Globus Toolkit 5.0 released

Just retweeting that the GT5.0 is now released. Although a big development over 4.0.x and 4.2.x, this doesn't include all the cool stuff that Crux will bring.

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.

InformationWeek.com - 5 Flavors of Cloud Computing

From the Nov 9, 2009 Issue (Cloud Security Handbook - p 10)

1. Software as a Service
2. Infrastructure as a Service
3. Storage as a Service
4. Platform as a Service
5. Hybrid Clouds

NSF TeraGrid GIS Workshop on Cyber-GIS

National Science Foundation TeraGrid Workshop on Cyber-GIS:

http://www.cigi.uiuc.edu/cybergis/index.php

February 2-3, 2010 - Washington, DC

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:

Complex geospatial systems and simulation of geographic dynamics
Computational intensity of spatial analysis and modeling
Data-intensive geospatial computation and visualization
High-performance, distributed, and/or collaborative GIS
Geospatial ontology and semantic web
Geospatial middleware, Clouds, and Grids
Open source GIS
Participatory spatial decision support systems
Science drivers for, and applications of Cyber-GIS
Spatial data infrastructure


For more information, please contact workshop co-chairs:

Shaowen Wang
National Center for Supercomputing Applications
University of Illinois at Urbana Champaign
shaowen@illinois.edu

Nancy Wilkins-Diehr
San Diego Supercomputing Center
University of California at San Diego
wilkinsn@sdsc.edu

HealthGrid 2010 conference: call for papers, posters and workshops - deadline Feb 15, 2010

HealthGrid 2010 conference: call for papers, posters and workshops

conference web site: http://paris2010.healthgrid.org/

KEY DATES
Call for papers, posters and workshops closes:
February 15th 2010

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

Call for papers and posters
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.
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:
A: ACCESSIBILITY
Challenges to making grids more accessible to bio-medical users
Scientific gateways
Workflow engines
Grid portals
Grid platforms
B: CORE TECHNOLOGIES AND KNOWLEDGE INTEGRATION
Grid technology versus web applications
Data privacy: confidentiality in distributed medical information systems – and the security challenges
Knowledge integration – knowledge management
Semantic techniques and the challenge of integrating heterogeneous biomedical data
Visualization in Grids
C: APPLICATIONS
Bioinformatics
Biomedical informatics
Medical imaging
Public health informatics
Genetics and epidemiological studies
Pharmaceutical R&D: drug discovery, clinical tests
Grid computing and the Virtual Physiological Human (VPH)
D: SOCIO ECONOMIC ASPECTS
Grid business aspects: sustainability and go-tomarket strategies
Experiences on production
Grid used in real business
Grid sociology: how to win society for Grids?
E: THE FUTURE OF GRIDS
Experiences with GP-GPU
Cloud computing, on demand computing
Nanomedecine

Call for workshops
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:
Topic: the workshop topic should be directly related to the conference topics listed in this call.
Duration: all workshops selected through this call will take place Monday afternoon. Duration can be 90 minutes or 210 minutes (including coffee break).
Targeted audience: what is the expected attendance (for room allocation) ?
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.
Name, affiliation and email address of the workshop submitter.

Code-A-Thon

I attended the NHIN CONNECT Code-A-Thon 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 wiki up with notes from the two days worth of sessions.

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.

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.

Vietnam welcomes three new grid sites; hospitals get new ‘HOPE’

.... HOPE (HOspital Platform for E-health) developed jointly at CNRS and HealthGrid in France, allows hospital sites to exchange medical information. HOPE is now installed at the Institute of Information Technology 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..
http://www.isgtw.org/?pid=1002120

Updated SDMX-HD Resource page

I updated the PHGrid wiki section on SDMX-HD.... with this link.

PHGrid Community Update

To the PHGrid Community:

Related to significant organizational change 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 PHGrid wiki (http://wiki.phgrid.net), and to PHGrid-related software in the Google code repository. 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).

-- Tom

So 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.

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.

Grid Computing Technologies for Geospatial Apps

Grid Computing Technologies for Geospatial Applications:

http://ifgi.uni-muenster.de/0/agile/


The gallery is here: http://ifgi.uni-muenster.de/0/agile/gallery.html


Standing room only !! or maybe just grab an open seat....

Project statistics

While creating the transition documentation, I ran some stats on the active code base (not including everying in old-projects) using cloc.

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 282 classes with 25k lines of Java, 2k lines of JSP, 6k lines of comments and documentation. Nothing massive, but it's a decent body of work.

Language	files	blank	comment	code
HTML	579	19160	9724	161640
Java	282	5420	5594	25656
Javascript	35	3098	2779	14490
XML	136	956	998	9448
XSD	20	146	99	4228
SQL	126	425	769	3840
JSP	20	357	95	2368
CSS	12	158	140	1460
Bourne Shell	1	2	0	7
SUM:	1211	29722	20198	223137

Enhanced PHGrid portal wireframe

So, as a step better than a jpg, the PHGrid portal demo is now web-based. Kudos to Chris.

Click HERE to launch...

Code transfer

I finished moving all of the active source projects from sourceforge to google code to support our transitioning off the project.

The following subprojects have been successfully moved (GIPSEPoisonService, GIPSEService, GIPSEServiceInstaller, gmap-polygon, gridviewer were all moved prevously:

• GridMedlee: from sf to gc.


• PHGridLanding: from sf to gc.


• SecureSimpleTransfer: from sf to gc.


• gipse-dbimporter: from sf to gc.


• gipse-store: from sf to gc.


• gipse-poly-web: from sf to gc.


• loader-gmaps-poly: from sf to gc. (this includes the CSVs for settng up the gridviewer GIS tables)


• npds-gmaps: from sf to gc.


• npds-gmaps-web: from sf to gc.


• poicondai: from sf to gc.)


• schemas: from sf to gc. (this includes the schemas and example xml for the GIPSE services)

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.

Successful GIPSEService test

Forgot to post that last week Ron Price and I successfully tested a deployment of the GIPSEService at the Denver DOH.

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 SVN repository).

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).

Sir Tim Berners-Lee: The Semantic Web Has Arrived and the Obama Administration is "Onboard"

http://www.beet.tv/2009/10/sir-tim-bernerslee-the-semantic-web-has-arrived-and-the-obama-administration-is-onboard.html

GAARDS Security implementation.

So, my next task for the coming months is to learn, tinker-with, and hopefully implement some cool bits of the GAARDS service as made by the folks up at Ohio State and their work with CaBIG and CaGrid. 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 summarize things as I understand them, and invite people to correct my summarizations...

Globus 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.

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 Verisign or Thawte. 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 unscalable.

Enter Dorian. Dorian is a GAARDS 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 username and password, or use their operating system credentials, or use a certificate issued by the Node itself instead of a larger third party.

The other critical component is Grid Trust Services (GTS) which allows for grids with different certificate sets to talk to each other and delegate which services on each grid are available to others. It also performs important syncing functions so that updates to access and authentication chains are propagated through the different grids.

There are other bits too, like GridGrouper which allows for simpler group paradigms (members of the group 'Gridviewer' would be able to access various gridviewers 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 GAARDS website

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 GAARDS will answer those use cases and which components are needed to do it.

Then, over the next couple of months, I'll need to implement those pieces and see what service modifications are needed to use them.

GIPSEPoison service move, and GIPSE Service Installers

The GIPSEPoison Service has now moved over to the google code repository (you can check out a read-only copy from http://phgrid.googlecode.com/svn/GIPSEPoisonService/trunk).

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: http://sites.google.com/site/phgrid/Home/service-registry/gipseserviceinstaller.

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.

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.

Open Source Installshield Equivalent

In 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.

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.

Screenshots and additional information can be found at: http://nsis.sourceforge.net/Screenshots

More code migration

I just finished moving over two additional subprojects from our sourceforge repository to the newer google code repository.

From now on, please access gridviewer and gmap-polygon 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.

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.

Note, we're not moving everything over to google code (yet) so there will be some time until all the subprojects come over.

Gridviewer Updates

Gridviewer was updated with the following changes(enhancements):

1. Default state of region query boxes is hidden. Seems to load cleaner.


2. GET Requests are now supported, meaning you can use a URL to generate a specific query.


3. Email link: Added an email link which generates a shorten URL (using bit.ly) and opens a pre-formatted email.


4. Light modifications to javascript for performance and general file size reductions.

http://ncphi.phgrid.net:8080/gridviewer/