-
- Browsing
- e-Science
- Made Paul's GLS Client Code available as open source via the following URL:
-
- Browsing
- Miscellanea
- NetBeans 6.1 is now available:
- Is it worth the pain of upgrading from 6.0.1? Darn - I only just got playing with 6.0.1 in an upgrade from 5.5... Go-go NetBeans :-)
- What can we learn from Grand Theft Auto IV?
- e-Science
- References
-
- Browsing
- Miscellanea
- e-Science
- Considering what SUMs are appropriate for MoSeS...
- Meeting with Junaid to catch up on last week and prepare for a possible SEE-GEO telecon tomorrow:
- Brief of the OGSA-DAI training/consultancy
- Junaid worked closely with Ally and would not have got very far without him :-)
- They installed the OGC OGSA-DAI extensions on VM04.manchester.ac.uk which Junaid has set up for use at NCeSS.
- Junaid accesses VM04.manchester.ac.uk via a gateway machine wittgenstein.ncess.ac.uk
- There were a few non-documented things that had to be done to configure the GLS.
- Ally mentioned these in his email.
- A detailed report to Michael/Chris is wanted.
- Brainstorm about GLS Security:
- We want a user-friendly experience.
- We have options, but it seems sensible to have some security handling in all component.
- We don't want it to be hard to manage the security:
- Proxy certificates (combining lifetimes with credentials) might be a good way forward.
- Discussion about virtualisation
- Junaid is to arrange to go to the Security workshop in Oxford:
- Richard Sinnott iss going :-)
- If Mark Birkin will not release MoSeS funds for this, I will approach June Finch to fund this via the NCeSS e-Infrastructure for the Social Sciences Project.
- Failing that we can use my Personal Research Fund (PRF)...
- NeSS
- Meeting with June Finch using Skype:
- Well I thought this was supposed to start at 14:00, but it seems June is not online...
- Meeting cancelled.
- GENESIS
- Browsing
- Provided feedback to Nanlin on the "Constraint Guided Algorithm" Paper
- We thought through modifying weights in an optimisation fitness function as a training strategy:
- A similar thing can be done in neural network classifier training.
- Hopefully we will write a paper togetehr on this looking at some population initialisation work started in MoSeS :-)
- Miscellanea
- e-Science
- GENESIS
- Established a NCeSS Sakai Portal : GENESIS worksite with the help of Xiaobo Yang (portal administrator).
- The URL for the GENESIS worksite is as follows:
- Added the RWiki Wiki Tool to the GENESIS worksite and made a home page publicly viewable at the following URL:
- Added the Password Reset Tool and Resources Tool
- Initialised my own wiki page on this worksite which is also publicly viewable via the following URL:
- MoSeS, NeSS, SEE-GEO
- Ally and Junaid seem to have made good progress with the GLS at the OGSA-DAI training :-)
- Thought of the day:
- In GENESIS, it is costed to spend in the order of two years researcher wages for software
- Surely it would be better to use free or open source alternatives and employ/develop software engineers?
- e-Science
- References
- Browsing
- Miscellanea
- Thought of the day:
- Nadir is a very down to Earth kind of name.
- Vania Dimitrova has been working to capture ontology from wiki tools: A semantic wiki to build a community for academic writing.
- e-Science
- Subscribing to JISC e-Framework email list...
- Data Integration and Dissemination (DIaD) is the acronym and name of a project run by James Reid at EDINA:
- I don't think there are any web pages about this yet, but I think I've seen a project plan about it which includes some exciting words about a cartogram service :-).
- The GeoLinking Service we are developing as part of the NCeSS e-Infrastructure for the Social Sciences Work Package 4.1 is very relevant and I look forward to collaborating on DIaD.
- OGSA-DAI Training:
- Sakai RWiki Tool link issue
- Ian Boston requested the Frame source HTML for the following issue:
- http://jira.sakaiproject.org/jira/browse/SAK-12262
- I provided this and look forward to progress :-)
- I maybe should think about filing another request based on my original desire to use a reference for links rather than a hard code as per my comment on 23-Nov-2007 09:59
- Browsing
- Requested geowebm consider adding The Centre for Computational Geography (CCG) to the list of Organisations and Projects on the web page accessible via the following URL:
- Thoughts of the day:
- Have you considered how to develop ontologies from resources like wikipedia and wikinfo?
- Geomorphometrics
- Progress on NextMap Cairngorm run:
- Iteration 3: Done Chunk ( 18, 9 )
- e-Science
- OGSA-DAI Training:
- Using OGSA-DAI to Grid enable data for the Arts, Humanities and Social Sciences - part 2, Web Based
- After another iteration (see next item) Ted got back to me with something that worked for testing OGSA-DAI Setup :-)
- [ogsa-dai005@tc07 ogsa-dai005]$ java uk.org.ogsadai.client.toolkit.gt.example.GTSecureSQLClient -u https://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai/ -d SwissProt_Metadata -q "select * from swissprot limit 10"
-
DRER ID: DataRequestExecutionResource
Data Resource ID: SwissProt_Metadata
Base Services URL: https://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai/
SQLQuery: select * from swissprot limit 10
uk.org.ogsadai.resource.request.status.COMPLETED
| accession | filename | name |
| Q6A814 | fasta_files/7d384f77856b40a1c84ec59672fbc626.fasta | Q6A814|ARGB_PROAC|Acetylglutamatekinase |
| Q99SH9 | fasta_files/f90ac6cf5420f4990e44db5ee0d4335a.fasta | Q99SH9|ATKA1_STAAM|Potassium-transportingATPaseAchain1 |
| Q97K30 | fasta_files/cc8ff4704d54216a026b9a2ae8c1710b.fasta | Q97K30|APEA_CLOAB|ProbableM18-familyaminopeptidase1 |
| Q17761 | fasta_files/0e3e7d896471468b6b79fbc8e3cde9d9.fasta | Q17761|6PGD_CAEEL|6-phosphogluconatedehydrogenase,decarboxylating |
| Q99XL6 | fasta_files/6a35dc1d226d83f8eedd96758277eb67.fasta | Q99XL6|ARGR2_STRP1|Argininerepressor |
| O42918 | fasta_files/f862c858aeff57fafec65dfc6d5e328d.fasta | O42918|AMY4_SCHPO|Alpha-amylase4precursor |
| P10538 | fasta_files/c004881332ac1a06fdd1df8dba2c9cd2.fasta | P10538|AMYB_SOYBN|Beta-amylase |
| Q8XDZ5 | fasta_files/b246c76324eea7df4fe09286b973874f.fasta | Q8XDZ5|ARNC_ECO57|Undecaprenyl-phosphate4-deoxy-4-formamido-L-arabinosetransferase |
| Q0BU70 | fasta_files/45e18226ca6d06d30df4c8bead400324.fasta | Q0BU70|ARGB_GRABC|Acetylglutamatekinase |
| O08915 | fasta_files/1091f29bdf22f2a5438f7512e39d41cc.fasta | O08915|AIP_MOUSE|AHreceptor-interactingprotein |
- Ted got back to me with my problem of yesterday:
-
You need to connect to the OGSA-DAI server on tc07 using tranport-level security as the server is deployed as such.
The URL should be https://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai/,
and other parameters should be no change.
However, you can't use XMLDBClient tool provided by the OGSA-DAI team because it does not support transport-level security.
There's only one SQL client that supports security.
Therefore, you need to write your own client for XMLDB client. But you can test SQL query like this:
java uk.org.ogsadai.client.toolkit.gt.example.GTSecureSQLClient -u https://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai/ -d SwissProt_Metadata -c "select * from swissprot limit 10"
- I tried a couple of things:
- Attempted test with what Ted suggested:
- [ogsa-dai005@tc07 ogsa-dai005]$ module load java ogsadai_wsrf
- [ogsa-dai005@tc07 ogsa-dai005]$ module list
-
Currently Loaded Modulefiles:
1) /dot 2) /globus/4.0.5 3) /java/1.5.0_07 4) /ogsadai_wsrf/3.0
- [ogsa-dai005@tc07 ogsa-dai005]$ java uk.org.ogsadai.client.toolkit.gt.example.GTSecureSQLClient -u https://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai/ -d SwissProt_Metadata -c "select * from swissprot limit 10"
-
Exception in thread "main" java.lang.IllegalArgumentException: There is no value for flag -q
at uk.org.ogsadai.client.toolkit.example.ClientBase.getSingleValue(Unknown Source)
at uk.org.ogsadai.client.toolkit.example.SQLClient.processParameters(Unknown Source)
at uk.org.ogsadai.client.toolkit.gt.example.GTSecureSQLClient.processParameters(Unknown Source)
at uk.org.ogsadai.client.toolkit.example.SQLClient.execute(Unknown Source)
at uk.org.ogsadai.client.toolkit.gt.example.GTSecureSQLClient.main(Unknown Source)
- Specifying port 8443:
- [ogsa-dai005@tc07 ogsa-dai005]$ java uk.org.ogsadai.client.toolkit.example.XMLDBClient -u http://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai -c listResources -d SwissProt_Resource
-
DRER ID: DataRequestExecutionResource
Data Resource ID: SwissProt_Resource
Base Services URL: http://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai
Command: listResources
DRER ID: DataRequestExecutionResource
Data Resource ID: SwissProt_Resource
Base Services URL: http://tc07.nesc.ed.ac.uk:8443/wsrf/services/dai
Command: listResources
Exception in thread "main" uk.org.ogsadai.client.toolkit.exception.ServerURLInvalidException: A problem occured initialising the server.
at uk.org.ogsadai.client.toolkit.ServerFactory.getWSDL(Unknown Source)
at uk.org.ogsadai.client.toolkit.ServerFactory.getServer(Unknown Source)
at uk.org.ogsadai.client.toolkit.ServerProxy.getServer(Unknown Source)
at uk.org.ogsadai.client.toolkit.ServerProxy.getDataRequestExecutionResource(Unknown Source)
at uk.org.ogsadai.client.toolkit.example.XMLDBClient.execute(Unknown Source)
at uk.org.ogsadai.client.toolkit.example.XMLDBClient.main(Unknown Source)
Caused by: java.net.SocketException: Connection reset
at java.net.SocketInputStream.read(SocketInputStream.java:168)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:256)
at java.io.BufferedInputStream.read(BufferedInputStream.java:313)
at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:606)
at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:554)
at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:571)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:939)
at java.net.URL.openStream(URL.java:1007)
... 6 more
- Investigating downloading and installing OGSA-DAI locally
- Browsing
- Thoughts of the day:
- Sometimes it is easier to learn by going through the motions and waiting for the reasoning to click into place:
- A significant amount of my maths learning was like this and it is slightly different than learning by example.
- Those learning the benefits of structuring information about their operations might do well to appreciate this before thinking too much about why one would want to do this and what the point of it all is ;-)
- My caveat for this general statement is that I am a scientist trying to model everything not a private company trying to exploit others for profit by keeping my business operations somewhat secret and playing a gambling/misinformation game...
- e-Science
- OGSA-DAI Training:
- Using OGSA-DAI to Grid enable data for the Arts, Humanities and Social Sciences - part 2, Web Based
- Thanks to Qingying Wen (Ted) I can login to tc07.nesc.ed.ac.uk via GSI-SSH.
- http://training.omii-europe.org/Tutorials/OGSA-DAI/SimpleWorkflowTC.html
- 2. Testing OGSA-DAI
- Problem:
-
[ogsa-dai005@tc07 ogsa-dai005]$ java uk.org.ogsadai.client.toolkit.example.XMLDBClient -u http://tc07.nesc.ed.ac.uk:8080/wsrf/services/dai -c listResources -
d SwissProt_Resource
DRER ID: DataRequestExecutionResource
Data Resource ID: SwissProt_Resource
Base Services URL: http://tc07.nesc.ed.ac.uk:8080/wsrf/services/dai
Command: listResources
DRER ID: DataRequestExecutionResource
Data Resource ID: SwissProt_Resource
Base Services URL: http://tc07.nesc.ed.ac.uk:8080/wsrf/services/dai
Command: listResources
Exception in thread "main" uk.org.ogsadai.client.toolkit.exception.ServerURLInvalidException: A problem occured initialising the server.
at uk.org.ogsadai.client.toolkit.ServerFactory.getWSDL(Unknown Source)
at uk.org.ogsadai.client.toolkit.ServerFactory.getServer(Unknown Source)
at uk.org.ogsadai.client.toolkit.ServerProxy.getServer(Unknown Source)
at uk.org.ogsadai.client.toolkit.ServerProxy.getDataRequestExecutionResource(Unknown Source)
at uk.org.ogsadai.client.toolkit.example.XMLDBClient.execute(Unknown Source)
at uk.org.ogsadai.client.toolkit.example.XMLDBClient.main(Unknown Source)
Caused by: java.net.ConnectException: Connection refused
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
at java.net.Socket.connect(Socket.java:516)
at java.net.Socket.connect(Socket.java:466)
at sun.net.NetworkClient.doConnect(NetworkClient.java:157)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:365)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:477)
at sun.net.www.http.HttpClient.(HttpClient.java:214)
at sun.net.www.http.HttpClient.New(HttpClient.java:287)
at sun.net.www.http.HttpClient.New(HttpClient.java:299)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:795)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:747)
at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:672)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:916)
at java.net.URL.openStream(URL.java:1007)
... 6 more
- I wonder what to do now...
- Browsing
- Thoughts of the day:
- Add a check sum signature to a file then create a new checksum. The two checksums and the verison information of the file can then be kept in a public look up registry. The registry can be used to confirm that a file is the version it claims to be.
- I suspect this is an old idea that many systems implement in some shape or form :-)
- Wonder iftwd work or ifthesowt wrong wit idea?
- Perhaps I should try to detail 3 thoughts for the day as Andy Hudson Smith advocates :-)
- Thanks to Mona Wong-Barnum, Data Services Portal Developer San Diego Supercomputer Center for the following gem:
- Being balanced is;
being secure enough to be vulnerable,
strong enough to be gentle,
wise enough to be humble,
powerful enough to serve others.
- CCG Java Group meeting:
- Met with Nikolaos Fyllas to show him how to add projects and libraries in NetBeans:
- Nikos has found a useful library Colt from Cern:
- It is useful for numerical work, but may be good for other things too.
- e-Science
- OGSA-DAI Training:
- Reading and writing to SRB space on NGS from a java program:
- srparget, srbpget and srbpput are the command line tools:
- I wonder if it is best to invoke these using System.exec()...
- Follow up from Cliff Brereton:
- MoSeS, NeSS
- Browsing
- Leeds Social Sciences Institute Seminar: Special Census Datasets
- e-Science
- General catch up meeting with Junaid
- Documentation
- Email "Journal list" from Junaid to Andy and Wei Jie on 2008-03-25
- Email "Developing a GeoLinking Service and making it available on the NGS" from Andy to Andy Richards cc Junaid and Ally Hume on 2008-04-16
- Junaid wanted to know exactly what was involved in developing the GLS and when everything is to be done :-)
- I tried to provide a brief of what we are doing...
- Junaid has been talking with Shiv Kaushal and having group meetings discussing the work
- It may be that the virtualisation route is the way forward and that there may be additional funding to investigate this.
- Hopefully Paul can be involved in developing an application for funds for this.
- Shiv is going to email Junaid some links.
- This sounds good and in tune with what Rob Allan suggested we could be looking at in e-Infrastructure for the Social Sciences project meetings this morning.
- Junaid happy to prepare a short presentation on GLS and related progress at the NeSS project meeting on 2008-05-15 :-)
- I am to re-send apologies for this meeting as I should be heading to the event:
- Junaid would be happy for his contract to be extended again for a further 6 month period.
- I want this to happen, so I will see with Mark Birkin what scope there is for keeping me on MoSeS funding for July and August.
- It would be good to offer Junaid as much time as is available for NeSS work on Work Package 4.1.
- Manchester are not paying Junaid for anything.
- June Finch hinted this morning that there may be additional funds that could be released to us from the NeSS project...
- I shall try to find out more about that in due course.
- I think that at the current rate of expenditure we are unlikely to have any financial resources left from our initial budget/allocation after 2008.
- Junaid argued the need for Role Based Access Control for the GLS Server on the NGS
- Junaid offered to present an outline of what we are doing in MoSeS and NeSS at the upcoming final part of OGSA-DAI training/consulting :-)
- There should be people from OMII-Europe there...
- Problems with OGSA-DAI training with the slowness of Virtual Machines, so little progress being made with this :-(
- Preparation for final part of OGSA-DAI training/consulting:
- Try to install SEE-GEO OGC OGSA-DAI extension on VM.
- Liaise further with Ally Hume once we hear back from Andy Richards.
- Important timings coming up:
- 2008-05-31 - end of SEE-GEO Project
- 2008-07-01 - end of Junaid's contract and Andy's allcoation on MoSeS
- 2008-08-31 - end of MoSeS
- 2009-12-31 - end of NeSS Project
- Need to keep an eye on SARoNGS and hope it is delivered on time :-)
- In a way NeSS project can help with this...
- NeSS
- References
- Browsing
- Completed Census User Survey for 2007
- SoG
- Attended Open Day Coffee Session
- The Oxford e-Research 08 Conference Committee informed me that my paper "Experience of e-Social Science: A Case of Andy Turner and MoSeS" has been accepted for the Oxford e-Research 08 Conference on the basis of the abstract I submitted 2008-03-11 :-)
- Emailed to start the registration process.
- I should organise my accomodation and look at the programme once it is detailed...
- e-Science
- Some thoughts on security from Pascal et al:
- NeSS, SEE-GEO
- Preparing for the NeSS Project meeting tomorrow:
- Great, June is using the wiki and has edited a page for the meeting and it now has an agenda :-)
- SEE-GEO OGSA-DAI with OGC geospatial extensions are now available:
- Browsing
- Completed a survey for OGC accessed via the following URL:
- Meeting with Cliff Brereton from IBM and Junaid Arshad
- Pre-meeting with Junaid
- Junaid wonders how does rSmart differ from Sakai?
- I wonder what is rSmart and how can IBM help us?
- Introductions at this informal meeting
- Cliff
- IBM Educational Representative pushing IBM products in the following categories
- Research Supercomputing
- Operational Research
- Open and Online Learning
- Rightly proud that IBM released Eclipse :-)
- rSmart sponsor of the Sky Project(?)
- Andy
- Junaid
- Andy outlined NCeSS and introduced MoSeS and NeSS work.
- Security discussion
- Importance of:
- data security
- confidentiality and commercial reasons (very expensive data).
- Securing other resources (computational, offices, portable deveices etc...)
- GeoSecurity
- Wants for fine grained control
- GeoXACML
- Junaid outlined his security work with:
- Sakai discussion
- Cliff gave us some low down on IBM products of interest:
- Tivoli Enterprise Manager
- Available under IBM Academic Initiative (Red Book)
- We need to register for this to install it.
- Closed source software suite
- Do OSS offerrings match up?
- Pointers from Cliff
- Caret, John Norman.
- As he tours UK academia, he will bear us in mind and point us out to other folk that might collaborate :-)
- Pointers for Cliff
- Visualisation:
- Ken Brodley, Andy Hudson-Smith CASA GeoVUE
- References
- e-Science
- References
- Browsing
- Registered a ESRCInfoCentre account for myself via:
- Ideas for dissertation topics
- In general I am interestied in anyone picking up any of the projects I have done and revising the work.
- This might involve:
- sourcing and re-licensing the data
- identifying what software to use
- generally improving documentation
- producing new research outputs
- Using neural networks to predict commuting variable values in census data.
- MASS
- Meeting with Thomas Mellor about dissertation topics:
- Tom not planning to revive RLF/1:
- It seems to much boring work and Tom would rather focus on an application like disaster management.
- I introduced the MEDALUS III/MedAction work I was involved in and suggested it might be of interest to revisit.
- The key thing is to select an application/thing of interest and source some data.
- To learn about neural networks it is best to have some quite large datasets to model with.
- Stress Survey
- Completed the Stressor Indicator Survey - Faculty of Environment accessed via:
- https://www.survey.bris.ac.uk/leedshss/env1
- Response to Part 2
- 9. Often
- 10. Often
- 11. Often
- 12. Always
- 13. Seldom
- 14. Seldom
- 15. Seldom
- 16. Seldom
- 17. Often
- 18. Always
- 19. Often
- 20. Often
- 21. Often
- 22. Often
- 23. Often
- 24. Seldom
- 25. Always
- 26. Sometimes
- 27. Sometimes
- 28. Seldom
- 29. Always
- 30. Seldom
- 31. Seldom
- 32. Sometimes
- 33. Neutral
- 34. Agree
- 35. Neutral
- 36. Neutral
- 37. Agree
- 38. Agree
- 39. Agree
- 40. Agree
- 41. Disagree
- 42. Neutral
- 43. Neutral
- 44. Agree
- 45. Neutral
- 46. I will make them publicly accessible under the item Stress Survey via the following URL:
http://www.geog.leeds.ac.uk/people/a.turner/personal/blog/archive/2008/04/#2008-04-14
Making the information public was not easily done. It could have been made a lot easier.
- e-Science
- Further communications on a Gateway to Access Census Data.
- Modified BSD License as per http://www.opensource.org/licenses/bsd-license.php for Paul's GLS Client Code:
-
Copyright (c) 2008, Paul Townend
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
* Neither the name of the University of Leeds nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- MoSeS
- Emailed Haibo asking for transport zone data:
- Browsing
- e-Science
- NeSS, SEE-GEO
- MoSeS
- Received a draft of an article about MoSeS and NGS users from Katie Weeks.
- Meeting With Paul :-)
- Trying to Get MoSeS Web Services NetBeans set up on my PC:
- For some reason NetBeans is not configuring tomcat properly and glassfish not working either...
- We tried various de-activations and activations, but nothing got tomcat appearing in the Services list...
- We called out geo-support (who have administrator role on my PC) to try to re-install:
- Unfortunately that did not work either...
- It's odd and we don't know what is happening and it seems no one else is having the same problem...
- I'm going to try another computer and failing that manually install and configure tomcat.
- Figured it out :-)
- A custom windows install allows for tomcat to be added, but for some reason this is not default as Paul says it is with the Mac OS.
- With such a custom install on my laptop, tomcat is listed as a Server :-)
- Although perhaps not completely working, this got me a bit further...
- Next I have a problem as I am using JDK1.6 and Paul was using JDK1.5...
- To use JAX-WS 2.1 with JDK 6, newer versions of API jars need to be in bootclasspath before rt.jar. To do this you can use Java endorsed mechanism to override what is in Java platform. The easiest way to do so is to copy all jars from the C:\Program Files\NetBeans 6.0.1\java1\modules\ext\jaxws21\api folder to C:\Program Files\Apache Software Foundation\Apache Tomcat 6.0.14\endorsed.
- Alas it is rarely simple with MoSeS!
- So I logged out and back in again as useradmin and did the copying then tried again and hey presto it worked perfectly :-)
- Browsing
- Getting to grips with NetBeans 6.0.1
- Something wierd happens when it starts loading, but it seems to recover.
- Hopefully that's not indicative of further problems...
- The following proxy configuration seemed to work:
- proxy www.leeds.ac.uk/proxy.pac
- port 3128
- http://www.netbeans.org/kb/kb.html
- Learning about Web Services
- Subscribed to the geowanking email list
- e-Science
- NeSS, SEE-GEO
- Communications with Jacqueline Carter (Jackie) from MIMAS about Access to Census Data
- Prompted by my email to Keith Cole about gateways to census data, Jackie telephone to get more of a brief from me and to let me know about relevant MIMAS progress and timelines :-)
- There is a Census Advisory Committee (CAC) meeting at the end of the month, do I want anything on the agenda for this?
- ESRC/JISC CAC oversees the Census support units, chaired by John Pullinger (ONS) and comprises representatives of the user community (http://www.mimas.ac.uk/about.html).
- Dave Rawnsley from the Census Dissemination Unit (CDU) is the person to liaise with in regard to this.
- Among other things, the information on the web pages that can be found via the following URLs give timetables for shibboleth adoption at MIMAS and EDINA respectfully:
- ...
- MoSeS
- Read Chengchao Zuo MSc 2007 Dissertation Thesis
- Used BHPS Wave 13 from 2004
- Meeting with Chengchao Zuo
- Chengchao has been working with Mark's IPS output and trying to link to that:
- This has been problematic as variables including accomodation type and occupation are not good fits in the IPS data (When aggregated to ward level for Leeds).
- He has tried doing some adjustments which have given some better results for mapping houseprice :-)
- Comparisons done with the land registry data I provided for him last year.
- Together we reconsidered linking the BHPS data with the Household SAR (HSAR) and Individual SAR (ISAR) Records
- The BHPS data we looked at come from Wave 13
- There are lots of variables some of which are also in the SAR data.
- There are several approaches:
- We can use the control constraints and optimisation constraint like approach to the population initialisation:
- Control constraints would be those variables values that had to match.
- Optimisation variables would be comparable and a fitness function could be derived from these to evaluate the fitness of the linkage.
- We can probably evaluate using a brute force search through all control constraining records or we could use a heuristic search like a genetic algorithm.
- Because the BHPS Wave 13 is such a small sample (approximately 15000 Individuals) I would have thought a brute force evaluation would be best and not take too long to calulate for the 4 million or so records in the HSAR and ISAR.
- For the most part the Household and Individual SAR variables are the same
- Age is one of the problem variables as it is so important and aggregated so differently.
- As I am unfamiliar with the BHPS I looked at it online:
- In the main Chengchao has been using two of the ten tables (household and individual respectively):
- We looked at the details of some specific variables:
- It would be good to go through the list of BHPS variables and find out which can be used for linking with the HSAR and ISAR variables
- Andy and Chengchao to meet about this again next week.
- Browsing
- e-Science
- SEE-GEO, NeSS, MoSeS
- GLS Client development
- Drafter some documentation to describe the GLS Client interface and emailed it to Chris Higgins and Richard Sinnott.
- I need to put this and the source code online...
- Browsing
- SoG
- Meeting with Thomas Mellor (Tom) about RLF/1
- Tom is considering what to do a dissertation topic and reviving RLF/1 and using it as a basis for some flood forecasting work has been suggested.
- We looked through the information on my blog from the meeting I had with Linda about this, see the item "2008-03-26" and "RLF Meeting with Linda See" on the web page at the following URL:
- I provided Tom with the web page files and the rlf1 directory.
-
- Hopefully based on this and feedback from other potential projects he can make a decision on what to do for his dissertation.
- He will look to Linda See, Paul Norman and Andy Evnas for further help and guidance.
- Via Simon Corne's brother Dave, I got Simon's email address and let him know about what we are doing.
- Simon might help us be aware of data and software licensing issues.
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Communications with Chris Higgins
- Wants me to get the GLS Client on geo-s12 operational and find out the status of the shibbolised https access version.
- Paul got the GLS EDINA GLS Client working on geo-s12 again :-)
- It had been broken since it was put on the NCeSS portal. Now both work.
- Trying to find out from Junaid about the status of the https shibbolised version of this client.
- MoSeS
- NeSS
- Browsing
- PC Upgrade
- In need of some new software installs:
- Put request in with geo-support.
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- OGSA-DAI training
- Started this off by copying Junaid's DVD and requesting the install of a VMWare player on my PC...
- MoSeS
- Meeting with Paul
- Paul showed me progress with the web services development :-)
- I should get NetBeans 6.x installed with all the bells and whistles.
- Planning to have another meeting on Thursday afternoon after a lunch with a visitor from China :-).
- Paul to talk with Jie about releasing the SLD creation code.
- It would be good if this were released with an open source license so it could be readily used by the rest of the e-Science community.
- Meeting with Junaid
- Discussed security
- This was in view of notes from various recent meetings.
- I'm still trying to get my head around how best to do security. There is a lot to consider.
- Junaid gave me the impression that it can all be done with a Role Based Access Control, but for this to work the roles have to be agreed on server and client sides.
- In this way a role can be stipulated as one which allows to operate (e.g. edit, view) the set of features (objects) with respective feature types in geospatial regions given by respective geometries.
- A concern then is not to unwittingly disclose in the role description itself whilst at the same time allowing the assignment of roles by some higher level administrator.
- The mind boggles!
- Sent Junaid the OGC GeoXACML standard.
- Browsing
- Deegree
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- SEE-GEO Meeting
- Telecon organised by Chris Higgins
- Agenda
- Introductions
- Scope of the proposed collaboration (see attached Grid_collab_v2.doc and the UniBW Use Case) including report on actions from Boston meeting. This is obviously the most substantial agenda item and I may ask individuals to expand on topics as appropriate, eg,
- AM on the OGC approach to security
- RS on Grid Security
- MJ on SARoNGS
- SS on the UniBW Use Case
- CKu on GDI-Grid objectives
- CKi on Deegree security plans
- Project management
- Milestones over next few months, ie, AGILE conference, Potsdam OGC TC, OGF23
- AOB
- Documentation
- Notes
- D-Grid using Globus Toolkit 4.0.5 web service component
- Going through the agenda:
- Introductions
- Scope of the proposed collaboration (see attached Grid_collab_v2.doc and the UniBW Use Case) including report on actions from Boston meeting. This is obviously the most substantial agenda item and I may ask individuals to expand on topics as appropriate, eg,
- European Persistent Testbed (EPT)
- MK getting familiar with Deegree
- Another EDINA colleague getting familiar with ebRIM and liaising with Andreas Poth.
- CH negotiating licenses for data from EuroGeographics
- AM on the OGC approach to security
- CH asks:
- What is the state of play with OGC access control?
- OWS4 SOAP WSDL and Web Services best practice?
- AM
- There was some discussion on security along the following lines:
- How many Policy Decision Point (PDP) can be used?
- Policy Enforcement Point (PEP)
- AM offered to provide a PEP
- To do this he needs a URL of WFS and what rights data model is on the WFS
- RS has:
- Working SAML and VOMS integration for PEP and PDP
- No XACML working with GT4 as yet.
- Shibboleth/SAML and XACML are somewhat alternative technologies
- MJ suggested pushing the VOMS attributes
- RS has this working with PERMIS but not XACML
- The security is complicated in a case where what is portrayed is based on what is allowed to be shown to a given user
- The case is not simply what actions and SLDs can be done, but based on what is returned and for where.
- I don't think the non geo-security people are appreciating this yet.
- Anyway, at the end of a roundabout discussion CH summarised that there was a need for GeoXACML
- Probably true, but is it needed for the use case?
- SAML is used to bind OGC clients
- AM is not familiar with Shibboleth
- WFS client does not follow a redirect
- How does shibboleth as an authentication service fit in with the OGC web services security?
- AM will look into this.
- RS will send AM appropriate shibboleth documentation.
- AM not aware of anyone working on OGC Authentication Interface Specification (AIS) that is technology neutral.
- SAML used in OWS4
- It seems there is scope for collaboration as GDI Grid people need to be working on this upto July too.
CH pushed for someone other than EDINA to develop a client.
- RS on Grid Security
- MJ on SARoNGS
- SS on the UniBW Use Case
- Currently different SLDs for each country for the Euroglobal map data are not there?
- Catalog and ebRIM
- CKu on GDI-Grid objectives
- CKi on Deegree security plans
- Project management
- There is no consortium agreement for this short term collaboration
- CH has fallen into the project managers role :-)
- Talk of setting up a Content Management System (CMS), mailing list and having regular telecons.
- Milestones over next few months, ie, AGILE conference, Potsdam OGC TC, OGF23
- AOB
- Next Meeting 2008-04-25 in Munich
- References/Reading
- Browsing
- Deegree
- Help with translation into English
- Review of "A Framework of Space-Time Modelling with Machine Learning for Environmental Data Forecasting" for Transactions of the Institute of British Geographers
- Notes to editor:
- This review is my opinion based on my limited understanding and knowledge of the subject and a reasonable amount of Web based searching in a couple of short sessions (a few hours work) since I agreed to review this article.
- In general this is good work and I appreciate the authors efforts in this important field of research.
- I am not convinced that a new framework is presented here, nor is it defined what this means.
- The article does not consider a new paradigm like Openshaw in 1999, but tries to outline a method (albeit a combination of techniques) that fits with that paradigm of Geographical Data Mining.
- The combination of techniques is brought to bear on measuring the correlations and trends in some geographic data and the application is new and interesting.
- The combination of techniques is shown to produce some better results than applying the results individually.
- Essentially, there is data pre-processing to generalise and generate useful variables that in combination can predict or explain another variable, and there is the pattern matching or model that does the prediction or explaination.
- I would like this work to reference and review the following which I have been involved in:
- I will suggest the authors consider this work.
- I'd like to suggest that the title be changed to something along the lines of:
- Combining STARMA and ANN for Environmental Data Forecasting: An Application to Climate Modelling in China
- Detailed notes to authors
- I'd like to suggest that the title be changed to something along the lines of:
- Combining STARMA and ANN for Environmental Data Forecasting: An Application to Climate Modelling in China
- I don't think that you are proposing a new framework with the so called "four-stage essential procedure", I think you are applying a basic and general modelling procedure that has been used countless times: prepare data, visualise/explore data, model, analyse results; and, repeat.
- I would like this work to reference and review the following:
- Overall, this is good work and I appreciate your efforts in this important field of research. However, the article should be polished further prior to publication.
- I will now suggest some detailed changes taking each section in turn.
- (Unfortunately the line numbers in the margin of my print out do not match those in the text, so I hope you can follow.)
- Abstract
- Page 1 line 16: replace "MAL" with "MAL" or remove "(MAL)"
- Page 1 line 17: remove "the"
- Page 1 line 24-30: apply not propose
- Page 1 line 32: remove "international"
- Section 1: Introduction
- Page 2 line 23: Start this sentance at STARMA removing "Due to the demanding significant increment..."
- Page 3 line 20: replace "testings" with "tests"
- Page 3 line 29: insert "than" between "when" and "the"
- Page 4 line 42: replace "The strongest" with "A"
- Page 6 line 15-21: This does not make sense to me!
- Page 7 line 42: remove "it is claimed" and add a reference
- Section 2.1
- Page 9: Insert reference to Openshaw S., Perrée T., Turner A.G.D., Turton I.J. (1998)?
- Section 2.2
- Page 12: change "white noise" to "can be considered random" or "are approximately random" or something or explain what the term "white noise" really means
- Section 2.3
- Page 16 line 42: Surely one can only remove outliers if they are known to be erroneous, or as part of say a monte carlo or combinatorial data removal?
- Page 17 line 7: Figure 1 is inconsistent as it does not use the term "ESDA"
- Section 3.1
- Page 18 line 47: remove "the China" and add "in China" at the end of the sentence
- Page 18 line 52: remove "international"
- Page 19 line 10: Why would they be normally distributed?
- Page 19: How is the training and validation data split? Please provide details.
- Page 19: The last two sentences are unclear. Please try again
- I have to admit that I then skipped to the conclusion.
- Section 4: Conclusion
- Page 28 line 41: remove "we successfully used" add "was used" after (MLA)
- Page 29: Remove "is proposed. Unlike most... this framework is indeed and integrated model that"
- Page 29 line 10: replace "space-time" with space and time.
- Page 29 second paragraph: this does not make it significant.
- Consider editing this in line with my previous comments
- Page 31 line 29: This is simply wrong. Feed forward back propogation nets limitted to one hidden layer need many more neurons to be as representative as ANN with two or more hidden layers. Even so there are pattern recognition tasks that can be carried out with ANN with two or more hidden layers, but not a single one.
- I hope this review helps.
- Accepted to review an article "Visual impression and curve accidents on rural roads" for Transportation Research Part F: Traffic Psychology and Behaviour.
- Browsing
- 2011 UK Census Output Consultation
- How exciting!
- Submitted two comments on the blog:
- http://www.ukcensusoutputs.net/blog/2008/03/10/forthcoming_themes#comment-60
- I would like a pseudo anonymised ouput from the 2011 Census. I don't care about the locations of individuals. It would be good to have this like the Household SAR for those in Households. The psuedo part of the annonymisation is that each individual is given a unique ID which is linked with name and address in a secure file that can be negotiated for linking by organisations like the cancer registry.
- http://www.ukcensusoutputs.net/blog/2008/03/25/data_feeds#comment-59
- I think the idea of a data feed is to provide data as required. This reduces the need for having multiple versions of datasets duplicated here and there. If done right then a user knows what version of data they are using and can access that same version at source even if a newer version is available, say for example, with some errors fixed. Good metadata is best for good feeds. Are there plans to feed user derived data as well as the provided data generated from source?
- OGC Grid Collision, MoSeS, NCeSS e-Infrastructure for the Social Sciences (NeSS)
- Using OGSA-DAI to Grid enable data for the Arts, Humanities and Social Sciences - part 2, Web Based
- Telephone call with Chris Higgins:
- Invited to join a meeting on Friday 2008-04-04
- SEE-GEO Security Telecon
- Richard Sinnott, Andreas Matheus, Christopher Kunz, Christian Kiehle, Mike Jones, Chris Higgins, Michael Koutoumpas, Andy Turner, Stefan Strobel, ...
- Main aim is to get Richard and Andreas collaborating to bash together Grid and OGC Security for Geospatial.
- SEE-GEO Meeting 2008-03-20
- Unresolved issue:
- Wanting detailed specifics of security of NCeSS demonstrator.
- An attempt to use GSI for all security was thought to be a waste of time.
- Basically Junaid was told to hang on while the problem of securing the data ends is solved.
- Whatever the protocol for communicating with the user in the system:
- It goes through client and or server and or round the side.
- MoSeS
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