Psitta Gen Calc

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madas
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Psitta Gen Calc

Post by madas » Wed Feb 06, 2013 1:07 pm

Hi,

i managed to finish the new Version of my GenCalc. Now you can calc IRNs, ARN, Alexandrines and Plumheads.
Beside the common base mutations it considers 'deep', dom. pied (possible as spangle), the multiple alleles blue with turq and Aqua, NSLino with bronze fallow and pastel and edged as sexlinked domiant Mutation.

prerequisites: Windows, .Net Framework 4 and Windows Installer 4.5
installation: visit this http://www.halsbandsittiche.de/PsittaGe ... ublish.htm Website and click the install button.
update: the application checks for updates on every start.
future: saving and loading calculations; calculate cross-over rates.

usage: to input the genetic makeup of the parents click on the arrow right to the button with the mutation name. then a new menu is open with all the available mutation for this species represented by checkbox foreach. To select a mutation as split click once, to select a mutation as color click twice and to deselect it click once again. :) To input a pallidino, bronze fallow NSLino or turquoiseblue please select the base allele means ino, NSLino or blue as color first and the second allele as split. If you like to input an aquaTurquoise then select both as split, same for pastelBronze fallow.

Hope you find it usefull. :)
If you find some bugs or scientific erros please feel free to write a commet. :D

greetings.

madas
Last edited by madas on Thu Feb 07, 2013 4:13 am, edited 4 times in total.

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Re: Psitta Gen Calc

Post by madas » Wed Feb 06, 2013 1:29 pm

To improve this little application i need some help. There are two language options that software is offering. A build in for the scientific view and a country-specific which should fit the needs of the breeders around the world.

Country-specific applied on the scientific mutation cinnamon means: in Germany "zimt", in the Netherlands "isabel", in France "i dont know" :) and so on.

So i would like to ask some of you to translate the scientific names to your country names. If translated please send it back to me via email so i can integrate it into the Software.

@Recio: https://www.dropbox.com/s/aj3ivkomtitmbci/fr-FR.xml
@Willy: https://www.dropbox.com/s/fltiu1cfpqps224/en-AU.xml
@Tienie or Deon: https://www.dropbox.com/s/rk4nemzxx495cjx/en-ZA.xml
@someone from UK: https://www.dropbox.com/s/9jzhnk9kd1yveyz/en-GB.xml
@someone from US: https://www.dropbox.com/s/92x7frau7n79mw3/en-US.xml

The Terms under GUI and INHERITANCE can remain (except for Recio). Important are the Terms under MUTATIONS.
You only have to change terms between XML-Tags. Example for cinnamon in Dutch: <CINNAMON>cinnamon</CINNAMON>
had to be changed to <CINNAMON>isabel</CINNAMON>

thx in advance.

madas

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Re: Psitta Gen Calc

Post by Johan S » Wed Feb 06, 2013 11:28 pm

Having developed software myself, I know that this is a big effort, so thanks Madas! I'm sure a lot of people will benefit from it, esp. since it takes more recent developments into account.

Unfortunately -
madas wrote:prerequisites: Windows, .Net Framework 4 and Windows Installer 4.5
I won't be able to use it. :cry: I'll have to wait until you feel like dabbling in mobile platform software development (Apple, Android, etc.). But fantastic effort none the less!

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Re: Psitta Gen Calc

Post by prodigy » Thu Feb 07, 2013 12:06 am

Hey Madas,

Looks great !

Installed with out a glitch on Windows 7

Any chance of an offspring export to note pad button in the next version this would make it the perfect tool ?

regards,

Peter

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Re: Psitta Gen Calc

Post by madas » Thu Feb 07, 2013 12:13 am

Johan S wrote:Unfortunately -
madas wrote:prerequisites: Windows, .Net Framework 4 and Windows Installer 4.5
I won't be able to use it. :cry: I'll have to wait until you feel like dabbling in mobile platform software development (Apple, Android, etc.). But fantastic effort none the less!
thx. Yeah i know but i haven't the time to learn a new (or two) programming language. So adapting this software on windows phone could be the first step.
But not in the next two or three months. :( And furthermore i am not a big fan of the apple hipe. Every year the same s**t in a new case for around 500€. :twisted:
So i am buying birds instead since I have more of it. :lol:

greetings.

madas

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Re: Psitta Gen Calc

Post by madas » Thu Feb 07, 2013 12:14 am

prodigy wrote:Hey Madas,

Looks great !

Installed with out a glitch on Windows 7

Any chance of an offspring export to note pad button in the next version this would make it the perfect tool ?

regards,

Peter
Try ctrl+v within notepad. It's already build in. :D

madas

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Re: Psitta Gen Calc

Post by prodigy » Thu Feb 07, 2013 12:40 am

YOU ARE THE MAN !

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Re: Psitta Gen Calc

Post by Johan S » Thu Feb 07, 2013 1:26 am

madas wrote:And furthermore i am not a big fan of the apple hipe. Every year the same s**t in a new case for around 500€. :twisted:
So i am buying birds instead since I have more of it. :lol:
Haha, neither am I, but Android is wonderful! :D

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Re: Psitta Gen Calc

Post by Recio » Thu Feb 07, 2013 3:46 am

madas wrote: ... future: saving and loading calculations; add dun-fallow, Khaki and perhaps indigo and sapphire to the mutation list; calculate cross-over rates....
Great work Madas,

I will send to you the French translation. Will you also make a Spanish version? If so ..let me know.

I like to see that in the future you want to "calculate cross-over rates" ... and correct for a common error we see in every genetic calculator.

Thanks Madas.

Recio

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Re: Psitta Gen Calc

Post by madas » Thu Feb 07, 2013 4:07 am

Recio wrote:
madas wrote: ... future: saving and loading calculations; add dun-fallow, Khaki and perhaps indigo and sapphire to the mutation list; calculate cross-over rates....
Great work Madas,

I will send to you the French translation. Will you also make a Spanish version? If so ..let me know.

I like to see that in the future you want to "calculate cross-over rates" ... and correct for a common error we see in every genetic calculator.

Thanks Madas.

Recio
If you translate your fr-FR.xml file then you can do it a second time for spanish but save as es-ES.xml. Then i only need to add the file. The rest is done by the programm. :)

Madas

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Re: Psitta Gen Calc

Post by madas » Thu Feb 07, 2013 4:12 am

indigo, sapphire, khaki and dun-fallow added. Restart the program for new update.

Happy calculating.

madas

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Re: Psitta Gen Calc

Post by Ring0Neck » Thu Feb 07, 2013 4:53 am

Brilliant Job Madas !! Thanks Heaps !

BTW Android/Wind Rules - Apples ... i feed my birds, nicely sliced.

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Re: Psitta Gen Calc

Post by trabots » Thu Feb 07, 2013 4:29 pm

indigo, sapphire, khaki and dun-fallow added. Restart the program for new update.
Including 'sapphire' gives an unproven mutation credibility when the full expression has never been produced. Like I keep saying, I have a 'sapphire' bred from an IndigoBlue. It is a Violet IndigoBlue Pallid which has a paler yellow head than what is usual for an IndigoBlue Pallid to go along with the reduced psitticin it shows. My knowing the parentage confirms to me that it is just variation. I won't have an image until I set it up for breeding. Let's have the df bird, not a bird with only one 'sapphire' gene!!! Let's have some images of a 'sapphire' if it is in fact real. Does anyone other than me on this forum have one? If not, why does it warrant such ready acceptance? Why isn't 'azure' included when it comes with the same Babu reference?

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Re: Psitta Gen Calc

Post by prodigy » Thu Feb 07, 2013 10:34 pm

First live application update to version 1.0.0.15 worked perfectly

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Re: Psitta Gen Calc

Post by Johan S » Thu Feb 07, 2013 11:30 pm

madas wrote:dun-fallow
Madas, do you have some pics? You can start a new topic to keep this one clean and to the point.
Last edited by Johan S on Thu Feb 07, 2013 11:42 pm, edited 1 time in total.

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Re: Psitta Gen Calc

Post by madas » Thu Feb 07, 2013 11:31 pm

Johan S wrote:
madas wrote:dun-fallow
Madas, do you have some pics? You can start a new topic to clean this one clean and to the point.
Tienie already started a topic here.

viewtopic.php?f=26&t=16511

greetings. :D

madas

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Re: Psitta Gen Calc

Post by Johan S » Thu Feb 07, 2013 11:43 pm

Thanks!

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Re: Psitta Gen Calc

Post by Recio » Tue Feb 12, 2013 12:56 pm

Hi Madas,

I was able to download the file into the dropbox but I could not change the words to translate. Maybe it is a problem wit my software???

Regards

Recio

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Re: Psitta Gen Calc

Post by madas » Tue Feb 12, 2013 1:12 pm

Hi Recio,

download and save as xml file. Then open it with notepad++ for example. And then change the words between the tag.
If you still are not able to change them then you can mail me a list with the translated words.

thx in advance.

madas

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Re: Psitta Gen Calc

Post by Recio » Tue Feb 12, 2013 2:50 pm

Hi Madas,

I have two left feet with computers ... so I will mail you directly the translation.

Recio

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Re: Psitta Gen Calc

Post by Johan S » Wed Feb 13, 2013 12:15 am

Recio wrote:Hi Madas,

I have two left feet with computers ... so I will mail you directly the translation.

Recio
That must be the problem! Rather try using your hands. People don't normally use their feet... :lol:

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Re: Psitta Gen Calc

Post by Carr.birds » Wed Feb 13, 2013 11:17 am

Stefan

Thanks great work. I think you can add Platinum to SL mutations.

Tienie

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Re: Psitta Gen Calc

Post by trabots » Wed Apr 03, 2013 5:25 pm

madas wrote: To input a pallidino, bronze fallow NSLino or turquoiseblue please select the base allele means ino, NSLino or blue as color first and the second allele as split. If you like to input an aquaTurquoise then select both as split, same for pastelBronze fallow.
Madas, I have just realised you use the same treatment as Gen Calc for heteroalleles except in reverse. Why is it that in TurquoiseBlue for instance, you treat Blue as visual and Turquoise you treat as split?? The bird is not Blue. Both Turquoise and Blue are each recessive mutations in their own right. There is no 'base allele', Blue is no more important genetically than Turquoise. We have species with only df Parblue mutations and no Blue yet discovered. In IRNs Indigo, Turquoise, Blue and possibly Emerald, all alleles, so share a locus and are all equally dominant over each other. What will happen if say Deep gets proven as allelic to Dark? Which is assigned 'base allele' status, first to be discovered? That is unscientific. As I have told Martin Razek, just treat them for what they are in fact, split for both Turquoise and Blue. Yours and Martin's treatment of alleles creates so much unnecessary confusion as evidenced on this forum all the time. One gene or 2 genes (except sex-linked hens so only one option), so simple.

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Re: Psitta Gen Calc

Post by Johan S » Wed Apr 03, 2013 11:47 pm

trabots wrote: just treat them for what they are in fact, split for both Turquoise and Blue. Yours and Martin's treatment of alleles creates so much unnecessary confusion as evidenced on this forum all the time.
Willy, I don't agree with the statement of the double split. That would mean that the bird will have the wildtype phenotype, like for example green / blue / fallow. We shouldn't treat alleles that way, as it will cause even more confusion. Or am I understanding your statement incorrectly and you don't mean that a TurquoiseBlue should be presented as green / blue / turquoise. :?:

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Re: Psitta Gen Calc

Post by madas » Wed Apr 03, 2013 11:55 pm

trabots wrote:
madas wrote: To input a pallidino, bronze fallow NSLino or turquoiseblue please select the base allele means ino, NSLino or blue as color first and the second allele as split. If you like to input an aquaTurquoise then select both as split, same for pastelBronze fallow.
Madas, I have just realised you use the same treatment as Gen Calc for heteroalleles except in reverse. Why is it that in TurquoiseBlue for instance, you treat Blue as visual and Turquoise you treat as split?? The bird is not Blue. Both Turquoise and Blue are each recessive mutations in their own right. There is no 'base allele', Blue is no more important genetically than Turquoise. We have species with only df Parblue mutations and no Blue yet discovered. In IRNs Indigo, Turquoise, Blue and possibly Emerald, all alleles, so share a locus and are all equally dominant over each other. What will happen if say Deep gets proven as allelic to Dark? Which is assigned 'base allele' status, first to be discovered? That is unscientific. As I have told Martin Razek, just treat them for what they are in fact, split for both Turquoise and Blue. Yours and Martin's treatment of alleles creates so much unnecessary confusion as evidenced on this forum all the time. One gene or 2 genes (except sex-linked hens so only one option), so simple.
Yeah i know. But it is like it is. At the moment i haven't the time to re-write the whole code (the little change to the checkbox behaviour results in a complete refactoring of the code, means calculation process and so on). And every change has to be tested for working as expected. :(

BTW: Why do we write bl*tq for the gen Symbol of the turq allele? Following your thoughts we should only write tq, right? I haven't assigned the base allele Status the blue or SLino or NSLino. I am only following this scheme at the moment.

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Re: Psitta Gen Calc

Post by trabots » Thu Apr 04, 2013 6:19 pm

Why do we write bl*tq for the gen Symbol of the turq allele?
Madas, "we" are those who use pure genetics code, ie: professional geneticists. We breeders don't need to use that code when we have names for these mutations which are far easier to understand. It angers me when parrot gurus use this code when 99% of breeders don't understand it. I don't know the code nor ever want to, but bl*tq is the heteroallele is it not? Wouldn't the homozygous Turquoise be tq*tq? It is just semantics justifying "base allele" for Blue because this code puts it first. The code would work equally well with tq*bl. What is the code for Indigo? for Deep? The code will always lag reality with regards to bird breeding so why ever use it in our context, that of breeding mutations?
At the moment i haven't the time to re-write the whole code (the little change to the checkbox behaviour results in a complete refactoring of the code
I fail to see how just treating allelic genes like every other gene for which your calculator already has the "code", is a problem. All it means is the birds which are double split for allelic mutations have a visual result. That difference is effected easily just with words. As I referred to before, what if Deep is found to be allelic to Dark? If you undertake the admirable task of creating a genetic calculator you should be willing and have the time always available to update it continually as these new mutations are discovered. This would be a piece of cake if one tick box = one gene and the other tick box = two genes. Declaring a heteroallele visual for one allele and split for another is absurd.

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Re: Psitta Gen Calc

Post by madas » Thu Apr 04, 2013 11:34 pm

trabots wrote: Madas, "we" are those who use pure genetics code, ie: professional geneticists. We breeders don't need to use that code when we have names for these mutations which are far easier to understand. It angers me when parrot gurus use this code when 99% of breeders don't understand it. I don't know the code nor ever want to, but bl*tq is the heteroallele is it not? Wouldn't the homozygous Turquoise be tq*tq? It is just semantics justifying "base allele" for Blue because this code puts it first. The code would work equally well with tq*bl. What is the code for Indigo? for Deep? The code will always lag reality with regards to bird breeding so why ever use it in our context, that of breeding mutations?
I don't agree here. Using genetic code resp. symbols does not cause any confusion as it is with "written" names. The gen code is clearly (100% correct) defining the bird makeup. So most People speeking on turquoise ringneck are refering in real to a turquoiseBlue. And you have always ask them "Do you mean homozygous or heterozyguos?". That's annoying too. But then using the gen code instead you are 100% sure what you speak about.

Your usage of the gen symbols isn't correct at all. bl*tq is a gen Symbol for only one allele. To represent the whole gen you need to alleles. Here are some examples for the blue locus (D is added due to the linkage between dark and the blue locus; there no offical gen Symbol for Indigo so i have used "in").

green: D+_bl+/D+_bl+
green /blue: D+_bl+/D+_bl
green /turquoise: D+_bl+/D+_bl*tq
blue: D+_bl/D+_bl
turquoiseBlue: D+_bl/D+_bl*tq
turquoise: D+_bl*tq/D+_bl*tq
aquaBlue: D+_bl/D+_bl*aq
turquoiseAqua: D+_bl*aq/D+_bl*tq
indigoBlue: D+_bl/D+_bl*in
indigoAqua: D+_bl*aq/D+_bl*in

and so on. Easy isn't it? :)
trabots wrote:It angers me when parrot gurus use this code when 99% of breeders don't understand it
And it angers me that the 99% of breeder aren't willing to learn some basic genetics. Bird breeding is more then combining two nice looking birds, feeding them, setuping nextboxes and waiting for the offspring to sell for good money. Even if your are a mutation breeder. We are responsible for the birds we breed with and so it's only fair to learn some (genetics) basic (include inheritance and gen codes). Without that you can't be sure what you sell to other people resp. you don't know if you got ripped of by the seller. And this at least one reason why we have such a big mistrust among the whole breeding community.
trabots wrote:I fail to see how just treating allelic genes like every other gene for which your calculator already has the "code", is a problem. All it means is the birds which are double split for allelic mutations have a visual result. That difference is effected easily just with words. As I referred to before, what if Deep is found to be allelic to Dark? If you undertake the admirable task of creating a genetic calculator you should be willing and have the time always available to update it continually as these new mutations are discovered. This would be a piece of cake if one tick box = one gene and the other tick box = two genes. Declaring a heteroallele visual for one allele and split for another is absurd.
Adding new mutation isn't a problem because the handling for all kind of mutations is already implemented on an abstract basis. But this abstract basis is working on the assumption that you have to input the allele base as color and the other allele as split. And the whole offspring is calculated under this assumption too.

My gen-calc was made as a byproduct then dealing resp. learning the Basic genetics for ringnecks resp. parrots. The whole project was made in my free time after a 10 hours working day. And i thought it would be nice to share it with you. I always welcome new suggestions but i think it is up to me whether and when i am able to implement them. Perhaps you are a pensioner i am not. So my free time is limited. And nearly 75% of the free time is dedicated to my bird hobby. So i don't think my family is willing that it reaches 100%. :D

greetings.

madas

PS: So lets wait what some other people think about your suggestion and then perhaps in two or three months i will be able to refactor the source code.

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Re: Psitta Gen Calc

Post by trabots » Fri Apr 05, 2013 11:09 pm

green: D+_bl+/D+_bl+
green /blue: D+_bl+/D+_bl
green /turquoise: D+_bl+/D+_bl*tq
blue: D+_bl/D+_bl
turquoiseBlue: D+_bl/D+_bl*tq
turquoise: D+_bl*tq/D+_bl*tq
aquaBlue: D+_bl/D+_bl*aq
turquoiseAqua: D+_bl*aq/D+_bl*tq
indigoBlue: D+_bl/D+_bl*in
indigoAqua: D+_bl*aq/D+_bl*in

and so on. Easy isn't it?
Madas, you are correct, I havn't a clue about the above dog's breakfast to the right of the colons, I just took an assumptive guess about bl*tq, sorry I was wrong. To the left of the colons we have what most breeders understand. Can you advise of a situation for us simple minded breeders where-bye assuming the correct names are used, the use of the code on the right will be more useful to us? Next time someone asks for a breeding outcome, why not use the geneticists' code to answer their query and let's see how many ??? we get?
And it angers me that the 99% of breeder aren't willing to learn some basic genetics. Bird breeding is more then combining two nice looking birds, feeding them, setuping nextboxes and waiting for the offspring to sell for good money. Even if your are a mutation breeder. We are responsible for the birds we breed with and so it's only fair to learn some (genetics) basic (include inheritance and gen codes).
It is not than they aren't willing, it is that the blinders go up as soon as they are faced with something other than words.
Why aren't all the genetic calculators converting the words to code first and displaying outcomes in code? Basic genetics is covered in Terry's book quite easily without the use of this code and in fact other than the introduction of symbols for mutations in the advanced portion of the book, the code is not used for breeding outcomes, he uses words alone.
this abstract basis is working on the assumption that you have to input the allele base as color and the other allele as split. And the whole offspring is calculated under this assumption too.
Yes but if you just group all alleles by locus and continue to use exactly the same tick boxes you use for all other mutations
with a note: 'Any two genes from this locus will produce a mutant phenotype and a bird can only have two genes from this locus, either two of the same or one each of any other two', the calculation is identical. You would just need a block to ticking more than two single gene boxes from this group or more than one double gene box. In fact if each mutation was treated tick*tick, ie: a tick for a gene, it becomes even simpler to use, it wouldn't matter whether a left side or right side box was ticked. Simple words could also then state the difference between the groups of incomplete and complete dominant mutations or that sex-linked hens can only have a single mutant gene. Things like cross-over and linkage, while needed technically for calculations are not needed by the users who just want outcomes.
My gen-calc was made as a byproduct then dealing resp. learning the Basic genetics for ringnecks resp. parrots. The whole project was made in my free time after a 10 hours working day. And i thought it would be nice to share it with you. I always welcome new suggestions but i think it is up to me whether and when i am able to implement them
As I said Madas that is admirable and I sincerely mean that. It seems however that every new calculator is set out to outdo the previous calculators and from what I see none tries to simplify things for the 99%ers. And to the expected question: Willy why don't you design a simpler to use genetic calculator? I just did above and all it needs is someone to slightly modify an existing one, skills which I do not have.

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Re: Psitta Gen Calc

Post by madas » Fri Apr 05, 2013 11:22 pm

Hi Willy,

I will See what i can do for you. But dont expect it within the next two months. Its breeding time here.

madas

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Re: Psitta Gen Calc

Post by madas » Sat Apr 06, 2013 1:05 pm

molossus wrote:Madas hi,
hope you all are having better weather.
Perhaps next week.

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Re: Psitta Gen Calc

Post by trabots » Sat Apr 06, 2013 10:03 pm

madas wrote:Hi Willy,

I will See what i can do for you. But dont expect it within the next two months. Its breeding time here.

madas
Madas, I am in zero hurry but thanks for that, again sincerely. Just trying to simplify things so more will get involved. The weather is fabulous here in Perth today.

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Re: Psitta Gen Calc

Post by madas » Mon Apr 08, 2013 2:20 am

trabots wrote:
madas wrote:Hi Willy,

I will See what i can do for you. But dont expect it within the next two months. Its breeding time here.

madas
Madas, I am in zero hurry but thanks for that, again sincerely. Just trying to simplify things so more will get involved. The weather is fabulous here in Perth today.
No Problem. You are welcome. :D

madas

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