Today I have been working on the use cases for a new little demo project I am dubbing PoiConDAI.
It is basically the consumption of a service that Dr. Jeremy has already created for listing Poison Control Center call volume data. I finalized some of the rough cases (as shown in the linked document) and tomorrow I will probably start playing more with AXIS and perhaps Introduce for making a quick client in anticipation of receiving the WSDL for the service.
Otherwise, I am working on next steps for RODSADai, including scalability improvements, security improvements, and a general design and design-process review with the folks of OGSA-DAI.
Tuesday, September 9, 2008
EARS, EpiInfo and Grid
Had very interesting meetings with two CDC teams :
1- the EARS team (early aberration reporting system)
2- the EpiInfo team
Both groups are very interested in working with the Grid research team -and investigating potential services based on their products that could be shared on the grid, as well as ways the grid could augment the value of their existing products. Should prove to be very interesting and fruitful. Will keep you all posted.
1- the EARS team (early aberration reporting system)
2- the EpiInfo team
Both groups are very interested in working with the Grid research team -and investigating potential services based on their products that could be shared on the grid, as well as ways the grid could augment the value of their existing products. Should prove to be very interesting and fruitful. Will keep you all posted.
JAMIA Article today
Greetings all:
The Sept/Oct 2008 Issue of The Journal of the American Medical Informatics Association came out today.
P. 705 - 706 In Response to: What Is a Grid?
Click HERE to read the article
The Sept/Oct 2008 Issue of The Journal of the American Medical Informatics Association came out today.
P. 705 - 706 In Response to: What Is a Grid?
Click HERE to read the article
Monday, September 8, 2008
New Listserv/Distribution Lists Created
Four new distributions lists have been created to enhance and simplify collaboration
ncphi@phgrid.net - Core NCPHI Group
poc1@phgrid.net - Initial Proof-of-Concept Group (NCPHI, Tarrant, Dallas & U. of Pitt)
public.health@phgrid.net - Specific focus on public health issues, business cases, use cases
technical@phgrid.net - Specific focus on technical issues relative to PHI Research Grid
Each of these distributions lists may be queried and manipulated using the following email addresses:
Help address ncphi-help@phgrid.net (for example, poc1-help or technical-help)
Subscription address ncphi-subscribe@phgrid.net (for example, poc1-subscribe or technical-subscribe)
Unsubscription address ncphi-unsubscribe@phgrid.net (for example, poc1-unsubscribe or poc1-unsubscribe)
ncphi@phgrid.net - Core NCPHI Group
poc1@phgrid.net - Initial Proof-of-Concept Group (NCPHI, Tarrant, Dallas & U. of Pitt)
public.health@phgrid.net - Specific focus on public health issues, business cases, use cases
technical@phgrid.net - Specific focus on technical issues relative to PHI Research Grid
Each of these distributions lists may be queried and manipulated using the following email addresses:
Help address ncphi-help@phgrid.net (for example, poc1-help or technical-help)
Subscription address ncphi-subscribe@phgrid.net (for example, poc1-subscribe or technical-subscribe)
Unsubscription address ncphi-unsubscribe@phgrid.net (for example, poc1-unsubscribe or poc1-unsubscribe)
Sunday, September 7, 2008
Linutop (Potential Grid Appliance - Hardware)
Linutop is a ready-to-use small computer, designed to reduce maintenance costs. Low maintenanceThe Linutop operating system is stored on an internal flash memory and cannot be altered by virus or mishap. Initial state can be recovered at each restart. Low deployment costsLinutop is delivered with free standard ready-to-use Linux software: Firefox, Open Office, VLC Media player... and can be easily customized with additional software. Energy savingWith no moving parts, Linutop offers a completely silent (0 dB), energy-efficient operation in an extremely small package. |
Open Source Collaborative Disease Surveillance Software
TriSano [pronounced "tri-SAH-no"]: http://www.trisano.org/
"Collaborative Software Initiative today announced the launch of the TriSano application and community. TriSano is an open source, citizen-focused infectious disease surveillance system that allows local, state and federal entities to collaborate for the good of public health. With TriSano, the Collaborative Software Initiative provides a forum in which subject matter experts (i.e., doctors, nurses and epidemiologists) and software developers work together to facilitate the creation of citizen-centric public health applications. This innovation ensures application features meet the specific requirements of each jurisdiction, allowing public health employees to achieve the goal of protecting lives."
"The TriSano™ Eye represents a zooming (micro/macro) view on disease detection and prevention. That is as close as I'm ever going to get to a bird of prey reference in a product. I love birds of prey. They have binoculars for eyes just like TriSano. Its true. Look it up: http://en.wikipedia.org/wiki/Bird_of_prey"
"Collaborative Software Initiative today announced the launch of the TriSano application and community. TriSano is an open source, citizen-focused infectious disease surveillance system that allows local, state and federal entities to collaborate for the good of public health. With TriSano, the Collaborative Software Initiative provides a forum in which subject matter experts (i.e., doctors, nurses and epidemiologists) and software developers work together to facilitate the creation of citizen-centric public health applications. This innovation ensures application features meet the specific requirements of each jurisdiction, allowing public health employees to achieve the goal of protecting lives."
"The TriSano™ Eye represents a zooming (micro/macro) view on disease detection and prevention. That is as close as I'm ever going to get to a bird of prey reference in a product. I love birds of prey. They have binoculars for eyes just like TriSano. Its true. Look it up: http://en.wikipedia.org/wiki/Bird_of_prey"
Wednesday, September 3, 2008
VBrowser Plug-in
I have been in contact with Piter De Boer, primary developer for vBrowser. Piter provided me with some direction and code for creating a custom plug-in for vBrowser. I was also added to the developer mailing for the vBrowser project. I'll begin exploring ways to add actual Grid Services to the vBrowser interface, starting with GridMedLee.
Peter's impression of the PHIN conference
Last week, I attended two Atlanta conferences, The first was the Public Health and Informatics Network (or PHIN) conference, and the second was Dragon*Con. This is why I was out Friday and yesterday: I needed to recuperate. What I learned at the PHIN conference is much more relevant to the interests of this blog.
First off, the demo of RODSAdai went okay on Monday, and blessedly it was the first event attended. That way, we showed it live and we got to answer questions about it and then we were done and I didn't have to worry about something crashing for the entire conference. It was very nice to see people talking the RODSAdai demo I did and the awesome VBrowser demonstrations Dan Washington set up, and it was inspiring to see all the philosophies amalgamated around our demos. There was a small hiccup in that the VPN timed out
The other big thing on Monday was getting to see Dr. Jeremy Espino's RODSAdai demo. His presentation was interesting because it focused on how to get people with similar intrests to contribute code to your project... and how to make your projects as friendly as possible for someone to go "Hey, I have this idea for how to .enhance your code to do this thing I need/want it to do" while still making sure said someone doesn't accidentally delete the source tree. I was actually used as a test case, because I was a developer chosen to code "how do we get information from these two unrelated RODS databases using GRID?" It was really neat because I also got some high praise for the quality of code I was contributing, and praise always makes me happy :D .
After the demonstrations. I went to dinner with a large bunch of Grid folk including Brian Lee, Jeremy Espino, Albert Lai (who is working to distribute the Natural Language Processor engine across grid), a CaBIG engineer, and a BE Architect whose names escape me. We talked a lot about the state of grid and what some of the impediments were to getting grid spread around the US and linking it up with the rest of the globe. The biggest thing I came away with is that we really need to have things in a tight little package, because going "take this box and run 'install' on this disk" is going to be the a lot easier sell to the beleaguered medical center sysadmin than "buy this box and then install these 400 programs in this order". It was lovely meeting everyone face to face.
On Tuesday, I attended the morning session while eating breakfast and heard a very good speech by a Georgia health official about why communities of practice are important... and then I went to the Enterprise Architecture Community of Practice and saw that there were a lot of things to sort out, including purpose and definition. After that I went to man the BearingPoint booth, where I sat in the paint station and asked people to complete parts of a paint-by-colors mural to be given away as a prize to a particular health center.
Finally on Tuesday, I went to the PHGrid concurrent session, where a lot of the things discussed on Monday night were reviewed again with a focus on Security and Performance.
Wednesday, I started by eating breakfast and going to the Plenary session which had a cool presentation about "PHIN 2018" which basically looked at how things were going to change slowly then rapidly over the future as goals were discussed and changed. , I attended a session for the evaluation of detection systems developed by the John Hopkins University Applied Physics Laboratory (JHU APL). The sessions were neat because they outlined the informatics and statistical analysis that went into detecting outbreaks. Basically, statistical analytical models were coded to detect outbreak conditions as they were appearing. The machines could then "learn" from mistakes (missed outbreaks, false alerts) and adjust their standards for statistical patterns accordingly. There were pretty cool examples of how the outbreaks were detected more accurately as time went on. Another speaker also went over his experiences in evaluating a new system designed for replacing the old one... complete with sitting behind the users, documenting the process, and seeing if that process would be supported or enhanced by the new system without introducing any new pain points. He did not reccommend the replacement, and it still hasn't been adopted as predicted. It was a great demonstration of a real world enterprise evaluation.
Then there was an awards lunch... and there was some conflict with people wanting to eat and talk rather than listen to the presenters. I think in the future the conference should have the "eat-and-talk" section of lunch, and then the "your food is gone, go outside if you need to keep chatting" presentation section. After that was the second section of the Enterprise Architecture CoP... and this time we made more progress for mapping our motives and definition. I think one of the best ideas was to make a "city map" for what a phin machine would be and who would be providing it.
Finally on Wednesday was the "Visualization and Analysis" panel... where I got to see all the cool Diginet work done by Carl Kincaide and Jim Tobias. They had basically done another version of a visualization and amalgamation tool that did the same sort of thing RODSAdai did, but they did it with a completely different platform. Thus, it shows a sort of convergent evolution and the ability to get the same results with different toolkits and starting environments.
On Thursday we spent the morning meeting with several different people. A lot were the coders from JHU APL, Jeremy and Albert were there, and the others were some of the Utah CaBIG coders... and we basically set up another Community of Practice that centers around "we've all met and talked about things lets keep on tabs with each other and what we are working on. The basic discussion was focusing on thing like making very easily deployable boxes and how to roll out some of these cool Proofs of Concept to production... and I sort of threw out there that one of the things that would need to be done is just to get one health department to try it, love it, rave about it, and then say "oh look, this is free and you can set it up too" and the desire for the ease the visualization or analysis will find more homes for our product and allow them to link up.
Overall the conference was very cool and I enjoyed meeting a bunch of the people I had worked with and probably will be working with well into the future.
First off, the demo of RODSAdai went okay on Monday, and blessedly it was the first event attended. That way, we showed it live and we got to answer questions about it and then we were done and I didn't have to worry about something crashing for the entire conference. It was very nice to see people talking the RODSAdai demo I did and the awesome VBrowser demonstrations Dan Washington set up, and it was inspiring to see all the philosophies amalgamated around our demos. There was a small hiccup in that the VPN timed out
The other big thing on Monday was getting to see Dr. Jeremy Espino's RODSAdai demo. His presentation was interesting because it focused on how to get people with similar intrests to contribute code to your project... and how to make your projects as friendly as possible for someone to go "Hey, I have this idea for how to .enhance your code to do this thing I need/want it to do" while still making sure said someone doesn't accidentally delete the source tree. I was actually used as a test case, because I was a developer chosen to code "how do we get information from these two unrelated RODS databases using GRID?" It was really neat because I also got some high praise for the quality of code I was contributing, and praise always makes me happy :D .
After the demonstrations. I went to dinner with a large bunch of Grid folk including Brian Lee, Jeremy Espino, Albert Lai (who is working to distribute the Natural Language Processor engine across grid), a CaBIG engineer, and a BE Architect whose names escape me. We talked a lot about the state of grid and what some of the impediments were to getting grid spread around the US and linking it up with the rest of the globe. The biggest thing I came away with is that we really need to have things in a tight little package, because going "take this box and run 'install' on this disk" is going to be the a lot easier sell to the beleaguered medical center sysadmin than "buy this box and then install these 400 programs in this order". It was lovely meeting everyone face to face.
On Tuesday, I attended the morning session while eating breakfast and heard a very good speech by a Georgia health official about why communities of practice are important... and then I went to the Enterprise Architecture Community of Practice and saw that there were a lot of things to sort out, including purpose and definition. After that I went to man the BearingPoint booth, where I sat in the paint station and asked people to complete parts of a paint-by-colors mural to be given away as a prize to a particular health center.
Finally on Tuesday, I went to the PHGrid concurrent session, where a lot of the things discussed on Monday night were reviewed again with a focus on Security and Performance.
Wednesday, I started by eating breakfast and going to the Plenary session which had a cool presentation about "PHIN 2018" which basically looked at how things were going to change slowly then rapidly over the future as goals were discussed and changed. , I attended a session for the evaluation of detection systems developed by the John Hopkins University Applied Physics Laboratory (JHU APL). The sessions were neat because they outlined the informatics and statistical analysis that went into detecting outbreaks. Basically, statistical analytical models were coded to detect outbreak conditions as they were appearing. The machines could then "learn" from mistakes (missed outbreaks, false alerts) and adjust their standards for statistical patterns accordingly. There were pretty cool examples of how the outbreaks were detected more accurately as time went on. Another speaker also went over his experiences in evaluating a new system designed for replacing the old one... complete with sitting behind the users, documenting the process, and seeing if that process would be supported or enhanced by the new system without introducing any new pain points. He did not reccommend the replacement, and it still hasn't been adopted as predicted. It was a great demonstration of a real world enterprise evaluation.
Then there was an awards lunch... and there was some conflict with people wanting to eat and talk rather than listen to the presenters. I think in the future the conference should have the "eat-and-talk" section of lunch, and then the "your food is gone, go outside if you need to keep chatting" presentation section. After that was the second section of the Enterprise Architecture CoP... and this time we made more progress for mapping our motives and definition. I think one of the best ideas was to make a "city map" for what a phin machine would be and who would be providing it.
Finally on Wednesday was the "Visualization and Analysis" panel... where I got to see all the cool Diginet work done by Carl Kincaide and Jim Tobias. They had basically done another version of a visualization and amalgamation tool that did the same sort of thing RODSAdai did, but they did it with a completely different platform. Thus, it shows a sort of convergent evolution and the ability to get the same results with different toolkits and starting environments.
On Thursday we spent the morning meeting with several different people. A lot were the coders from JHU APL, Jeremy and Albert were there, and the others were some of the Utah CaBIG coders... and we basically set up another Community of Practice that centers around "we've all met and talked about things lets keep on tabs with each other and what we are working on. The basic discussion was focusing on thing like making very easily deployable boxes and how to roll out some of these cool Proofs of Concept to production... and I sort of threw out there that one of the things that would need to be done is just to get one health department to try it, love it, rave about it, and then say "oh look, this is free and you can set it up too" and the desire for the ease the visualization or analysis will find more homes for our product and allow them to link up.
Overall the conference was very cool and I enjoyed meeting a bunch of the people I had worked with and probably will be working with well into the future.
Tuesday, September 2, 2008
Phin Conference Experience
Hi all, here's my phin conference experience. Considering the fact that I have never attended a professional conference of this size, its safe to say, I was truly impressed. At the same time, it gave a lot of perspective on where we fit in the big picture. I especially liked the format, where they kept 3 speakers per session so it never felt like its dragging. But all in all a lot of information to consume and analyze. I really liked the session about MedLEE and the application outlining the research grid services by Wayne Loschen. Also had a long chat with Ron Price about the various aspects of security evaluation of the Grid. I also enjoyed Vaugh Mcmullin's presentation about the impelementing a Data Grid leveraging Secure reliable transport, clustered node data sets using existing open source and concepts utilized by PHIN with one particular point of emphasis being making application device independent. To add further, it was a really good idea to assemble on thurday, following the conference, with all the grid collaborators and outline next steps and focussing on preventing redundancy of work. All in all, I would say an enriching experience which will lead to bigger things in terms of Grid research.
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