tag:blogger.com,1999:blog-76168992451735578522024-03-06T01:50:27.981-05:00Public Health Grid (PHGrid) - Research and DevelopmentCollaborating with our partners to achieve a secure, easy-to-use, technical and social infrastructure for solving large-scale public health problems. Creating an intuitive and powerful user experience. Developing an inexpensive and lightweight data and computational grid infrastructure. Developing robust and intuitive standards-based grid services. Facilitating national health IT integration efforts.Tom Savel, MDhttp://www.blogger.com/profile/03779019277404173906noreply@blogger.comBlogger722125tag:blogger.com,1999:blog-7616899245173557852.post-47770931638316343672010-01-25T11:17:00.004-05:002010-01-25T11:23:28.823-05:00Globus Toolkit 5.0 releasedJust retweeting that the <a href="http://www.globus.org/news.html#164">GT5.0 is now released</a>. Although a big development over 4.0.x and 4.2.x, this doesn't include all the cool stuff that <a href="http://confluence.globus.org/display/CRUX/Crux">Crux</a> will bring.<br /><br />Although the community has pledged support for the 4.x releases through (at least) the end of 2010, there is a recommendation to upgrade to 5.0.0 immediately.Brian Alexander Leehttp://www.blogger.com/profile/04154356447489829768noreply@blogger.com6tag:blogger.com,1999:blog-7616899245173557852.post-8777599463768077412010-01-04T12:01:00.001-05:002010-01-04T12:03:50.085-05:00InformationWeek.com - 5 Flavors of Cloud ComputingFrom the Nov 9, 2009 Issue (Cloud Security Handbook - p 10)<div><ol><li>Software as a Service</li><li>Infrastructure as a Service</li><li>Storage as a Service</li><li>Platform as a Service</li><li>Hybrid Clouds</li></ol></div>Tom Savel, MDhttp://www.blogger.com/profile/03779019277404173906noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-73747421081196121892009-12-24T08:56:00.002-05:002009-12-24T08:58:33.663-05:00NSF TeraGrid GIS Workshop on Cyber-GISNational Science Foundation TeraGrid Workshop on Cyber-GIS:<br /><br />http://www.cigi.uiuc.edu/cybergis/index.php<br /><br />February 2-3, 2010 - Washington, DC<br /><br />The NSF Cyber-GIS workshop will take place in conjunction with the 2010 UCGIS Winter Meeting at Doubletree Hotel, Washington, DC. The workshop will focus on the following themes and topics: <br /> <br />Complex geospatial systems and simulation of geographic dynamics <br />Computational intensity of spatial analysis and modeling <br />Data-intensive geospatial computation and visualization <br />High-performance, distributed, and/or collaborative GIS <br />Geospatial ontology and semantic web <br />Geospatial middleware, Clouds, and Grids <br />Open source GIS <br />Participatory spatial decision support systems <br />Science drivers for, and applications of Cyber-GIS <br />Spatial data infrastructure <br /> <br /><br />For more information, please contact workshop co-chairs: <br /><br /> Shaowen Wang<br />National Center for Supercomputing Applications<br />University of Illinois at Urbana Champaign<br />shaowen@illinois.edu <br /><br />Nancy Wilkins-Diehr<br />San Diego Supercomputing Center<br />University of California at San Diego<br />wilkinsn@sdsc.eduJim Tobiashttp://www.blogger.com/profile/05595788727239094443noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-82570046252835792592009-12-21T15:53:00.000-05:002009-12-21T15:56:55.053-05:00HealthGrid 2010 conference: call for papers, posters and workshops - deadline Feb 15, 2010HealthGrid 2010 conference: call for papers, posters and workshops<br /><br />conference web site: <a href="http://paris2010.healthgrid.org/">http://paris2010.healthgrid.org/</a><br /><br />KEY DATES<br />Call for papers, posters and workshops closes:<br />February 15th 2010<br /><br />The eighth HealthGrid conference will take place June 28-30 2010 at University Paris XI in Orsay (France). Every year, this conference is the opportunity to discuss the state of the art for the integration of grid practices into the fields of biology, medicine and health. This year, it will take place just at the time the European Grid Initiative will start federating the national grid initiatives and propose its resources to the Research Infrastructures. The conference program will include a number of high profile keynote presentations complemented by a set of refereed papers, which will be selected through the present call. Out of the selected papers, the best will be invited for oral presentations and the others for poster presentations. All the selected papers will be published in the book series „Studies in Health Technology and Informatics“ published by IOS Press and referenced in Medline, Scopus, EMCare and Cinahl Databases<br /><br /><u>Call for papers and posters</u><br />Contributions should be made as full research papers (up to 5,000 words in length and maximum 10 pages). Selection for oral or poster presentation will be based on the content of the submitted papers, the originality of their contribution, technical quality, style and clarity of presentation, and importance to the field. Oral presentations could include demonstrations.<br />All papers must be submitted electronically. Please refer to the conference website for upload instructions. The guidelines for authors and support tools are those of the series „Studies in Health Technology and Informatics“ (see URLs below). Papers are invited in, but not limited to, the following areas and topics:<br /><u>A: ACCESSIBILITY</u><br />Challenges to making grids more accessible to bio-medical users<br />Scientific gateways<br />Workflow engines<br />Grid portals<br />Grid platforms<br /><u>B: CORE TECHNOLOGIES AND KNOWLEDGE INTEGRATION<br /></u>Grid technology versus web applications<br />Data privacy: confidentiality in distributed medical information systems – and the security challenges<br />Knowledge integration – knowledge management<br />Semantic techniques and the challenge of integrating heterogeneous biomedical data<br />Visualization in Grids<br /><u>C: APPLICATIONS<br /></u>Bioinformatics<br />Biomedical informatics<br />Medical imaging<br />Public health informatics<br />Genetics and epidemiological studies<br />Pharmaceutical R&D: drug discovery, clinical tests<br />Grid computing and the Virtual Physiological Human (VPH)<br /><u>D: SOCIO ECONOMIC ASPECTS<br /></u>Grid business aspects: sustainability and go-tomarket strategies<br />Experiences on production<br />Grid used in real business<br />Grid sociology: how to win society for Grids?<br /><u>E: THE FUTURE OF GRIDS<br /></u>Experiences with GP-GPU<br />Cloud computing, on demand computing<br />Nanomedecine<br /><br /><strong><u>Call for workshops<br /></u></strong>This year, the conference Program Committee calls for workshops. On Monday afternoon, June 28th 2010, parallel workshops are scheduled from 2.30 pm to 6pm. Workshop proposals should include the following information:<br />Topic: the workshop topic should be directly related to the conference topics listed in this call.<br />Duration: all workshops selected through this call will take place Monday afternoon. Duration can be 90 minutes or 210 minutes (including coffee break).<br />Targeted audience: what is the expected attendance (for room allocation) ?<br />Format: do you wish to invite the speakers or to call for contributions? The contributions to the workshops will not be included in the conference proceedings.<br />Name, affiliation and email address of the workshop submitter.Muzna Mirzahttp://www.blogger.com/profile/00554628838743401720noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-89111035032612934712009-11-24T09:09:00.003-05:002009-11-24T09:15:46.913-05:00Code-A-ThonI attended the <a href="http://www.connectopensource.org/pages/viewpage.action?pageId=24510467">NHIN CONNECT Code-A-Thon</a> in Portland, Oregon last week. It was two days of developers planning out and working on the next release of the NHIN CONNECT software (v2.3). There's a <a href="http://www.connectopensource.org/display/CONNECTWIKI/Code-a-thon+Wiki+%28Fall+2009%29">wiki</a> up with notes from the two days worth of sessions.<br /><br />But the interesting, relevant piece was when they started talking about future architecture. Two of the future topics (out of probably 20 or so) were grid computing and cloud computing. Because of the distributed nature of NHIN (CONNECT nodes everywhere), we had a short discussion about how data and computing power can be spread around in a distributed manner. Specifically, the question of hadoop and map-reduce was brought up about how jobs can be spread out over NHIN and NHIN-compatible systems.<br /><br />On the whole, a pretty remarkable mini-con. This is a new approach to Federal open source projects and refreshing that OSS has come so far.Brian Alexander Leehttp://www.blogger.com/profile/04154356447489829768noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-7179156682909245652009-11-04T10:59:00.001-05:002009-11-04T11:01:38.008-05:00Vietnam welcomes three new grid sites; hospitals get new ‘HOPE’.... HOPE (<a href="http://eu-acgt.org/news/newsletters/summer-2009/single-article/archive/2009/july/article/hope-hospital-platform-for-e-health.html" target="_blank">HOspital Platform for E-health</a>) developed jointly at CNRS and <a href="http://healthgrid.org/" target="_blank">HealthGrid</a> in France, allows hospital sites to exchange medical information. HOPE is now installed at the <a href="http://www.ioit.ac.vn/pages/index.asp?lang=1" target="_blank">Institute of Information Technology</a> in Ho Chi Minh City, formerly Saigon, for testing. All going well, it will be installed in the primary Ho Chi Minh hospital.... read more..<br /><a href="http://www.isgtw.org/?pid=1002120">http://www.isgtw.org/?pid=1002120</a>Muzna Mirzahttp://www.blogger.com/profile/00554628838743401720noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-70046771853404158712009-10-27T10:02:00.001-04:002009-10-27T10:03:56.175-04:00Updated SDMX-HD Resource pageI updated the PHGrid wiki section on SDMX-HD.... with <a href="http://groups.google.com/group/sdmx_hd/web/links?_done=%2Fgroup%2Fsdmx_hd%3Fhl%3Den%26&hl=en">this </a>link.Tom Savel, MDhttp://www.blogger.com/profile/03779019277404173906noreply@blogger.com4tag:blogger.com,1999:blog-7616899245173557852.post-29859317200772347102009-10-23T04:47:00.000-04:002009-10-23T04:48:23.886-04:00PHGrid Community UpdateTo the PHGrid Community:<br /><br />Related to significant <a href="http://blogs.sciencemag.org/scienceinsider/2009/08/new-chief-order.html">organizational change</a> currently underway, the internal team supporting the PHGrid activities within NCPHI has transitioned to other projects. To assist in this transition, we have provided many updates to PHGrid documentation (technical and project) posted to the <a href="http://wiki.phgrid.net/">PHGrid wiki</a> (http://wiki.phgrid.net), and to PHGrid-related software in the <a href="http://code.google.com/p/phgrid/">Google code repository</a>. If anyone has any questions relating to this change, or PHGrid software / services, please don't hesitate to contact me. We look forward to continued PHGrid research activities upon completion of the reorganization. It has been my sincere pleasure to work with the NCPHI PHGrid team (Brian, John, Peter, Dan, Chris, Moses, Joseph).<br /><br />-- TomTom Savel, MDhttp://www.blogger.com/profile/03779019277404173906noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-26436677115036190842009-10-19T17:27:00.002-04:002009-10-19T17:30:37.125-04:00So long and thanks for all the fish...Thank you to everyone I've worked with over the years as part of the public health informatics research grid project. I've met some extremely bright individuals and had a chance to collaborate with some extremely rare organizations and groups.<br /><br />Although moving off the project formally (i.e. I won't get paid for contributing), I'll still be participating through the loose system of collaboration that the project uses to create the blog, wiki and software elements.Brian Alexander Leehttp://www.blogger.com/profile/04154356447489829768noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-63493359691656290832009-10-17T16:40:00.003-04:002009-10-17T16:43:55.523-04:00Grid Computing Technologies for Geospatial AppsGrid Computing Technologies for Geospatial Applications: <br /><br />http://ifgi.uni-muenster.de/0/agile/<br /><br /><br />The gallery is here: http://ifgi.uni-muenster.de/0/agile/gallery.html<br /><br /><br />Standing room only !! or maybe just grab an open seat....Jim Tobiashttp://www.blogger.com/profile/05595788727239094443noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-85785268392267904192009-10-16T10:27:00.002-04:002009-10-16T10:41:46.795-04:00Project statisticsWhile creating the transition documentation, I ran some stats on the active code base (not including everying in <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/old-projects/">old-projects</a>) using <a href="http://cloc.sourceforge.net">cloc</a>.<br /><br />I'm not really a fan of measuring quality by number of lines of code (since good programmers produce fewer lines of code than bad but busy programmers), and a lot of this is boilerplate, etc. But I think it's worth noting that with just a limited team, we made <strong>282 classes</strong> with <strong>25k lines of Java</strong>, <strong>2k lines of JSP</strong>, <strong>6k lines of comments and documentation</strong>. Nothing massive, but it's a decent body of work.<br /><br /><table><tr><td>Language</td><td>files</td><td>blank</td><td>comment</td><td>code</td></tr><tr><td>HTML</td><td>579</td><td>19160</td><td>9724</td><td>161640</td></tr><tr><td>Java</td><td>282</td><td>5420</td><td>5594</td><td>25656</td></tr><tr><td>Javascript</td><td>35</td><td>3098</td><td>2779</td><td>14490</td></tr><tr><td>XML</td><td>136</td><td>956</td><td>998</td><td>9448</td></tr><tr><td>XSD</td><td>20</td><td>146</td><td>99</td><td>4228</td></tr><tr><td>SQL</td><td>126</td><td>425</td><td>769</td><td>3840</td></tr><tr><td>JSP</td><td>20</td><td>357</td><td>95</td><td>2368</td></tr><tr><td>CSS</td><td>12</td><td>158</td><td>140</td><td>1460</td></tr><tr><td>Bourne Shell</td><td>1</td><td>2</td><td>0</td><td>7</td></tr><tr><td>SUM:</td><td>1211</td><td>29722</td><td>20198</td><td>223137</td></tr></table>Brian Alexander Leehttp://www.blogger.com/profile/04154356447489829768noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-28014276616839115842009-10-14T13:45:00.002-04:002009-10-14T13:47:39.828-04:00Enhanced PHGrid portal wireframeSo, as a step better than a jpg, the PHGrid portal demo is now web-based. Kudos to Chris.<br /><br />Click <a href="http://app.mockflow.com/mockflow/view.jsp?pid=PB82DFFCB99DA777EA055CE36063BAF24&id=B6CEFE3AFF9681EAB44FCE3713944352">HERE</a> to launch...Tom Savel, MDhttp://www.blogger.com/profile/03779019277404173906noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-23907170556276171642009-10-14T13:36:00.005-04:002009-10-14T16:38:44.151-04:00Code transferI finished moving all of the active source projects from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/">sourceforge</a> to <a href="http://code.google.com/p/phgrid/source/browse/">google code</a> to support our transitioning off the project.<br /><br />The following subprojects have been successfully moved (<a href="http://code.google.com/p/phgrid/source/browse/#svn/GIPSEPoisonService">GIPSEPoisonService</a>, <a href="http://code.google.com/p/phgrid/source/browse/#svn/GIPSEService">GIPSEService</a>, <a href="http://code.google.com/p/phgrid/source/browse/#svn/GIPSEServiceInstaller">GIPSEServiceInstaller</a>, <a href="http://code.google.com/p/phgrid/source/browse/#svn/gmap-polygon">gmap-polygon</a>, <a href="http://code.google.com/p/phgrid/source/browse/#svn/gridviewer">gridviewer</a> were all moved prevously:<br /><ul><br /><li>GridMedlee: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/GridMedlee/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/GridMedlee">gc</a>.</li><br /><li>PHGridLanding: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/PHGridLanding/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/PHGridLanding">gc</a>.</li><br /><li>SecureSimpleTransfer: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/SecureSimpleTransfer/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/SecureSimpleTransfer">gc</a>.</li><br /><li>gipse-dbimporter: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/gipse-dbimporter/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/gipse-dbimporter">gc</a>.</li><br /><li>gipse-store: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/gipse-store/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/gipse-store">gc</a>.</li><br /><li>gipse-poly-web: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/gipse-poly-web/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/gipse-poly-web">gc</a>.</li><br /><li>loader-gmaps-poly: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/loader-gmaps-poly/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/gipseloader-gmaps-poly">gc</a>. (this includes the CSVs for settng up the gridviewer GIS tables)</li><br /><li>npds-gmaps: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/npds-gmaps/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/npds-gmaps">gc</a>.</li><br /><li>npds-gmaps-web: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/npds-gmaps-web/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/npds-gmaps-web">gc</a>.</li><br /><li>poicondai: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/poicondai/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/poicondai">gc</a>.)</li><br /><li>schemas: from <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/schemas/">sf</a> to <a href="http://code.google.com/p/phgrid/source/browse/#svn/schemas">gc</a>. (this includes the schemas and example xml for the GIPSE services)</li><br /></ul><br />The sf projects will be left intact so as not to break any links, but all activity will be made on the google side from today onward.Brian Alexander Leehttp://www.blogger.com/profile/04154356447489829768noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-72759842819452642692009-10-14T10:13:00.003-04:002009-10-14T10:16:26.572-04:00Successful GIPSEService testForgot to post that last week Ron Price and I successfully tested a deployment of the GIPSEService at the Denver DOH.<br /><br />Ron, working with Art Davidson, set up a synthetic aggregate data set and then he deployed an instance of the GIPSEService (8/31 gipse spec from the <a href="http://code.google.com/p/phgrid/">SVN repository</a>).<br /><br />I was then able to submit a test query from the NCPHI Lab using lab credentials that was successfully processed by the GIPSEService and sent back a response document containing the relevant observation set. Also, I tested with inappropriate credentials from unauthorized locations and I was not able to access the service (as expected since Ron's security controls prevent access by unauthorized users or locations).Brian Alexander Leehttp://www.blogger.com/profile/04154356447489829768noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-40138926326111461282009-10-09T20:02:00.002-04:002009-10-09T20:02:54.733-04:00Sir Tim Berners-Lee: The Semantic Web Has Arrived and the Obama Administration is "Onboard"<a href="http://www.beet.tv/2009/10/sir-tim-bernerslee-the-semantic-web-has-arrived-and-the-obama-administration-is-onboard.html">http://www.beet.tv/2009/10/sir-tim-bernerslee-the-semantic-web-has-arrived-and-the-obama-administration-is-onboard.html</a>Tom Savel, MDhttp://www.blogger.com/profile/03779019277404173906noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-28672804919080826102009-10-08T17:12:00.002-04:002009-10-08T17:50:44.515-04:00GAARDS Security implementation.So, my next task for the coming months is to learn, tinker-with, and hopefully implement some cool bits of the <span class="blsp-spelling-error" id="SPELLING_ERROR_0">GAARDS</span> service as made by the folks up at Ohio State and their work with <span class="blsp-spelling-error" id="SPELLING_ERROR_1">CaBIG</span> and <span class="blsp-spelling-error" id="SPELLING_ERROR_2">CaGrid</span>. After a few preliminary readings of white papers and discussions with other people who have investigated various security models, I'm going to try and <span class="blsp-spelling-corrected" id="SPELLING_ERROR_3">summarize</span> things as I understand them, and invite people to correct my <span class="blsp-spelling-error" id="SPELLING_ERROR_4">summarizations</span>...<br /><br /><span class="blsp-spelling-error" id="SPELLING_ERROR_5">Globus</span> works with X.509 certificates. To save a lot of complicated two-stepping, I'd say the easiest way to think of a certificate is as a licence with a special key embedded in them. Two nodes wanting to talk to each other have to present their certificates order to access services and establish secure communication, and the nodes have to "trust" each others certificates.<br /><br />The way to get "automatic" trust without having to add keys into individual trust stores would be to have all the certificates issued by a trusted third party like <span class="blsp-spelling-error" id="SPELLING_ERROR_6">Verisign</span> or <span class="blsp-spelling-error" id="SPELLING_ERROR_7">Thawte</span>. This is like getting a passport or a drivers license as ID instead of having a business card with your name on it. It is also expensive, and to have to do it for every node on the grid beyond 5-node grids is pretty much <span class="blsp-spelling-error" id="SPELLING_ERROR_8">unscalable</span>.<br /><br />Enter Dorian. Dorian is a <span class="blsp-spelling-error" id="SPELLING_ERROR_9">GAARDS</span> component and is essentially a Grid Service that allows other authentication methods to be used to access the grid. On one hand, it allows for someone to say "people authenticated by [method] at [node] are allowed to access these grid services". Thus, instead of having to have a certificate, one might just need to enter a <span class="blsp-spelling-error" id="SPELLING_ERROR_10">username</span> and password, or use their operating system credentials, or use a certificate issued by the Node itself instead of a larger third party.<br /><br />The other critical component is Grid Trust Services (<span class="blsp-spelling-error" id="SPELLING_ERROR_11">GTS</span>) which allows for grids with different certificate sets to talk to each other and delegate which services on each grid are <span class="blsp-spelling-corrected" id="SPELLING_ERROR_12">available</span> to others. It also performs important syncing functions so that updates to access and authentication chains are propagated through the different grids. <br /><br />There are other bits too, like <span class="blsp-spelling-error" id="SPELLING_ERROR_13">GridGrouper</span> which allows for simpler group paradigms (members of the group '<span class="blsp-spelling-error" id="SPELLING_ERROR_14">Gridviewer</span>' would be able to access various <span class="blsp-spelling-error" id="SPELLING_ERROR_15">gridviewers</span> on different nodes... ) and Web Service Single Sign On which would allow an easy port for web applications to gain access to grid services... and you can read about it at the <a href="https://www.cagrid.org/display/gaards/Home"><span class="blsp-spelling-error" id="SPELLING_ERROR_16">GAARDS</span> website </a><br /><br />Either way, I am at the periphery of understanding right now. I hope within a couple of days to have a really good grip on how security works now (and it's limitations) use cases for what we need, and a stronger correlation to how <span class="blsp-spelling-error" id="SPELLING_ERROR_17">GAARDS</span> will answer those use cases and which components are needed to do it.<br /><br />Then, over the next couple of months, I'll need to implement those <span class="blsp-spelling-corrected" id="SPELLING_ERROR_18">pieces</span> and see what service modifications are needed to use them.Peter White with Deloittehttp://www.blogger.com/profile/17191553251151047642noreply@blogger.com1tag:blogger.com,1999:blog-7616899245173557852.post-19388342980043684732009-10-07T16:15:00.003-04:002009-10-07T16:45:29.539-04:00GIPSEPoison service move, and GIPSE Service InstallersThe GIPSEPoison Service has now moved over to the google code repository (you can check out a read-only copy from <a href="http://phgrid.googlecode.com/svn/GIPSEPoisonService/trunk">http://phgrid.googlecode.com/svn/GIPSEPoisonService/trunk</a>).<br /><br />But, one of the things that I have been doing has been making an ant-fueled bundle that will install both the GIPSEPoisonService and the GIPSEService with a single ant command. You can read about that here: <a href="http://sites.google.com/site/phgrid/Home/service-registry/gipseserviceinstaller">http://sites.google.com/site/phgrid/Home/service-registry/gipseserviceinstaller</a>.<br /><br />It essentially uses a properties file to download code from a repository, deploys other service-specific properties files to the downloaded code, and then calls the downloaded code's build and deploy scripts. <br /><br />The idea is that for future service deploys, I can just email Dan a zip with the appropriate properties files and say "unzip this as [user] and then run 'ant all'". My next hope is to try and see if I can make a mvn based download script so that I can make similar installers for things like GIPSEService. The other cool thing is that both ant and mvn should be easily callable by the NSIS installer that Dan found.Peter White with Deloittehttp://www.blogger.com/profile/17191553251151047642noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-3398586231751920202009-10-05T13:42:00.002-04:002009-10-05T13:59:24.685-04:00Open Source Installshield EquivalentIn an effort to reduce the complexity of installing grid nodes, I have been evaluating Open Source products that will allow us to create an automated installer. The goal is to have a user download grid software from PHgid and execute the install program that would install a node with minimal user interaction.<br /><br />Nullsoft Scriptable Install System (NSIS) is one noteworthy product that stands up to this task. NSIS requires low system overhead, it's Windows compatible, scriptable, and it supports multiple compression methods. <br /><br />Screenshots and additional information can be found at: <a href="http://nsis.sourceforge.net/Screenshots">http://nsis.sourceforge.net/Screenshots</a>Daniel Washingtonhttp://www.blogger.com/profile/02605239879049567214noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-37699847377341691532009-10-02T17:42:00.003-04:002009-10-02T17:48:40.154-04:00More code migrationI just finished moving over two additional subprojects from our <a href="http://phgrid.svn.sourceforge.net/viewvc/phgrid/?sortby=date#dirlist">sourceforge repository</a> to the newer <a href="http://code.google.com/p/phgrid/source/browse/#svn/">google code repository</a>.<br /><br />From now on, please access <a href="http://code.google.com/p/phgrid/source/browse/#svn/gridviewer/trunk">gridviewer</a> and <a href="http://code.google.com/p/phgrid/source/browse/#svn/gmap-polygon/trunk">gmap-polygon</a> through google code. The sf version will stick around for a while to minimize inconvenience of repository switching, but eventually it will be replaced with just a pointer to the google code repository.<br /><br />We're switching to google's site for a few minor reasons: 1) the issue tracking / wiki software is better. It lets you create pretty clean workflows through their tagging system; 2) the code review feature is useful; 3) their Subversion server is quite faster than sourceforge's; and 4) it's easy to switch, so we can switch back to sourceforge if it becomes better.<br /><br />Note, we're not moving everything over to google code (yet) so there will be some time until all the subprojects come over.Brian Alexander Leehttp://www.blogger.com/profile/04154356447489829768noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-30182779079941808692009-10-01T13:26:00.006-04:002009-10-01T13:30:06.324-04:00Gridviewer Updates<span class="Apple-style-span" style=" white-space: pre-wrap; font-family:'Lucida Grande';font-size:11px;">Gridviewer was updated with the following changes(enhancements): <br /><ol><br /><li>Default state of region query boxes is hidden. Seems to load cleaner.</li><br /><li>GET Requests are now supported, meaning you can use a URL to generate a specific query. </li><br /><li>Email link: Added an email link which generates a shorten URL (using <a href="http://bit.ly/">bit.ly</a>) and opens a pre-formatted email.</li><br /><li>Light modifications to javascript for performance and general file size reductions.</li></ol> <br /><a href="http://ncphi.phgrid.net:8080/gridviewer/">http://ncphi.phgrid.net:8080/gridviewer/</a></span><br /><br/>chris mcilvoyhttp://www.blogger.com/profile/03893222570885810558noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-9864220417215711432009-09-29T16:36:00.002-04:002009-09-29T16:49:41.387-04:00GIPSEPoison supporting zipcodes, now onto easier installersSo, after a lot of planning, I finally managed to get general zip5 and zip3 support working in the GIPSEPoison service. I got it so that the service would only ever have to make two calls to the NPDS-poison service (one for states, one for zips) and that it could return zip3 and zip5 and state results simultaneously, and checked in the code after testing it.<br /><br />The next thing I am planning to work on is some ant scripting for building and deploying the service in one simple command. The hope is that it will turn the install process for this service into a simple command thus turning about ten steps into about a two step process (one if you are repeating the process or just installing a patch).<br /><br />Otherwise, it seems the farther future involves the generation of more services, more intricate installers, portals and other service/viewer aggregators. My hope is to just start creating things that make fetching and installing these items as easy as possible.<br /><br />CheersPeter White with Deloittehttp://www.blogger.com/profile/17191553251151047642noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-75974667529445229622009-09-28T14:38:00.003-04:002009-09-28T14:44:23.513-04:00Unsupported Class Version ErrorThe error:<br />Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file<br /><br />Explanation:<br />This happens when you have compiled a jar file with a newer version of Java and executing it with an older version of Java.<br /><br />The Solution:<br />Either upgrade that Java version on the executing machine or recompile the code with the correct version.Daniel Washingtonhttp://www.blogger.com/profile/02605239879049567214noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-9014660482055085472009-09-25T11:08:00.002-04:002009-09-25T11:16:30.302-04:00Gridviewer deploymentThe latest version of Gridviewer has been deployed this morning on the training node. It has all the latest security additions.<br /><br />http://ncphi.phgrid.net:8080/gridviewer/chris mcilvoyhttp://www.blogger.com/profile/03893222570885810558noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-54469020124243624112009-09-24T16:10:00.004-04:002009-09-24T16:26:53.463-04:00Invalid Encoding Name in Tomcat 6Here's an error message you may come across when deploying Globus to Tomcat 6. This error message happens when Tomcat is started.<br /><br /><br />SEVERE: Parse Fatal Error at line 1 column 40: Invalid encoding name "cp1252".org.xml.sax.SAXParseException: Invalid encoding name "cp1252".<br /><br />Use the following procedure to correct the error:<br /><br />1. Change directory to %CATALINA_HOME%\conf<br />2. Open tomcat-users.xml in a text editor<br />3. Look at the first line of the file and change encoding='cp1252' to encoding='utf-8'<br />4. Save the file and restart TomcatDaniel Washingtonhttp://www.blogger.com/profile/02605239879049567214noreply@blogger.com0tag:blogger.com,1999:blog-7616899245173557852.post-25361440227022816172009-09-24T10:58:00.004-04:002009-09-24T11:34:09.334-04:00A web-based portal for PHGrid - Initial screenshots for discussionI keep thinking about the public health workforce….and their most-likely perspective on our PHGrid activity. My thought is, what matters to them is that they are provided a new, robust and intuitive resource at their disposal that makes their work easier - not that it's a cool technology based on the globus toolkit, and leverages grid computing.<br /><br />Thus, to better demonstrate to the public heath community the potential capability of the PHGrid architecture and ecosystem, I created some wireframe mockups articulating my thoughts around a web-based PHGrid portal. The goal of this is to demonstrate to users that PHGrid is not just about 1 GIPSE (aggregate data) service and 1 web-based geographic mapping "viewer" (i.e., a PHGrid Gadget)- but about a dynamic ecosystem potentially consisting of hundreds of different PHGrid resources (services, applications, Gadgets, etc) created by many and shared among many. This portal would provide a user-friendly, single, secure, access point to PHGrid resources (services, applications, Gadgets, Data, Computational power, etc.).<br /><br />These wireframe screenshots are very crude….have many errrors, and are in no way exhaustive. They are at least a starting point for discussion.<br /><br />Of course, there may end up being many more features of the portal - but I really do see it requiring 3 fundamental components:<br /><br />1. <a href="http://8516705459778631629-a-1802744773732722657-s-sites.googlegroups.com/site/phgrid/Home/resource-documents/PHGridPortalMainPage.jpg?attachauth=ANoY7cpauK0p1JDe2_qpUlDs3UOQyKe81d5fCfRouSUWv11KTy59MwrKHBpZM4wXXolECL43e2GVKIQ-JHAuqkjFuXB2DrtVg7WCLqRZfIu5c_s8mMjUeu4PvbykhejKvbwn5aOd2JTPYcgZbAozkN67RXA71_gAQLo4JkjkBSh-G1vWPfNrwI335w7Ym-sgKc-k2O86SUHeNlKQAvG3eFLSRPI0cL1FV31s7r8EyNowjPPuRY2_fy4%3D&attredirects=0">General, secure, customizable PHGrid dashboard</a>. I see this as a combination of MyYahoo, iGoogle, and iTunes for PHGrid. It combines, for example, social networking, eLearning, news, alerting, and statistics.<br /><br />2. <a href="http://8516705459778631629-a-1802744773732722657-s-sites.googlegroups.com/site/phgrid/Home/resource-documents/PHGridPortalDirectoryPage.jpg?attachauth=ANoY7coGERaazNDD-OV_S2f9Fct55xQg1c9PG0LB_FU5YSf24ilGuVnNWV3ahMjA3pBs1_mf9D22_G-37iBFfsY9XRABfYFsrkxsRxtzR4qHf06zXLWHmbg81vIPWcJzaX1012tPs-7950tJOWdZs5AGOOfT0hxf3RpX2tLgVj7i8okn0woS7Vn30pVLnMIehdnycU8fsueFur46PP3-OQS9k52NISSNO04rgsG8LE3bSevd4v2kzNrpgHVnfiYrUGHhdOJirg-Q&attredirects=0"> Real-time directory of available PHGrid resources</a>. This combines features of an automated standards-based (UDDI) registry with integrated social aspects of eBay and Amazon.com. Users can quickly look for specific resources (services, applications, etc), examine their strengths and weaknesses, and ultimately request access to the resource. In other words, this part of the portal provides user-friendly access to a dynamic PHGrid resource ecosystem.<br /><br />3. <a href="http://8516705459778631629-a-1802744773732722657-s-sites.googlegroups.com/site/phgrid/Home/resource-documents/PHGridPortalMyGridPage.jpg?attachauth=ANoY7cruWluM3stWnh-W_Yi0tqV-7U6v0BObwZykjzt4YY60kfSEm-MS-0gbLeHOpIpXDUQjSQ_ETJA3qlg-R9-vyucbXLeYKFjFcCC7qPlAgMl-gX5wELItPX5NuwJGcDBM5uk5T27OGTwBl9trDT3u2vBKHcLEAun1qJIy-v_bkrEz1Kj9OenH2bjCHyqv7gyrp37O-G1kH6ettkxr0c7AGRNAfiW8yejlQbCW-kkvqN-SxR57CIjFZ9VMX8NFO5kFBXb98d2E&attredirects=0"> MyGrid</a> - A user-defined PHGrid "workbench." This part of the portal allows users to customize a pallet of resources which are important / relevant to them - and which simplifies the process of organizing PHGrid resources.<br /><br />Depending on the access control requirements - the user may be able to obtain immediate access to the resource- or may have to wait for the resource provider to grant access. Some resources may even require a document to be filled out and submitted. As can be seen in the Access Status feature of the site, this feature will allow the requesting user to monitor the status of his/her request - regardless of the specific process. Once the user has been granted authorization, he/she can use the Service/Gadget Automation tool to create ad-hoc and recurrent workflows / macros - tying together multiple resources. This would have aspects of both the taverna workbench and yahoo pipes. Clearly this area needs a lot of work..but I feel it may grow into a much larger aspect of the site.<br /><br />Here is an example of a workflow (i.e., a macro) that could be created and saved - to be run at any time - or automated to run on a recurrent based:<br /><br />After logging into the system with their secure credentials, a state epidemiologist goes to the MyGrid part of the portal. They then complete the following steps:<br /><br />1. Requests specific data elements from data source X [service a]<br />2. Combines this data with data from source y [service b]<br />3. Runs a Natural Language Processing (NLP) engine on one data field from source y to convert a large chunk of text from a family history field into discrete coded data elements [service c]<br />4. Performs geospatial analytics on the newly generated data set z [service d]<br />5. Visualizes the analytic output using specific criterial [gadget e]<br />6. Creates images from the visualization tool and exports them to a web-based tool to be accessed by his/her colleagues at the local and county health departments within that state [service f and gadget g]<br />7. The user saves this workflow, and configures it to run every night at midnight.<br /><br />I look forward to others thoughts on this. My hope is that we can create a very rough mock-up of this in the near future. It's my belief that it is only through the creation of a resource such as this, that we can clearly articulate the real value of PHGrid's robust, secure, SOA-based architecture / ecosystem to the overall public health community, and not just to the IT and informatics savvy public health workforce.<br /><br />Thanks! TomTom Savel, MDhttp://www.blogger.com/profile/03779019277404173906noreply@blogger.com3