Getting Started

From ICISWiki

Contents 1 What can ICIS do for me? 2 What needs to be done to set up a new ICIS system 2.1 A. Set up the Germplasm Management System 2.2 B. Set up the Data Management System 2.3 C. Set up the Gene Management System and the Inventory System 2.4 D. Set up local data management systems for breeding teams or genetic resources groups. 3 Where can I get the latest ICIS software and documentation? 4 What are the system requirements to run ICIS? 5 ICIS training and training materials

What can ICIS do for me?

• Bioinformatics and crop information systems in rice research pdf
• Generation Challenge Programme (GCP): Standards for Crop Data pdf
• The International Rice Information System. A Platform for Meta-Analysis of Rice Crop Data pdf
• Linking genotype to phenotype: the International Rice Information System pdf

What needs to be done to set up a new ICIS system

The following steps need to be taken to get an ICIS based system up and running for any crop. If there is already a Central Database for your crop most of the steps in A, B and C may already be done, in any case you will need to work with the administrator of that central database to ensure compatibility with your local installation.

Firstly, identify a database administrator and a data curator and data manager(s). These can all be the same person if you want, but they need skills in database administration, and understanding of database designs, an understanding of the crop, the breeding systems, and the data, as well as skills in managing and manipulating data with excel, ACCESS or SQL. This 'team' should familiarize themselves with ICIS, and the best resource for that is this ICIS Wiki. The empty database and software can be downloaded from the ICIS Communication project on CropForge as indicated below. Once this is done the following steps can be taken (there is more technical help with some of these steps here):

A. Set up the Germplasm Management System

1. Review historical pedigree information and decide how well it has been recorded and hence how easy it will be to parse into an ICIS system. This is a data management task (not a user task) and the data manager needs lots of help from breeders and germplasm people to get it done right. Decide how much historical data is worth the effort of converting. Important sets are germplasm collection catalogues and international testing nurseries.
2. Review the list of germplasm development methods in ICIS and check that all the ones in use for the current crop are available. If not, define them. (It may be useful to delete ones which are never used for the crop to reduce confusion, but never re-use identifiers).
3. Compile a list of germplasm collection and development locations and load these into the ICIS location management tables.
4. Decide on naming conventions for germplasm an nurseries.
5. Develop scripts and procedures to convert historical pedigrees to ICIS format. (ICIS administrators at IRRI, CIMMYT or GCP can help with this)

B. Set up the Data Management System

1. Make a trait dictionary. This requires reviewing all traits usually recorded for the crop and specifying some detail about how those traits are related, described and measured. A template has been developed for this purpose and is on the MBP wiki site. This dictionary does not have to be complete as new traits can always be added, but it helps to get a good basis.
2. Review historical evaluation data and decide how much is important to be loaded.
3. Compile a list of germplasm evaluation locations and load these into the ICIS location management tables.
4. Decide on naming conventions for trials.
5. Annotate historical evaluation data with the Trait Identifiers and the Germplasm Identifiers, Loation Identifiers using an ICIS Workbook so that these data can be directly loaded into the database.

C. Set up the Gene Management System and the Inventory System

1. These systems can be set up later depending on the urgency for storing genetic data and seed inventory data. They take quite a bit of workflow definition to make sure they are compatible with lab and storage practices.

D. Set up local data management systems for breeding teams or genetic resources groups.

1. Identify research groups who need to use the data management system. Decide whether they have the capacity to run the system themselves or need to have a central unit or an application manger run the system and deliver them lists and fieldbooks in a conventional way.
2. For each team set up a local database connected to the central which has been established.
3. Confirm that all breeding methods, locations, traits, and naming conventions are suitable for the team, else add them.
4. Make sure that the group's current germplasm sets and nurseries are in the local or central system, so that all current germplasm has identifiers. This uses similar methods to section A above and needs to be done by a data manager.
5. Train the users of the system in the techniques they need to use. This is best done with a general overview followed by what might be called 'context sensitive training'. That is, when they need to do a task - prepare a nursery, prepare a stock list, generate a fieldbook etc they can call on someone to come and show them how to do it, and then do it themselves the next time with less help. It is not always possible to do it this way and some training material is available for adaptation to different crops (See below).

<input type="hidden" id="gwProxy"></input><input type="hidden" id="jsProxy" onclick="jsCall();"></input>

Where can I get the latest ICIS software and documentation?

• ICIS Software download site CropForge
• Release notes Ver 5.5 notes
• Installer download Ver 5.5.1 zip
• Technical documentation Ver 5.5 TechDoc

What are the system requirements to run ICIS?

ICIS training and training materials

TDM Breeders Training Course 5.5