Hi Andreas, All,

First of all my best wishes for a happy and prosperous New Year.

I believe there is some confusion with ToxModel, just because during the
summer we worked in parallel in a similar use case, which just by chance we
called ModelTox. There are a few differences between the two use cases, but
the main difference is that ModelTox aims to create and compare multiple
models, while ToxModel creates a single model. If I am not wrong, we have
agreed upon the implementation of ToxModel. I also did not manage to find
any documentation on ToxModel on the Web page, so I searched over my e-mail
archive and I found the word file that is attached. 
For reference, documentation of ModelTox can be found at
http://www.opentox.org/data/documents/partner/wp/1/use-cases/usecasesclass3/
usecaseclass3cata/UC%203.A.5/view
and certainly we need to change the name of this use case to avoid any
further confusion.

Best regards,
Harry  

-----Original Message-----
From: development-bounces at opentox.org
[mailto:development-bounces at opentox.org] On Behalf Of Andreas Karwath
Sent: Tuesday, January 05, 2010 11:33 AM
To: tobias.girschick at in.tum.de; opentox development mailing list
Subject: Re: [OTDev] Usecase development roadmaps

Hi Tobias & all,

I have added the pages (in form of articels) to the testing part in  
the development section of the opentox web page:
http://www.opentox.org/dev/testing/use-case-development

This includes two pages (FastTox and ToxModel) as well as an issue  
tracker for both of them. The pages are enabled for commenting.
What is still required is a use case specific mailing list - or we use  
this one right here (OTDev).

I started filling in the FastTox use case - more or less as a  
placeholder for the real workflow.

I will be unable to participate in todays meeting, however. I will try  
to work on it tomorrow afternoon , or Thursday.

Just for clarification - would you have a description for ToxModel? As  
I could not find any on the web page.

Cheers,

a.karwath


On 05 Jan 2010, at 09:45, Tobias Girschick wrote:

> Hello Martin, All,
>
> I think that the following use cases are relevant for ToxModel:
>
> 3.A.1,
> 3.A.2,
> 3.A.3,
> 3.A.5,
> 3.B.1 (maybe in a simplified version, where the user just applies a
> selection algorithm)
> 3.C.1,
> 3.C.2,
> 3.C.5 (?)
>
> regards,
> Tobias
>
> On Mon, 2010-01-04 at 15:05 +0100, Martin Guetlein wrote:
>> Hello All,
>>
>> I hope everybody has had nice holidays.
>>
>> On Wed, Dec 23, 2009 at 2:12 PM, Andreas Karwath
>> <karwath at informatik.uni-freiburg.de> wrote:
>>>
>>> 3.) Could one help me, to identify the ToxModel in our use case
>>> szenarios? Is this mapping correct?
>>>
>>>       FastTox : 3.A.1 Given a chemical structure, predict an  
>>> endpoint  ( http://www.opentox.org/partners/usecases/3a1
>>> )
>>>               if so which version? Original, IST or TUM?
>>>
>>>       ToxModel:
>>>               3.A.2 Given a set of endpoint data, develop and  
>>> store a predictive
>>> model ( http://www.opentox.org/partners/usecases/3a2 )
>>>       or:
>>>               3.A.5 (was originally 3.A.8) Given set of data for  
>>> endpoint,
>>> develop, internally validate and store multiple predictive models  
>>> ( http://www.opentox.org/partners/usecases/3a5
>>> )
>>>
>>
>> It would be very nice if people could help us to select the use  
>> cases,
>> that are related to ToxModel and FastTox. This is needed to create  
>> the
>> roadmaps on the opentox webpage,
>>
>> Best regards,
>> Martin
>>
>>
>
>
> -- 
> Dipl.-Bioinf. Tobias Girschick
>
> Technische Universität München
> Institut für Informatik
> Lehrstuhl I12 - Bioinformatik
> Bolzmannstr. 3
> 85748 Garching b. München, Germany
>
> Room: MI 01.09.042
> Phone: +49 (89) 289-18002
> Email: tobias.girschick at in.tum.de
> Web: http://wwwkramer.in.tum.de/girschick
>
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development

Dr. Andreas Karwath
Research Assistant
-----------------------------
Autonomous Intelligent Systems / Machine Learning Lab
Institute for Computer Science
Albert-Ludwigs-Universität Freiburg
Georges-Köhler-Allee 079
D-79110 Freiburg
Germany
-----------------------------
+49 (0)761 203 8029 (office)
+49 (0)761 203 8007 (fax)
www.karwath.org (web)
karwath at informatik.uni-freiburg.de (work)
andreas at karwath.org (private)
andreas.karwath (skype)



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