Breeding software

[ChrisK]

Wondering what software the breeders here, amateur and professional, use for tracking their crosses, visualizing pedigrees etc.

[janezee]

Sounds like a family tree program would work, eh? Maybe?
Perhaps a lot more accessible than a dedicated program.

But I've been out of the mainstream of applications for the last 14 years or so.

They just might have easier ways to do it yourself these days. I'm curious to know, too.

[Tom Wagner]

For potatoes...I have been using a really old dos database pedigree program developed by Dr Steve Love of Aberdeen Idaho. I started with the pedigree data provided for potatoes from the Idaho breeding program and augment it with my own data...or updates from Idaho. It is contained on a old computer that I saved just for the pedigree data only. The program was programed by floppy disks given to me. I have no idea how to update the data to a modern computer or share it with anyone.

It has about 5,000 or so potato varieties with an ancestry chart and all.

I typed in many of my own clones and data from many breeding programs

[ChrisK]

I found Peditree put out by Wageningen Univ. and Pedigraph from Univ. of MN. Might try playing around with them. The breeders and field folks at work use PRISM, but I don't need that kind of power or the expense that comes with it!

There's got to be something better than Excel. Google returns many apps aimed at amateur animal breeding...guessing those don't handle selfs well though.

[jennifer28]

Originally Posted by ChrisK

I found Peditree put out by Wageningen Univ. and Pedigraph from Univ. of MN. Might try playing around with them. The breeders and field folks at work use PRISM, but I don't need that kind of power or the expense that comes with it!

There's got to be something better than Excel. Google returns many apps aimed at amateur animal breeding...guessing those don't handle selfs well though.

Chris-

This sounds like something that could be built and not too terribly difficult to build. If I understand what you are wanting it is a database that stores the data on each variety and the successive filial generations? And then you need a way to look at the data so you would want something that would run queries on the database? And it is NOT designed for multiple users to be entering data in paralell, but it is just for one person to use at a time, at a home garden or a single garden site?

If it were me, I would build it with Perl script and store the data in a MySQL database but that is because I like Perl and I am a nerd.
A sad, perl-loving nerd.
But you could just import the MS Excel files into an access database. Then you can run queries in access to look at the data you want. You can also export that data back into excel if you want to.

I would recommend the book Access Database Programming by Steven Roman if you wanted to do it yourself. I like your idea of making something like this. If I were to make something like this, I would definitely give it to you. If you happen to have any database programmer friends, perhaps you can bribe them into making it for you. OR maybe there is someone here on this forum who has already done something like this with Access?

[ChrisK]

Thought about Access or similar but I don't have the skill yet for something as advanced as I'm thinking with phenotype notes, pictures etc that would then output something like:

http://www.brianmahieu.com/lnm_pedigree.html

I might be able to get one of the bioinformaticians at work to build me something in exchange for a case or two of homebrew or tomatoes!

I was thinking a tree like above for the released dwf varieties would be kind of cool on the dwf project web pages. Folks could see the development of the final line released and the variation it came from. I have one I did manually in PowerPoint, of all things, for the Muddy lines to date.

Thanks for the tip on the Access programming book!

[RebelRidin]

As it turns out, I develop in Access. It's my favorite. I just spent today converting and recompiling a suite of apps from Access 97 to 2010. I was amazed how stable the code was across all those versions over time. Practically no mods required to get them up and running.

I find Access to be a very flexible fast-track development platform. With the database structures to anchor it, the design tools it provides and VBA to extend it... I describe it as Visual Basic on steroids.

Any app built can be compiled and distributed for runtime use royalty free too. 2010 even packages your application up into a freestanding installation package for you... super easy distribution and deployment.

Unless you are looking for a web based app... I highly recommend it.

PS - Defining a good data structure and getting the desired outputs defined are the toughest parts of any project like this. In other words... If you know how to organize it and know what you want from it, that's at least half the battle.

[dice]

For people comfortable with Linux, you might find something useful
(and likely free) here for geneology tracking:
http://www.extension.org/pages/32521...tics-101-video

There is also a geneology program (for humans) that is free, runs on
multiple operating systems, called "Gramps" that you might be able
to use for tomato breeding as well. It has its own web site,
with some screen shots so you can see what it looks like:
http://sourceforge.net/projects/gramps/

Gramps is also included on the (free) Linux Genealogy CD (free in
the sense that you can download the cd image, burn it to a cd-r,
boot the cd-r, and you are running Linux from cd with Gramps
included; no charge, and it will not write to your hard drive containing
windows unless you tell it to; great, low-risk way to get a look at
Linux and Gramps at the same time): http://blog.eogn.com/eastmans_online...-released.html

(I immediately thought of Linux because this is the sort of thing
that a programming student might write for a class assignment
or a fun summer project or because some relative needed it or
whatever, and it would likely be open source and GPL, meaning
inspectable by expert programmers for security holes and free
for anyone to use.)

If Gramps is usable for this, though, it runs on Linux but does not
require it (there are versions for Windows, Mac OS X, etc).

[samyaza]

dice : if you run a distribution including a packages management program (such as Debian, Red Hat, Archlinux...), Gramps must be in your official repository.

[ChrisK]

Gramps looks interesting but how do animal genealogy programs handle plants as far as selfing?

[John3]

For those who are interested here's a portable ver (fits on a usb drive) of Gramps (notice on the left side click one of those for the apps they have for other things)
here's the link http://portableapps.com/apps/education/gramps_portable
Note I think it's on the home page but somewhere at that site they will talk with the developers to expand or enhance the apps they offer or create new apps from the main app.

[dice]

Originally Posted by samyaza

dice : if you run a distribution including a packages management program (such as Debian, Red Hat, Archlinux...), Gramps must be in your official repository.

And so it is (Gentoo Linux): gramps-3.2.5 is the stable version on 32-bit
x86 (probably on 64-bit, too, but that computer is presently awaiting
a part).

Originally Posted by ChrisK

Gramps looks interesting but how do animal genealogy
programs handle plants as far as selfing?

Good question. I have not installed or used Gramps, so I do not what
it would make of that (would sanity checking the input report an
error for "same mother and father" for a generation).

I came across a site with a huge number of apps for genetics, but a lot
of them seemed to be written in some legacy language called "R" and
ran on Unix, VMS, etc.

(The "R" language: http://en.wikipedia.org/wiki/R_language
I guess it as not as obscure as I thought. Anyone with classes in
statistics in the last couple of decades probably at least knows
about it. The bookmark for the site with the long list of genetics
programs is on my other not currently booting computer, but most
of it seemed pretty specialized, ie for genetics as rocket science,
rather than a general purpose generational tracking program.
There might be some of those in there, but I did not have
days to comb the list to find out.)

edit:
Looking at the Gentoo ebuild (script for compiling the package),
gramps-3.2.5 is considered the most stable version on 32-bit and
64-bit x86, PowerPC, and Sparc platforms. gramps-3.2.6 and
gramps-3.3.1 are both considered "testing" versions by the
Gentoo ebuilds on those same platforms. It seems to store
the data in a Berkeley db database and use a python interface
to the database, but mostly be written in C. Disabling an
error check for mother-father identity (selfing) if it has one
would probably be straightforward for a C (or maybe python)
programmer.

Getting the gramps developers to add a compile-time
configuration switch to disable it might seem like a wierd
request, though. (On operating systems like Windows, where
the users all use downloaded, pre-compiled binaries, someone
with a Windows developer environment to compile it in would
have to archive a pre-compiled version of gramps with that
error-checking hack to make it publicly available for download.)

But yes, the source code is there, the license is GPL_2, no one
is going to object if someone modifies it to adapt it specifically
to generational tracking for plant breeding. This ends up being
on-going code maintenance, though (tracking bugs reported to
the upstream developers for gramps, and maintaining the parts
that someone modified to keep them in sync with bug fixes
and changes incorporated into the canonical version of gramps).
One would need Windows and/or Mac OS X developer
environments to make pre-compiled versions available to users
on those platforms.