WebIRO is designed to provide a common platform to

• view/edit pedigrees with pedIRO. For details, please visit the pedIRO descriptions.
• to sort files issued of a sequencing machine and format them into the standart linkage format with genIRO. For details, please visit the genIRO descriptions.
• compute lodscores lodIRO or snpIRO. For details, please visit respectively lodIRO descriptions and snpIRO descriptions.

This platform uses Javascript, AJAX, DOM and CSS webtechnologies and also SVG files to display some pictures. For more informations about the compatibilities with your web browser, please have a look to the about sections.

Your webIRO team manager.

pedIRO is a tool to visualise pedigrees by uploading files in the standart pedigree file format. It can also be used to create a pedigree from scratch.

For both uploaded and freshly created pedigrees, you are able to add, delete and modifiy members sex (male, female), diagnostic (healty, affected) and status (alive, dead).

A standart pedigree file format contains the following headers:

Familly Name	UPN	Father ID	Mother ID	Sex	Diag.	Status

Where:

• Familly Name is the name of the familly(ies) contained in your pedigree
• UPN (the Unique Primary Number) is used to identify in a unique manner members of your familly.
• Father ID is where you put the UPN of the father of this member. If this is a founder member, you have to put 0 (zero) as UPN value.
• Mother ID is where you put the UPN of the mother of this member. If this is a founder member, you have to put 0 (zero) as UPN value.
• Sex can have one of the following values:
  • 0 is for an unknown sex
  • 1 is for a male
  • 2 is for a female
• Diag. (Diagnostic) can have one of the following values:
  • 0 is for an unknown diagnostic
  • 1 is for a healthy diagnostic
  • 2 is for a deseased diagnostic
• Status can have one of the following values:
  • 0 is when we dont know whether the member is alive or not
  • 1 is when the member is alive
  • 2 is when the member is dead

GenIRO is a tool to automatically create a per chromosome based standart linkage analysis file that can be used with lodIRO. Basically you need a standart pedigree file format slightly modified uploaded together with a per panel based markers data file(s) exported from a sequencing machine software.

A modified pedigree file formated for GenIRO contains the following headers:

Familly Name	UPN	Father ID	Mother ID	Sex	Diag.	Status	ADN Number

Where:

• Familly Name is the name of the familly(ies) contained in your pedigree
• UPN (the Unique Primary Number) is used to identify in a unique manner members of your familly.
• Father ID is where you put the UPN of the father of this member. If this is a founder member, you have to put 0 (zero) as UPN value.
• Mother ID is where you put the UPN of the mother of this member. If this is a founder member, you have to put 0 (zero) as UPN value.
• Sex can have one of the following values:
  • 0 is for an unknown sex
  • 1 is for a male
  • 2 is for a female
• Diag. (Diagnostic) can have one of the following values:
  • 0 is for an unknown diagnostic
  • 1 is for a healthy diagnostic
  • 2 is for a deseased diagnostic
• Status can have one of the following values:
  • 0 is when we dont know whether the member is alive or not
  • 1 is when the member is alive
  • 2 is when the member is dead
• The ADN number contains the per member ADN number given when samples where sequenced.

A standart exported file has the following headers:

Sample File	Sample Name	Panel	Marker	Allele 1	Allele 2
2007-01-16_A13161-P37_009.fsa	A13161-P37	Panel37-HD5-V2.5	D3S2748	112	260

where:

• The first row is the original file name that contains the raw data but is actually ignored by our software.
• This column is primordial to sort the data on a per member basis. By using the value that directly follows the key word A in this file who is the ADN Number of a member and the ADN Number given into the last row of the uploaded pedigree, we are able to make the correspondance for post treatements.
• This column is actually not necessary and is actually disregarded by our software.
• This columns contains the marker key word
• The last two columns are actually the alleles values.

In our lab we are currently using genemapper from Applied Biosystems to produce this kind of file. This is the main reason of the above headers format. Because this software is currently under developement, we would like to move in the near future to more simple header designed as:

Sample	ADN	Panel	Marker	Allele 1	Allele 2

where:

• The first column contains the sample file name (as above).
• The ADN number to make the correspondance between this file and the pedigree.
• The panel number actually again not absolutly necessary but may be util in some way in the future.
• The Marker number
• The two Alleles values.

LodIRO is a tool dedicated to the linkage analysis. You have to provide a pedigree file and markers data files, select which statistical tool(s) you want for the computation, adjuste the statistical parameters and proceed to the results. For now, only the autoscan and genehunter computation algorithms are available. In the near future we will add merlin and allegro.

SnpIRO

AmIRO is an Animal Manager developped to manage the mouse facilitie at the Institute. It is based on a MySQL database to store data and a web interface to manage the animals, users, autorisations and to provide tools for research matching criterias, tracabilities and statistics.

We provide on the amIRO website the possibility to test it with a low level of authorisation (guest/guest) and so less possibilities that are available for peoples having a high authorisation level. This is because this website is also a testing platform used for developpement of the futur stable release available in the institute.

This facility is not yet available in english. It is planned but not yet done!

If you think this tool can be usefull for you, please use the contact form for more informations.

Contact

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This sections will provide you some tips&tricks to enjoy at the maximum this platforme. First of, this is your actuall web browser settings:

Description	Your settings
Web browser / OS:	CCBot/1.0 (+http://www.commoncrawl.org/bot.html)
Javascript is:
SVG is:

About CSS3

First off, this web site uses the CSS3 styles and is mostly compliants with W3C. As fare has we know, most browser like

• Firefox [2.0.4]
• Iceweasel [2.0.0.2]
• Safari [2.0.4]

can handle CSS3 , but at least ie6 doesn't! This incompatibilities is mostly due to css3-selectors .

About SVG

PedIRO uses the SVG file format to display pedigrees. Althoug here, as far as we know, only

• Firefox [2.0.4]
• Iceweasel [2.0.0.2]

can natively interprete SVG files. With an optional plugin available on the adobe website,

• iExplorer [6.0]

can handle this file format. If you want to test your navigator for SVG compatibilities, try it here .