Talk:Guide Plant Breeding Technician IT

I see there a lot of formatting problems and will work on fixing them.

I will add internal links and subsections when I learn more.


 * Here is howto make make the general pages for internal links Howto write a new Object page on Wikihowto. Its how we link to related howtos and link to wikipedia for definitions.  For instance i made one for plants with your page on it.  Thanks for the amazing guide.  I bet it is one of the best if not the best on Wikihowto ZyMOS 04:00, 5 April 2007 (UTC)
 * But there is no rush to add them. you have obviously already done a ton of work.

PROPOSAL
 * This Wikihowto is for someone interested in the subject of Plant Breeding (Maize, Barley, Triticale and Beans) but who may not have much in the way of resources. It should give one a detailed inside view of the processes involved in plant breeding [operating a plant breeding facility ???] and be very practical. A computer simulation videogame might be better but this Wiki could possibly be used as an information source. I would like it to be accessible to a young person in other countries like Belize,Mexico, Argentina, India, or Russia but I don't know what technologies would be appropriate to discuss in those countries.Perhaps someone from CIMMYT could assist in the edited versions of this Wiki.Dynamically created alternative versions based on country or region might be an idea.

I'm not sure what the best title is. I've called it "Plant Breeding Technician IT" because it is written for someone taking over use of the computer as their main duty but it's quite obsolete as far as modern plant breeding operations such as Monsanto's go. It might be called an operations manual or 'The Mechanics of Plant Breeding Field Operations'.


 * NOTE:This is NOT a wiki on Plant Breeding or Genetics.

Robert W. Jugenheimer wrote a book entitled "Corn: Improvement, Seed Production, and Uses (1976, reprinted 1985) that contains some of the information I want to convey but the references to punch cards and addressograph plates are obsolete and the material I write about is not mentioned in detail by Dr. Jugenheimer but only mentioned in a short miscellaneous section.

I would like the Wiki to include detailed accounts of various alternative ways of doing things and not get stuck on just one way of doing things.

I want the Wiki to be INCLUSIVE and to encourage inclusion of people with an interest in plant breeding in the work of plant breeding.People with Ph.D's in Plant Breeding can act as overseers and mentors of the plant breeding work.

I will probably move the PREFACE and IMPROVEMENT SECTIONS to this DISCUSSION page.However, there are points in the preface and improvement sections that I would like to see in the edited Wiki.

PREFACE
These notes pertain primarily to the record keeping and report generation work I did for a private plant breeding project from Jan. 1995 to Jan. 2000.

One of the things I learned working on this project is that there is a lot that can be done by a handful of dedicated people working together to achieve a goal despite a small budget. It’s possible to start small.

WHY I WROTE THESE NOTES
 * If you don’t write up your post and put it into the hands of your successor, you or your immediate senior will have to repeatedly re-train others and answer questions about the post long after you have vacated the post.

At my current place of employment my supervisor is finding this out as a result of a large employee turn-over for introductory positions.He is having to repeat instructions over and over. In addition, despite the billion dollar status of the business, documentation on the use of data loggers for inventory and ordering is not available to the employees that use them and even the supervisor didn’t know that certain functions were available. When the barcode reader on a machine was not working, the supervisor instructed people to enter the 12 digit bar code manually, which can be tedious. After an employee made a verbal statement within the hearing of the manager about getting a datalogger with a working barcode reader to avoid having to enter long digit strings, the manager showed the supervisor a few days later how to switch to the smaller 6 digit ordering ID when doing inventory work. The supervisor then passed this verbally along to the employee. So one of the reasons I am writing this material down, even though it may be as obsolete as a book on computer punch cards, is to pass on to my successor (and if that person becomes ill, anyone filling his/her position) information regarding my work that may, or may not, still have some usefulness.

If there is a software disaster such as occurred to my predecessor, the emergency methodology that my predecessor passed on to me and that I am writing down here, despite it’s many limitations, may come in handy. I don’t expect that to happen as commercial plant breeding software with extensive bug testing and large numbers of users is now available.This was not the case in  the mid 1980’s and even into the early 1990’s when proprietary customized programs were the only option one had. My successor may very well go through these notes and mark out entire passages as ‘NO LONGER APPLICABLE’, ‘NOT USED’, ‘SUPERSEDED by MS-ACCESS or AGROBASE 2’ etc. but perhaps these notes could be used as a superstructure for an improved set of notes on the office hat and using an electronic version of these notes, one  could more easily make changes to the notes. .

There is an educational reason for writing this material down. Someone interested in the work could get an idea of what goes on. It would be interesting to make a PLANT BREEDING COMPANY multi-media simulation with elements from ELECTRONIC ARTS’ SIM FARM, MS 3D-MOVIEMAKER, camcorder video and something like the tall-red-berry plant breeding simulator (Kweker) on the Wageningen University Plant Breeding website. The proposed simulation would take one through the specifics of the plant breeding work on a yearly cycle with an actual product at the end of a 10 or 20 year cycle.

Another reason I am writing this material down is that, despite all of its errors and ommissions, it might prove useful to someone in a developing country that would like to help with plant breeding but has very little money. Plant Breeding was being done long before computers were invented and before the phrase ‘genetic engineering’ was ever coined. Even if one doesn’t have access to electricity or an obsolete computer, database software and spreadsheet software, these notes will allow one to get an idea of the work that one might do and the flow of the processes. Maybe there is a quipu methodology that works as good as paper records or computer spreadsheets and databases.

I would also like to promote what I call a ‘self-initiated distributed processing’ approach to the plant breeding work rather than the monolithic ‘professional’ multinational company approach. This would be a co-operative approach similar to participatory plant breeding.I have witnessed 2 groups of people and an individual in different fields of endeavour that took the initiative regarding some matter and pooled their resources and accomplished things, while other professionals sat with their feet on their desk saying things were impossible.

There is very little information in a written form regarding the data processing and report generation work involved in plant breeding. Much of it appears to be proprietary knowledge held by individual companies or it’s considered too obvious to put into writing. It might be buried in Government archives and journals.

As of 2003, there is a handbook that lists breeding software but the software and formulas are geared towards advanced genetics and statistics rather than record keeping methodologies. A Canadian software company called AGRONOMIX started selling a pretty good plant breeding program in the late 1990’s but I haven’t had a chance to test it yet. It looks quite good in the internet demonstrations. It’s also quite expensive and so is the training to use the program. A 3 day course costs about $1000. During the years that I was working on this project and even after, in 2003, I visited several Universities and Colleges in Canada looking for written material regarding the work I was doing and couldn’t find anything specifically on the subject. The only book I found was Robert Jugenheimer's United Nations FAO publication on Plant Breeding from the late 1950’s that didn’t get into specifics regarding day to day operations. The use of computers was mentioned but only in a vague way and there was nothing on how paper records were kept. It may be that the material I was seeking is in agricultural colleges somewhere in Canada but the pragmatic nature of the work inclines me to think that plant breeders and technicians didn’t bother to write it down because much of it is quite obvious to them, everyone has a different system and it’s something one does rather than reads about. If someone has written down the specifics of the day to day operations it‘s probably held as proprietary information by the plant breeding company. There are a few books by cereal breeders (wheat, barley, triticale etc.) that get into methodology but again, there is nothing specific regarding how records were kept or what reports were generated.

As someone who had perfect marks in his grade 10 agricultural class, I was surprised to find that at 15 I was taught more about Mendelian and non-Mendelian genetics and subsurface drainage than I ever saw being used by the plant breeders and agricultural producers in the area I was now working in 16 years later. There are some good reasons for this but it’s a good example of the difference between the practical and academic worlds.

As a result of my experiences, I question the teaching of Genetics found in most College and first year University Biology textbooks (I seem to have covered all that material and a bit more in my grade 10 Agriculture Class).I hear in Belgium, high school students have created transgenic plants.

Plants don't appear in the field with genotype tags.The schools have things backwards and most of the Punnett square work is only for academic games like trivial pursuit. It would be better to start with a broader viewpoint with DNA, chromosomes and genes rather than with the historical work of Gregor Mendel.Then one could say, Genetics, not Mendelian and non-Mendelian genetics.Mendel's work is only known because a later researcher,DeVries, needed to show prior art for the same reason that Microsoft referenced Xerox Parc in the dispute over the Macintosh GUI.(In that case there was a clear sequence from Xerox to Apple, however).

The perception of the history of Plant Breeding is distorted by the erroneous impression that there was an historical sequence that went from Mendel's work straight to the work of DeVries and others. This type of erroneous historical impression is quite common as teachers and schools distort the historical sequence to explain things.It occurs often in Physics and even appears in some accounts of the development of computer GUI's.A classic physics example is reference to Dr. Einstein's E= mc^2 formula and atomic weapons, as if Einstein went from the 1905 paper with it's mention of radium salts (see glow in the dark clocks) straight to atomic weapons creation. There is evidence from the 1930's that Dr. Einstein thought of his work as having potential only for use by Cosmologists and theoreticians but he didn't see any practical applications of it.In the popular realm, however, there was quite a bit of hysteria about atomic weapons.There was a chemist named Frederick Soddy who worked with Rutherford, and Dr. Soddy gave lectures before 1900 on nuclear physics and chemistry (published in 'The Interpretation of Radium, 1909').Dr Soddy's book influenced H.G. Wells to write a science fiction story involving atomic weaponry (The World Set Free, 1914) that influenced Leo Szilard (bit of a chain reaction here)to develop the idea of nuclear chain reaction in 1933.Throughout the 1920's there were a lot of science fiction stories that talked about atomic bombs and atomic energy as if it was real,while scientists who didn't want to be lynched as Alchemists,like Rutherford, claimed it was all 'moonshine'.

Another classic physics example is citation of the work of Michelson and Morley or even to ideas of Poincare as leading Einstein to develop relativity. These things helped explain the significance of the paper to students after 1905 and did occur earlier, but they were not causal influences.That is, Dr. Einstein didn't go straight from reading Poincare's papers and the Michelson-Moreley experimental results to 'On the Electrodynamics of Moving Bodies'.

Perhaps a technician or professional in the field of plant breeding would be angered enough by the poor quality of this wiki and the author's ignorance to write a more professional account of her day to day work, and the specifics of the research methodology and computer software used.

TWO-FINGER METHODS
 * In Teaching Thinking (1976), Edward De Bono wrote about two-finger typing skills as distinguished from touch typing ‘full’ typing skills. Two-finger typewriting skills allow one to “quickly acquire a level of skill and competence to cope with a specific situation.... yet in a wider context it is a block to further development of typing skills.  A person with touch typing skills can cope better in a wider context.”

The methods given in my notes regarding the use of spreadsheet and database programs to create the valuable final products of the post are at most a two-finger skill. They were adopted to cope as quickly as possible with a serious software problem using available equipment and readily available, inexpensive alternative software but their application is very limited in scope. They don’t scale up to working with thousands of varieties and plots. Just trying to upgrade from the VP-Planner spreadsheet/database program to Excel, I ran into serious problems that only seem to be resolvable by employing Visual Basic or a commercially available program. Things that took hours to do with the mid 1980’s VP-Planner spreadsheet/database program, can be done in a few seconds with a few mouse clicks with modern software.

I am structuring these notes with a description of the Valuable Final Products of the post listed first, to help give one a wider context than specific application program mouse clicking instructions would. I have also tried to concentrate more on what is needed rather than on the exact procedures to produce it that would be limited to one program. The comments on the procedures could possibly be used in designing a customized program.

I don’t know what actually happened with the original customized DBASE program that was created using CLIPPER. It’s claimed that a relative referencing error resulted in several years of data being unreliable as the results were not kept together properly by the program. As if that wasn’t enough, the company had a major hard drive failure without adequate back up even though the company’s data processing requirements were small to modest in size. A year’s worth of data wasn’t more than 25 MB. During the years I worked on the project, the data kept was never over 4 MB per year but less data was being produced. The number of rows and plots grown was reduced as well as the number of traits for which data was being collected.

In accordance with Murphy’s law, an automated data collection device in the combine had a cracked motherboard that couldn’t be repaired because the manufacturer went out of business. Our fledgling plant breeding company could not afford to replace the expensive automated data collection system so my partner used a manual procedure.

IMPROVEMENTS
I’m well aware that the methodology presented in the following chapters is very crude, inefficient and antiquated. It’s not presented as any kind of systems analysis output-based or otherwise. It’s merely presented as a methodology that worked and was inexpensive. It also has a flexibility that the customized program that failed for the predecessor company didn’t have. That company had access to far more money and professionals and still went through a data processing hell. Obtaining a commercial program such as Agronomix’s AGROBASE 2 or a customized program would certainly be a lot better than the spreadsheet and database methodology.

'''It can be very easy as a spectator to sit back and criticize many of the methods and the makeshift equipment that were used. The important thing, however, is to recognize that there is something that can be done and doing it, instead of standing on the side lines wishing for a huge budget or approval from a self-appointed certifying body that wants all growers of potted violets to have degrees in Horticultural Science and Plant Breeding.

'''It's ‘what you do with what you have' that really counts. The company and its employees can grow and learn more each year and things can be improved as one goes along.'''

(NOTE: I would like something like the bolded sentences above to be in the Wiki somewhere.)

Perhaps one day the company will be able to afford purchasing commercial software (now that there is such a thing) or hiring a Systems Analyst and programmers to create a customized program (A plug for D.W. Brown and his Object-Oriented Analyses of ‘The Outhouse Bathroom Boutique’ and the  ‘Royal Korona Yacht Club’ ).

Navigation
I had two pages named BEANS that caused a navigation problem.I changed 6.BEANS to 6.Phaseolus Vulgaris L.
 * you could also try something like Beans (cultivation), beans (planting), or beans (black, pinto) or what ever applies ZyMOS 22:48, 4 April 2007 (UTC)

=Great guide= This article is amazing, Thank you so much. at the bottom of the page you mentioned you wanted to link to a specific part of the page in the link. The only way to do this is to link to an ancor on the page so the link would be something like this http://howto.wikia.com/wiki/Guide_Plant_Breeding_Technician_IT#Seedlists. however the origonal page has to be programed (html) to have an anchor, like this html tag '' . I looked at the pages code and it didn't seem to have these tags. So as far as i know there is no way to do this, unless you can edit that other page ZyMOS 04:00, 5 April 2007 (UTC)

= Comments by Laserblue = Thanks for your positive comments and helpful information.

A professional plant breeder would probably disagree with you and say something like 'the author is incompetent' or 'he doesn't know what he's talking about'. I admit the quality of the information and the style of writing is poor.I want it to look more like the Wikipedia articles.I'm thinking I should split it up into different wikis for each crop type to make it shorter and more manageable.
 * Well its true, i know nothing of the plant breeding world, But even if it is out of date, that is the beauty of wiki. Many knowledgeable people can fill in the gaps. ZyMOS 17:05, 22 April 2007 (UTC)

My Notebook Covers and this entire wiki might be regarded as a joke by anyone that uses modern software, automated seed packaging and field equipment and a tablet computer or Harvest Master ^TM data collector in the field.

I'm just trying to learn how to make a wiki.It also appears to be an easy way to get my notes together into a printable version but I don't know how to deal with spreadsheets I had embedded in some documents.

It would be nice if a young person could peek over the shoulder of people at work, and that's basically what I'm trying to present.Perhaps, a person with more experience and a University degree could use this wiki as a stub for a better article.
 * Well i can't say i know what you are talking about, but i can help in wikifying it. Ill help split it up and you can correct it if i organize it poorly. Thanks again ZyMOS 17:05, 22 April 2007 (UTC)

=Organization= I split up the page into several sections. Please check it out thoughtly to make sure i didn't delete anything. I kept a backup at Guide Plant Breeding Technician IT/temp. If i miss organized something or you have a better idea, please fix it. Thanks again, ZyMOS 18:15, 22 April 2007 (UTC)

So this is how I add a comment
I'm looking over the sections and I like the way you have split up the material.

I'm not sure I like "Using Plant Breeding Software" as a section title and I think I messed something up trying to change the title to "Viable Software".

There could be a section on using plant breeding software but that sounds very specific.I would like to structure this wiki along the lines of how to get the job done if you can't get the fancy, complicated software but you can get MS-Office or other similar software [added much later - like OPEN OFFICE! Calc and Writer].

The ICIS wiki has some nice looking pages on how to use ICIS that would be nice to emulate. For example, there is "UPLOADING CROSS HISTORIES AND PEDIGREE NOTES FROM HISTORICAL RECORDS TO A LOCAL ICIS DATABASE" By Shawn Yates (yatess@agr.gc.ca) and Dr. Fran Clarke (clarkef@agr.gc.ca) Agriculture and Agri-Food Canada, SPARC, Swift Current, Saskatchewan, Canada at http://cropwiki.irri.org/icis/index.php/Uploading_pedigree

Besides looking really great, however, it sure seems a complicated business to get one's old data into a local ICIS database.There are a lot of bells and whistles in ICIS!

Maybe people could find someone to create a LINUX Hobby Plant Breeder's Distro.

New name
This wiki needs a better name. Any suggestions?
 * Guide to being a hobby plant breeding technician with a computer and working on a shoestring budget?
 * Guide to being a plant breeding technician
 * a little more formal
 * Antipatterns in plant breeding?
 * Guide to setting up a Plant Breeding xxx
 * Guide to organizing a Plant Breeding xxx
 * Im not sure of the appropriate word for xxx

=other= See if this is useful, i was looking up links for the equipment list http://www.hgca.com/tools.output/114/114/Tools/Agronomy%20Calculators/Grain%20Moisture.mspx?fn=grainMoisture

grain moisture and weight loss calculation link
Looking over the entire HGCA website, I would not add it as a reference although it does sponsor cereals research and has research papers online.This Wiki is on operations or mechanics involved in plant breeding rather than plant breeding so I would rather let a Wiki on Barley, Triticale, Cereals Production or Cereals Breeding use it as a reference. It's a very nice website.

The HGCA link regarding kg weight loss per tonne of dried seed is for the large quantities harvested and dried by agricultural producers. A plant breeding facility or hobby breeder would not usually be harvesting tonnes of seed.However, one could use the calculator if one was producing Breeder's seed or Foundation seed.

In the local area, agricultural producers don't dry grain other than maize.

Researchers don't dry samples of Maize Yield Trials but just do a calculation. The calculator wouldn't be very useful since one is going to have many samples rather than just one.

A simple formula in Excel can be used and applied to all samples. The final desired moisture value is 15.5% moisture. In the calculation of yield, the water lost by drying is obtained by multiplying the harvested Plot Weight by the percentage of moisture difference between the harvest value and 15.5%.

(Plotwt * ((Harvested Moisture value - 15.5% final moisture value)/100)

This is then subtracted from the harvested Plot Weight to give a Plot Weight at 15.5% moisture.

Regarding the other calculators, most of them don't appear to be very applicable.The calculators are for agricultural producers.For example, the Yield Calculator only converts from tons/acre to tonnes per acre and vice versa which is of no help when one has only a few kgs from plots 100's of times smaller than an acre or a hectare.There are several agronomic calculators and the Green Area Index Tool that are certainly interesting and there is also interesting information on pages of many of the other calculators.

I don't see any listings re: equipment used in research at the HGCA website.
 * cool, thanks for the info ZyMOS

=Batch upload script=

On one of your pages you mentions u needed a batch uploader for pictures check out this User:ZyMOS/Meta:upload

=Cleaning and prettyfying= If cleand up some of the pages, and added some images to make it pretty and more readable. I think you will aprove, but if I made some errors or screwed something just fix my ignorance. Hope u like it ZyMOS 19:10, 19 April 2008 (UTC)