Greetings all...
Those who know me...know that I am a profound PHIN evangelist. This year's conference had a significantly different feel from the previous years - and was...a great conference.
I moderated many sessions - and all were very strong and well attended. Of course, I thought that the GRID-related sessions were outstanding.
Take-away issues: There was a lot of buzz around "grid" - and it's clear that over the next few months, a lot of coordination and communication needs to take place.
From the sessions and ad-hoc meetings I attended, it is very clear to me that we have just cracked open the door into the world of grid / distributed computing. What's behind that door? Something amazing... of this I have no doubt. What will it look like? Time will tell - and that's the beauty of research and discovery.
We are discovering the pieces of the puzzle - and with the amazing collaborative effort of our national and international partners....it's clear that we will be making amazing progress in the months ahead. It's a true privilege to be part of this effort.
Just think for a moment about a few of the pieces of the puzzle we have discovered:
Taverna (essentially yahoo pipes for distributed computing)
DCQL
VBroswer
Globus
MonALISA
OGSA-DAI
GridGrouper
Gridifying Services via caGRID tools
As we work closely with our public health partners - we look forward to providing the public health community powerful new tools and resources.
I can only imagine the progress we will have made - before the 2009 PHIN Conference.
Saturday, August 30, 2008
Friday, August 29, 2008
PHIN Impressions
Pros:
I found the PHIN conference to be a valuable learning experience. I particularly enjoyed visiting the vendors in the exhibit hall and viewing the various Public Health technology solutions.
The session that I enjoyed the most was the Natural Language Processor presentation. The speaker was enthusiastic about the technology and provided insight on real world use cases. It was also nice to understand the technology that we are currently integrating with grid.
Last but not least, I would like to thank the person who came up with the PHIN bag idea. It works great as a laptop bag!
Cons:
I didn’t enjoy the lunch sessions because I had a difficult time hearing the speakers due to the noise level in the room. A separate networking lunch would have been instrumental in reducing the amount of chatter during those sessions.
I found the PHIN conference to be a valuable learning experience. I particularly enjoyed visiting the vendors in the exhibit hall and viewing the various Public Health technology solutions.
The session that I enjoyed the most was the Natural Language Processor presentation. The speaker was enthusiastic about the technology and provided insight on real world use cases. It was also nice to understand the technology that we are currently integrating with grid.
Last but not least, I would like to thank the person who came up with the PHIN bag idea. It works great as a laptop bag!
Cons:
I didn’t enjoy the lunch sessions because I had a difficult time hearing the speakers due to the noise level in the room. A separate networking lunch would have been instrumental in reducing the amount of chatter during those sessions.
My First PHIN Conference Experience
My first PHIN conference experience was awesome. I started my conference experience on Sunday attending two pre-conference sessions, Web2.0 for Public Health and PHIN101, both sessions were very good and provided a wealth of useful information. The next three days were packed with many interesting presentations covering everything from GIS applications to vocabulary. I have included links to some of the tools and projects that were mentioned during some of the sessions I attended, enjoy.
Tools/Projects:
Eclipse Open Health Framework - http://www.eclipse.org/ohf/
Cobertura - http://cobertura.sourceforge.net/
JFreeChart - http://www.jfree.org/jfreechart/
Selenium - http://selenium.openqa.org/
Taverna - http://taverna.sourceforge.net/
ConceptHub - http://www.concepthub.org/wiki/Main_Page
Creative Commons - http://creativecommons.org/
Thin Wire - http://sourceforge.net/projects/thinwire/
Open ID - http://openid.net/
Cruise Control - http://cruisecontrol.sourceforge.net/
Ivy - http://ant.apache.org/ivy/
Public Health Partners - http://phpartners.org/
*** Orange Data Mining - http://www.ailab.si/orange - very interesting gui programming tool using python scripts
Tools/Projects:
Eclipse Open Health Framework - http://www.eclipse.org/ohf/
Cobertura - http://cobertura.sourceforge.net/
JFreeChart - http://www.jfree.org/jfreechart/
Selenium - http://selenium.openqa.org/
Taverna - http://taverna.sourceforge.net/
ConceptHub - http://www.concepthub.org/wiki/Main_Page
Creative Commons - http://creativecommons.org/
Thin Wire - http://sourceforge.net/projects/thinwire/
Open ID - http://openid.net/
Cruise Control - http://cruisecontrol.sourceforge.net/
Ivy - http://ant.apache.org/ivy/
Public Health Partners - http://phpartners.org/
*** Orange Data Mining - http://www.ailab.si/orange - very interesting gui programming tool using python scripts
Thursday, August 28, 2008
Grid UI Update
Here are couple of more UI's for the Grid, I found
1) http://wiki.arcs.org.au/bin/view/Main/FileTransferSGGCUsageGuide
from Australian research collaboration service which has the capabililty for gridFTP, third party transfers, and also a cool feature which is multi replica transfers. Its sort of like bittorrent with the variation like when we have a large file whose copy exists in several locations, we can specify multiple locations from where we want to get the file which will potentially create a local copy of the file faster.
2) The other one is http://commons-vfs-ui.sourceforge.net/ which is a Commons VFS implementation from Apache. It provide support for Storage Resource Broker and GridFTP.
1) http://wiki.arcs.org.au/bin/view/Main/FileTransferSGGCUsageGuide
from Australian research collaboration service which has the capabililty for gridFTP, third party transfers, and also a cool feature which is multi replica transfers. Its sort of like bittorrent with the variation like when we have a large file whose copy exists in several locations, we can specify multiple locations from where we want to get the file which will potentially create a local copy of the file faster.
2) The other one is http://commons-vfs-ui.sourceforge.net/ which is a Commons VFS implementation from Apache. It provide support for Storage Resource Broker and GridFTP.
Face to face collaboration
Due to people being in town for the PHIN conference, we had a face to face meeting this morning with many of the phGrid collaborators.
It's nice to finally put faces to voices and email addresses and even though telepresence is useful, there's still no beating flesh and blood for easily communicating. Although we still had a dial in line as some of us couldn't be there in person.
We talked with Pittsburgh, WashingtonU, UtahU, Johns Hopkins APL, Ohio State BMI, Columbia University and NCPHI Lab.
We recapped the services built and demonstrated and also talked about next steps.
The immediate agreed upon next steps are to plan out how to connect together the services developed by different groups, set up some sort of simple description set of each service to let others know about service information, link to each others public source code repositories, find some specific public health use cases to drive future development and extend our current set of services.
There's actually a lot more around next steps but it is too much to describe in this post. Over the next week, we're collecting the next steps together and will post some more ideas for future proof of concept projects.
We also talked about some ways to approach collaboration and source control. Ohio State has two really good examples of how they do it:
CaGrid Incubator
CaGrid GForge
It's nice to finally put faces to voices and email addresses and even though telepresence is useful, there's still no beating flesh and blood for easily communicating. Although we still had a dial in line as some of us couldn't be there in person.
We talked with Pittsburgh, WashingtonU, UtahU, Johns Hopkins APL, Ohio State BMI, Columbia University and NCPHI Lab.
We recapped the services built and demonstrated and also talked about next steps.
The immediate agreed upon next steps are to plan out how to connect together the services developed by different groups, set up some sort of simple description set of each service to let others know about service information, link to each others public source code repositories, find some specific public health use cases to drive future development and extend our current set of services.
There's actually a lot more around next steps but it is too much to describe in this post. Over the next week, we're collecting the next steps together and will post some more ideas for future proof of concept projects.
We also talked about some ways to approach collaboration and source control. Ohio State has two really good examples of how they do it:
CaGrid Incubator
CaGrid GForge
Tuesday, August 26, 2008
PHIN Conference
The blog has been quiescent this week because the entire team has been at the 2008 PHIN Conference in Atlanta, GA demoing and talking about grid, as well as learning more about public health informatics.
Friday, August 22, 2008
I wasn't able to get the demo to ncphi.phgrid.net yet.
While the demo is set up and running on our internal servers... and we have a way to get into the internal servers for the Phin conference, and while I was able to get the databases and ogsadai bits installed on Dallas (I think) and NCPHI (I know)... I will not be able to get jboss on NCPHI and the demo available for public consumption.
I faced a lot of hurdles that delayed me, including limited server access due to higher priority testing and a 4:00 PM brownout/surge that killed all of our virtual machines. I was tooting along despite that when at 5:30, I discovered that dallas wasn't accessible on port 8443. That is the port OGSA-DAI operates on, and without it I won't be able to see one of the databases needed for the demo.. as a RODSAdai demo isn't that impressive with only one server.
I also tried getting JBoss installed on the NCPHI node, only to find that there were lots of errors generated on startup and a realization that port 8080 is blocked coming in.
Thus, we are facing a big case of interrupted ports, and no-one is in the building who can un-interrupt them.
At least the internal demo is working, and very neat I think.
I faced a lot of hurdles that delayed me, including limited server access due to higher priority testing and a 4:00 PM brownout/surge that killed all of our virtual machines. I was tooting along despite that when at 5:30, I discovered that dallas wasn't accessible on port 8443. That is the port OGSA-DAI operates on, and without it I won't be able to see one of the databases needed for the demo.. as a RODSAdai demo isn't that impressive with only one server.
I also tried getting JBoss installed on the NCPHI node, only to find that there were lots of errors generated on startup and a realization that port 8080 is blocked coming in.
Thus, we are facing a big case of interrupted ports, and no-one is in the building who can un-interrupt them.
At least the internal demo is working, and very neat I think.
Thursday, August 21, 2008
Remaining SRGM Test Cases
The latest version of SRGM_POC test case document is on the wiki right now with test case 4G to be revisited with either a little more elaboration or a change of approach. I am currently working with Vaughn Mcmullin on that. Apart from that, the case 4J ) Evaluate user interface projects for RFT management and operation (including, but not limited to, job starting/stopping/resuming, route management) ( Req. No 16) is what I am looking into. Early in our work we came across vbrowser which covered a lot of ground, in terms of functionality, as one of the possible UI's. So before we move further in this area, upon Brian's recommendation, I am posting a couple of features that we would want to zero in on while evaluating various UI's
1) Support for manual/interactive as well as automatic transfers. Although, as discussed ,automatic transfers could be more of an added feature rather than a basic requirement.
2) Ability to see the status of jobs going on at any particular time by being able to provide a way to query the persistent storage.
3) Capability to stop the jobs manually in the middle of a transfer, which could remove parts of payload already transferred.
4) As we know,Vbrowser is applet based so making a decision whether we would like to have a web based UI for our purpose.
5) Raj(from Globus) mentioned in one of the calls that they do have a UI implementation also so I will be following up with him whether their implementation covers some of these already.
I also found another UI implementation for GridFTP of WISENT, which is an eclipse based, cross-platform, open-source GridFTP client which allows to transfer, view progress and delete files. Although it would be interesting if they provide support for RFT. Please feel free to check out the url (a flash presentation of the application)
http://bi.offis.de/gridftp/screens/gridftp.htm
Please feel free to add what you would think, could be a feature of the UI for GridFTP.
1) Support for manual/interactive as well as automatic transfers. Although, as discussed ,automatic transfers could be more of an added feature rather than a basic requirement.
2) Ability to see the status of jobs going on at any particular time by being able to provide a way to query the persistent storage.
3) Capability to stop the jobs manually in the middle of a transfer, which could remove parts of payload already transferred.
4) As we know,Vbrowser is applet based so making a decision whether we would like to have a web based UI for our purpose.
5) Raj(from Globus) mentioned in one of the calls that they do have a UI implementation also so I will be following up with him whether their implementation covers some of these already.
I also found another UI implementation for GridFTP of WISENT, which is an eclipse based, cross-platform, open-source GridFTP client which allows to transfer, view progress and delete files. Although it would be interesting if they provide support for RFT. Please feel free to check out the url (a flash presentation of the application)
http://bi.offis.de/gridftp/screens/gridftp.htm
Please feel free to add what you would think, could be a feature of the UI for GridFTP.
VBrowser
Communicated through email with Piter T. de Boer from the Informatics Instituut at the University of Amsterdam. We plan to discuss our use of VBrowser as an application and as a plugin development framework after the PHIN Conference next week.
Piter is our first contact with the team developing VBrowswer
Piter is our first contact with the team developing VBrowswer
Wednesday, August 20, 2008
caGrid: DCQL Federated Query Processor News
One thing that Ron just learned regarding DCQL is that the Federated Query Processor (FQP) in caGrid will not support delegation until caGrid1.3 which should be out early 2009. So, currently one can do a federated query with authentication (https only), but authorization does not work.
For instance when we tried this at Utah our data grid services rejected the query from the FQP because the query came in under user workflow and workflow is not authorized.
For instance when we tried this at Utah our data grid services rejected the query from the FQP because the query came in under user workflow and workflow is not authorized.
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