ICIS Mini-Workshop 2007

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ICIS Mini-Workshop 2007, IRRI, March, 26-30, 2007

Participants

• IRRI

Graham Mclaren

Richard Bruskiewich

Arllet Portugal

Beth Sison (IMS)

Warren Constantino (WorkBook)

Candy Pimentel (SetGen, GMSSearch)

Weng Valerio (GEMS)

Ching Habito (Diagnostic/Validation Tools )

William Eusebio (LAuncher /GMSInput)

Vivay Salazar (ICIS Help)

Ella Herrera (GRIMS)

Ruaraidh Hamilton (GRIMS)

..

• CBWA: Canola Breeders Western Australia

Cameron Beeck

• VIDA Australia

Selwyn Ellis

• Bayer CropScience

John de Leon

• Nunhems

Casper aan den Boom

• Monday: March, 26

1. Introduction and short of update of participants of their current status of ICIS.

2. Outcome of meetings at IRRI concerning possible changes at database structure and modules

-Conduct a general review of the ICIS schema to identify, document and prioritize for implementation, what changes (in schema, documented use, etc.) may be required by recent experiences with the IRGCIS and INGER integration.

-Conduct a general review of the ICIS schema to identify, document and prioritize for implementation, the required features of a “next Generation (CP)” ICIS interface..

Proposed database changes:

• STUDY table: Add UserID field, Add folder structure functionalities as in LISTNMS table
• Add DMSCHANGES table to store changes made in Studies by ICISWorkBook. Still to investigate if CHANGES eventually also can be stored in DMSATTR table
• Start using DMSATTR table also RequesterID that need to be linked to a List for GeneBank needs.
• Consider adding of permanent columns to LISTDATA tables for PLOT SIZE (request Nunhems) and REMARKS (Request Bayer). Also investigate possibility of storing information of possible extra permanent LIST columns in DATATTR.
• For further intergration of GRIMS probably one extra "GRIMS" table might be necessary in ICIS.
• In future maybe some other changes are required for further integration with the genomic site, Richard mentioned CHADO db structures.

3. Feature Requests: Mainly FR’s are discussed that have larger impacts for ALL users, like:

a. SetGen: Management Neighboorhood for Derivative AND Generative GID’s

There is more then one definition for Neighboorhood, see also CropWiki The general feeling is that ICIS-users likes to do more with Neigboorhoods. Currentlty only the Management Neighboorhood can be stored via the [-] button in SetGen. This looks fine. Extra functionalities that will be required for Management Neighboorhood are a possibility to EDIT this via EDIT GMS, and a possibilty to start Management Neighboorhoods via the [B-] button.

Other Neighboorhoods, like "Derivative Neigboorhood for n-steps" and "Generative Neigboorhoods" probably can be made easily available by dll-functions. Arllet and Casper will further investigate ths.

b. SetGen: Have unique GID table OVER more LOCAL databases

Therefore NO new function is required, this can be easy done via identifying a "last local GID" in the INSTLN table. By identifying different "last local GIDs" in the different local ICIS implementations every implementation will have it own sets of GIDS.

c. SetGen: Columns in (SetGen) Lists

(Number of Columns (CropForge FR-ID=427, Order of Columns CropForge FR-ID=428, Column Headers CropForge FR-ID=429)

These request will have quite some impact on SetGen and also on the WorkBook. Decided is to start a FeatureRequest on CropForge where the programming impact of these changes will be described and discussed. After discussion it will be decided when and how to implement these requests.

d. SetGen/GMSSearch: Can we support lowercase next to UPPERCASE names in SetGen/GMSSearch

Yes, this is possible, but also need to be described first further in a FeatureRequest (CF_FR-ID=30) on CropForge. Items that should be clear are eg. Where to define Upper/Lowercase option, where might it interfere with the STANDARDIZE names function, How to deal with "CROSS 117" and "Cross 117", are they different names Yes or No etc..

e. GMS Search Layout: On CropForge, FeatureRequestID=177, Ruaraidh Hamilton has made some proposals to change the layout of GMSSearch. Also Nunhems has some ideas to improve GMSSearch.

Discussed items to improve will be specified at CropForge, item: FeatureRequestID=177

f. ICISWorkBook: Implement FolderStructure for Studies (CropForge; FR-ID=431)

The general opion is that we need for Studies a similar folder structure as for List. In general functionalities should be the same as for List (Lock, Hide, Finalize etc.) It still need to be discussed what should be done with Studies that will be deleted from the database by a user. Should we maintain real deleting from the database as is done now, or should we implement a similar system as is implemented for List, where for deleted lists we change the STATUS to 9 and maintain all data in the database, but do no show them anymore to the users.

For more Feature Requestst see also CropForge-Tracker.

4. ICIS Web Site - the Next Generation; what functionality do the various end user communities (breeding, genetic resources, evaluation network) need on the ICIS web site? How can this functionality be coherently developed into one web site application (i.e. storyboard the flow of web page navigation?)

Richard showed progress so far, user interface looks very promissing, but it looks like that another library should be used and that the code partly should be re-written.

• Tuesday: March, 27

1. 'ICIS 5.4 and further; What features do we want in next ICIS versions.(Can ICIS 5.4 be released in Canada?) Are Delphi and VBA the program languages that should be used in (long-term) future (version 6?)?

Decided is that only a few high priority bugs will be solved in ICIS 5.3. From then all changes will be made in ICIS 5.4. Goal is to release an ICIS 5,4 package at the 2007 Workshop at Canada.

For the moment Delphi and VBA are satisfied for all stand-alone applications. For the long-term the goal is that the Browser-based (Java) Web-interface also can be used in "stand-alone" ICIS versions.

2. Feature Requests for ICIS. See CropForge-Tracker for more info.

3. Agenda ICIS Developers Workshop 2007 AAFC. See updates on agenda at CropWiki page.

4. Bi-lateral meetings.

• Wednesday: March, 28

1. MarkerData and ICIS: What is the current status of GEMS? How are which data stored? Which tools are used?

Weng showed a very interesting use-case about loading, linking and presenting SSR marker data and phenotypic data. For this use-case Weng has used the latest functionalities of the ICIS-WorkBook and GEMS. For retrieving the data back from the database PostGres and mySQl are compared as databases. Conclusion is that PostGres is much faster than mySQL. IRRI uses external output tools as GGT and GVT for vizualisation. See for more info CropWiki.

Nunhems is following the same approach, but using Oracle databases for storing data.

2. Testing ICIS modules, Help-files ICIS, ICIS-manuals. How to improve?

Vivay gave a nice presentation about the new ICIS-Help that is currently developed. This is a dynamic BrowserBased help, currently created with RoboHelp. This looks very promising! Ideas are exchanged about where and how to make this help available, probably on CD, but also live via Internet. An ICISWiki page is started to put ideas/remarks for topics that need to become available in ICIS Help.

Nunhems shows the Nunhems Breeding Help, which is also a BrowserBased Help which is created with Help&Manual, a simular tool as RoboHelp. The Nunhems Breeding Help is not only for ICIS at Nunhems, but also for other Breeding-Related-IT issues.

3. Bi-lateral meetings.

Wednesdayevening: March, 28

Workshop dinner

• Thursday: March, 29

1. More bi-lateral meetings

2. ......

• Friday: March, 30

1. More bi-lateral meetings

2. ....