make a simple recommendation to use existing HTTP digest authentication, leaving DAS software to implement the components independently. Secondly, a DAS-specific delegated authentication model based around a trusted third party (probably the DAS registry) as the identity provider. >> >> Each proposal has its own advantages and disadvantages in terms of both security and implementation considerations which we now need to debate within the community before we come up with a recommendation, so I have summarised both proposals on the wiki: >> http://www.biodas.org/wiki/DAS1.6E#Authentication >> > I didn't participate in the fine details of the discussion last friday, but I wondered afterwards if anyone had considered adopting the Globus authentication model. Grid based authentication for programmatic web services has now been around for a number of years in a number of guises (the Globus toolkit is the one I know of), and may already address all the requirements and concerns raised at the meeting. > > My 2c.. > Jim. > > ps. I can point out some people who may be worth approaching regarding Globus or Shibboleth style third-party ident/auth middleware if people wish. Definitely worth a shout, I'll do some research. From gthorisson at gmail.com Wed Apr 14 07:33:16 2010 From: gthorisson at gmail.com (Gudmundur A. Thorisson) Date: Wed, 14 Apr 2010 12:33:16 +0100 Subject: [DAS] authentication summary In-Reply-To: References: <4BC4A076.4030901@compbio.dundee.ac.uk> Message-ID: <3CDE9329-04DC-4533-B6BE-189FB7FE9EB9@gmail.com> Hi all. To add my $0.02 to the debate; I whole-heartedly support the delegated auth model, but suggest we try to tease apart the authentication step on one hand (user proving to the DAS registry who he is), and the authorisation-related things on the other (does the authenticated user have access to a given server, or source within a server, or possibly even more fine-grained controls; user managing/requesting access to sources; and more). Also, as something of an alternative approach to "heavier" grid security solutions, it may be worth considering a more Web 2.0 style delegated authz approach based on OAuth (http://oauth.net). In the photo sharing-and-printing example scenarios illustrated in the two tutorials referenced below, one could envision the DAS registry as the site where the photos are hosted (the OAuth provider), and the DAS client as the photo-printing site (the OAuth consumer): http://hueniverse.com/2007/10/beginners-guide-to-oauth-part-ii-protocol-workflow/ http://www.wdvl.com/Authoring/Authorization/OAuthIntro/Jaswinder_Singh03042010.html However, I'll admit that it isn't entirely obvious to me how to accommodate the DAS servers themselves as additional players in these scenarios, unless (as Andy's writeup mentions) the servers accepts tokens issued by the registry. The following may be also useful to the discussion. We have an ongoing project in our group where we're exploring a number of scenarios very similar to the delegated model described by Andy, with a central AtomPub server and authz schemes centred on Atom feeds and feed entries (some of which are protected and others which are not). An authz scenario of particular interest involves a standalone application, from which a user with submission privileleges uploads genetic variation data via a RESTful POST to the central Atom store. The relevance to the present discussion that the submission app above can probably be considered as analoguous to a standalone DAS client, and the central Atom store analoguous to the DAS registry. The model we are keen to use for this is very similar to Flickr photo-uploads, where the user authorises the Flickr Uploadr standalone application (http://www.flickr.com/help/tools/) to send photos to Flickr on his behalf. Importantly, the user does not enter user/pwd credentials in the standalone app itself, but rather is sent to the central website where he signs in (if not already authenticated) and authorises the app. Subsequently, the app can upload data to the until de-authorised by the user, or the token expires (if time-limited). This would seem to address the issue Andy listed regarding trusting 3rd party DAS client with one's password. Our aim here is to try and keep the authz/authn sequence simple for users and leverage their familiarity with social networking tools, and also to simplify implementation of the standalone app (BTW there will be several of those, implemented by others) and other Web-based apps connecting securely to the Atom store. Also, we're trying to generally keep things simple implementation-wise and "secure enough" for our purposes, and thus we're trying to avoid deploying full-blown grid security toolkits which would likely be overkill. Whether the same holds for DAS authn/authz in terms of the level of security required and other factors, I don't know at this time, and will leave open for debate. Hope these musings are helpful!! Best regards, Mummi, Leicester -- Gudmundur A. Thorisson, Brookes lab Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK Tel: +44 (0)116 229 7273 On 13 Apr 2010, at 18:17, Andy Jenkinson wrote: > On 13 Apr 2010, at 17:48, Jim Procter wrote: > >> Thanks for posting this, Andy. >> >> >> On 13/04/2010 14:44, Andy Jenkinson wrote: >>> Afterwards, two proposals emerged: firstly, that the DAS specification make a simple recommendation to use existing HTTP digest authentication, leaving DAS software to implement the components independently. Secondly, a DAS-specific delegated authentication model based around a trusted third party (probably the DAS registry) as the identity provider. >>> >>> Each proposal has its own advantages and disadvantages in terms of both security and implementation considerations which we now need to debate within the community before we come up with a recommendation, so I have summarised both proposals on the wiki: >>> http://www.biodas.org/wiki/DAS1.6E#Authentication >>> >> I didn't participate in the fine details of the discussion last friday, but I wondered afterwards if anyone had considered adopting the Globus authentication model. Grid based authentication for programmatic web services has now been around for a number of years in a number of guises (the Globus toolkit is the one I know of), and may already address all the requirements and concerns raised at the meeting. >> >> My 2c.. >> Jim. >> >> ps. I can point out some people who may be worth approaching regarding Globus or Shibboleth style third-party ident/auth middleware if people wish. > > Definitely worth a shout, I'll do some research. > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From asidhu at biomap.org Mon Apr 26 04:45:05 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Mon, 26 Apr 2010 16:45:05 +0800 Subject: [DAS] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 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 rmb32 at cornell.edu Mon Apr 26 18:02:11 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 15:02:11 -0700 Subject: [DAS] Google Summer of Code - accepted students Message-ID: <4BD60D63.1040400@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Tue Apr 27 01:52:57 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 22:52:57 -0700 Subject: [DAS] Google Summer of Code - accepted students Message-ID: <4BD67BB9.3000804@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Sat Apr 3 20:09:27 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sat, 03 Apr 2010 13:09:27 -0700 Subject: [DAS] Google Summer of Code is *ON* for OBF projects! Message-ID: <4BB7A077.4070802@cornell.edu> Hi all, Reminder: GSoC student proposals must be submitted to Google by April 9th, 19:00 UTC. That's less than a week away. Students: you should ALREADY be working with mentors on the project mailing lists, they can help you get your proposal into shape. So far, we have 5 proposals submitted to our org in Google's web app. Keep them coming, and let's see some really good ones! Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Sun Apr 4 04:37:38 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Sat, 03 Apr 2010 21:37:38 -0700 Subject: [DAS] Reminder: GSoC student applications due April 9, 19:00 UTC Message-ID: <4BB81792.8060001@cornell.edu> Hi all, Sending this again with a different subject line, just in case. GSoC student proposals must be submitted to Google through their web application by *April 9th, 19:00 UTC*. That's less than a week away. Students: you should ALREADY be working with mentors on the project mailing lists, they can help you get your proposal into shape. So far, we have 6 proposals submitted to our org in Google's web app. Keep them coming, and keep them good! Rob Buels OBF GSoC 2010 Administrator From andy.jenkinson at ebi.ac.uk Tue Apr 13 13:44:23 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 13 Apr 2010 14:44:23 +0100 Subject: [DAS] authentication summary Message-ID: Hi all, First of all, thank you to those of you who attended last week's DAS Workshop. I thought we had some interesting talks and, as ever, some productive and thought provoking discussions. As a follow up to the third day's discussion on authentication, I thought I would provide a quick summary: There was an initial overview about the prospect of adopting OpenID delegated authentication in DAS (which is already used by the DAS registry and some DAS clients). Specifically, the core reliance of OpenID on HTTP browser redirects makes in unsuitable for DAS server-server communications. Afterwards, two proposals emerged: firstly, that the DAS specification make a simple recommendation to use existing HTTP digest authentication, leaving DAS software to implement the components independently. Secondly, a DAS-specific delegated authentication model based around a trusted third party (probably the DAS registry) as the identity provider. Each proposal has its own advantages and disadvantages in terms of both security and implementation considerations which we now need to debate within the community before we come up with a recommendation, so I have summarised both proposals on the wiki: http://www.biodas.org/wiki/DAS1.6E#Authentication Please feel free to edit as necessary, and comment on the list. Cheers, Andy From andy.jenkinson at ebi.ac.uk Tue Apr 13 17:17:48 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 13 Apr 2010 18:17:48 +0100 Subject: [DAS] authentication summary In-Reply-To: <4BC4A076.4030901@compbio.dundee.ac.uk> References: <4BC4A076.4030901@compbio.dundee.ac.uk> Message-ID: On 13 Apr 2010, at 17:48, Jim Procter wrote: > Thanks for posting this, Andy. > > > On 13/04/2010 14:44, Andy Jenkinson wrote: >> Afterwards, two proposals emerged: firstly, that the DAS specification make a simple recommendation to use existing HTTP digest authentication, leaving DAS software to implement the components independently. Secondly, a DAS-specific delegated authentication model based around a trusted third party (probably the DAS registry) as the identity provider. >> >> Each proposal has its own advantages and disadvantages in terms of both security and implementation considerations which we now need to debate within the community before we come up with a recommendation, so I have summarised both proposals on the wiki: >> http://www.biodas.org/wiki/DAS1.6E#Authentication >> > I didn't participate in the fine details of the discussion last friday, but I wondered afterwards if anyone had considered adopting the Globus authentication model. Grid based authentication for programmatic web services has now been around for a number of years in a number of guises (the Globus toolkit is the one I know of), and may already address all the requirements and concerns raised at the meeting. > > My 2c.. > Jim. > > ps. I can point out some people who may be worth approaching regarding Globus or Shibboleth style third-party ident/auth middleware if people wish. Definitely worth a shout, I'll do some research. From gthorisson at gmail.com Wed Apr 14 11:33:16 2010 From: gthorisson at gmail.com (Gudmundur A. Thorisson) Date: Wed, 14 Apr 2010 12:33:16 +0100 Subject: [DAS] authentication summary In-Reply-To: References: <4BC4A076.4030901@compbio.dundee.ac.uk> Message-ID: <3CDE9329-04DC-4533-B6BE-189FB7FE9EB9@gmail.com> Hi all. To add my $0.02 to the debate; I whole-heartedly support the delegated auth model, but suggest we try to tease apart the authentication step on one hand (user proving to the DAS registry who he is), and the authorisation-related things on the other (does the authenticated user have access to a given server, or source within a server, or possibly even more fine-grained controls; user managing/requesting access to sources; and more). Also, as something of an alternative approach to "heavier" grid security solutions, it may be worth considering a more Web 2.0 style delegated authz approach based on OAuth (http://oauth.net). In the photo sharing-and-printing example scenarios illustrated in the two tutorials referenced below, one could envision the DAS registry as the site where the photos are hosted (the OAuth provider), and the DAS client as the photo-printing site (the OAuth consumer): http://hueniverse.com/2007/10/beginners-guide-to-oauth-part-ii-protocol-workflow/ http://www.wdvl.com/Authoring/Authorization/OAuthIntro/Jaswinder_Singh03042010.html However, I'll admit that it isn't entirely obvious to me how to accommodate the DAS servers themselves as additional players in these scenarios, unless (as Andy's writeup mentions) the servers accepts tokens issued by the registry. The following may be also useful to the discussion. We have an ongoing project in our group where we're exploring a number of scenarios very similar to the delegated model described by Andy, with a central AtomPub server and authz schemes centred on Atom feeds and feed entries (some of which are protected and others which are not). An authz scenario of particular interest involves a standalone application, from which a user with submission privileleges uploads genetic variation data via a RESTful POST to the central Atom store. The relevance to the present discussion that the submission app above can probably be considered as analoguous to a standalone DAS client, and the central Atom store analoguous to the DAS registry. The model we are keen to use for this is very similar to Flickr photo-uploads, where the user authorises the Flickr Uploadr standalone application (http://www.flickr.com/help/tools/) to send photos to Flickr on his behalf. Importantly, the user does not enter user/pwd credentials in the standalone app itself, but rather is sent to the central website where he signs in (if not already authenticated) and authorises the app. Subsequently, the app can upload data to the until de-authorised by the user, or the token expires (if time-limited). This would seem to address the issue Andy listed regarding trusting 3rd party DAS client with one's password. Our aim here is to try and keep the authz/authn sequence simple for users and leverage their familiarity with social networking tools, and also to simplify implementation of the standalone app (BTW there will be several of those, implemented by others) and other Web-based apps connecting securely to the Atom store. Also, we're trying to generally keep things simple implementation-wise and "secure enough" for our purposes, and thus we're trying to avoid deploying full-blown grid security toolkits which would likely be overkill. Whether the same holds for DAS authn/authz in terms of the level of security required and other factors, I don't know at this time, and will leave open for debate. Hope these musings are helpful!! Best regards, Mummi, Leicester -- Gudmundur A. Thorisson, Brookes lab Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK Tel: +44 (0)116 229 7273 On 13 Apr 2010, at 18:17, Andy Jenkinson wrote: > On 13 Apr 2010, at 17:48, Jim Procter wrote: > >> Thanks for posting this, Andy. >> >> >> On 13/04/2010 14:44, Andy Jenkinson wrote: >>> Afterwards, two proposals emerged: firstly, that the DAS specification make a simple recommendation to use existing HTTP digest authentication, leaving DAS software to implement the components independently. Secondly, a DAS-specific delegated authentication model based around a trusted third party (probably the DAS registry) as the identity provider. >>> >>> Each proposal has its own advantages and disadvantages in terms of both security and implementation considerations which we now need to debate within the community before we come up with a recommendation, so I have summarised both proposals on the wiki: >>> http://www.biodas.org/wiki/DAS1.6E#Authentication >>> >> I didn't participate in the fine details of the discussion last friday, but I wondered afterwards if anyone had considered adopting the Globus authentication model. Grid based authentication for programmatic web services has now been around for a number of years in a number of guises (the Globus toolkit is the one I know of), and may already address all the requirements and concerns raised at the meeting. >> >> My 2c.. >> Jim. >> >> ps. I can point out some people who may be worth approaching regarding Globus or Shibboleth style third-party ident/auth middleware if people wish. > > Definitely worth a shout, I'll do some research. > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From asidhu at biomap.org Mon Apr 26 08:45:05 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Mon, 26 Apr 2010 16:45:05 +0800 Subject: [DAS] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 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 rmb32 at cornell.edu Mon Apr 26 22:02:11 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 15:02:11 -0700 Subject: [DAS] Google Summer of Code - accepted students Message-ID: <4BD60D63.1040400@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator From rmb32 at cornell.edu Tue Apr 27 05:52:57 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Mon, 26 Apr 2010 22:52:57 -0700 Subject: [DAS] Google Summer of Code - accepted students Message-ID: <4BD67BB9.3000804@cornell.edu> Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator