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Louis Kessler's Behold Blog

Digitizing and Going Paperless - Thu, 5 Jan 2017

When I was reviewing the #RootsTech 2017 Schedule several months ago to see what sessions I would be interested in attending, I was particularly attracted to the talk by Janine Adams and Brooks Duncan on “Go Paperless: Digitize & Streamline Your Research”, on Friday at 11:00 a.m., described as:

Going paperless is about much more than saving trees and a clean desk. More and more genealogy enthusiasts are discovering the benefit of having the document they need, right when they need it in electronic form—and being able to easily share their documents with others. Turning at least some of your paper into an organized, electronic system can help alleviate the paper overload that can come with exploring your family history. This session will give concrete, specific information on tools and best practices for going paperless from two people who live and breathe it.

I’ve followed Janine’s Organize Your Family History blog for a long time, and I look forward to hearing her in person. She is joined by Brooks Duncan, who I didn’t know about before. He runs the DocumentSnap website whose raison d’être is to help people go paperless.

Brooks recommends the Fujitsu ScanSnap which is a higher level sheet feed scanner than you might be accustomed to. It scans at 25 pages per minute, which is 50 sides per minute because it does both sides at once. It then can output right to searchable PDF. Brooks can instruct you how to best use the scanner, use the software that comes with it, and set up automated jobs for it to perform different scanning tasks.

When I retired from Manitoba Hydro, I had a bookcase with about 100 binders chock full of information that I assembled over my 36 year career. During my last two months, I spent a bit of time every day at one of our companies high powered multipurpose printers scanning the important documents and turning them into searchable PDFs that I could place appropriately on our network where the staff would be able to find them if they needed them after I was gone.

The scanner function was a WOW to me. This machine was about 45 ppm and I could go through a binder of 25 documents totalling 800 pages in about an hour. This includes time for the invariable jam-ups, usually caused by a staple I missed when I was preparing the pages. But I was able to review, assess, cull and digitize the entire bookcase in less than an hour a day over those 2 months.

WP_20170104_23_19_13_ProOf course, that left me with the desire to do the same at home. I’ve got 40 years of genealogy material, programming info, marketing tips, photos, business cards, travel information and stuff – lots of stuff – that needs to be gone through. Just look at what my bookshelf in my office looks like! I was definitely a binder person. But I’ve also got a very full 3 drawer vertical file and boxes in the closet and basement ready to be gone through. This is probably 10 times as much as what I had at work to go through. At work, we had a “trim” about 8 years ago when we were moving to our new Head Office downtown. I’ve never had the luxury of a “trim” at home yet.

To do such a big task, you must make it easy. And you need a good equipment and tools to help you. I learned the value of having a good scanner at work, so my first course of action was to get a good scanner for home. The 2 page per minute sheet feeder on my Epson Workforce 645 was okay for small jobs, but just wouldn’t cut it for this task. I love that ink jet printer. It’s worked flawlessly for the past 6 years. Ink is a bit expensive, but hey, can’t complain about how its performed.

I was not familiar with Fujitsu equipment, which Brooks was recommending. WP_20170104_23_09_55_ProEpson had a similar sheet feed scanner, also 25 ppm, the DS-560 which I could get here in Canada for $450 compared to $640 for the ScanSnap. I was very happy with all the Epson products I had used up to now, and the software that would come with the scanner would also work with my printer if I got the Epson.

I started checking for the best prices and came across a great offer by CDW Canada on the Epson scanner higher end of the same DS model. Their regular price for the Epson WorkForce DS-860 was $1,374, somewhat more than I was willing to pay. But an unbelievable pre-new year’s 50% off offer suddenly made that product a consideration. It was effectively the same as the DS-560, but it has a 65 pm engine! Yes, that’s over a page a second! 130 sides per minute! I jumped at this and ordered the product. It was delivered two days ago.

It’s small, fits on the corner of my desk, and weights only about 10 pounds. And it’s impressive. Check out this video:

Now, we weren’t quite done. I set everything up. The scanner worked perfectly and I set up a job to automatically create the searchable PDFs for me. But the button on the scanner, which was one-press scanning using any one of 10 custom jobs I could select from, was not working. The button was supposed to start the Document Capture Pro software that did the work.

I found that the trouble was in the Control Panel –> Scanners and Cameras, that the programs that I could select from to assign to the scanner’s Start Button event did not include “Document Capture Pro” as an option. The documentation for the DCP software said that it should.

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This button is sort of a necessity, since it adds the “touch” of convenience that is necessary for a task to be repeated over and over. I searched the web to see if there was a way to add DCP to the list. Microsoft seemed to indicate that if it wasn’t listed, it couldn’t be added. But one answer said that it’s just a registry entry, and could be done like this. Okay. I could do that, but I didn’t have the GUID of the Document Capture Pro software. Searching the registry, I couldn’t find it either.

So I called up Epson support. I believe I was talking to Singapore. The first level of support didn’t know enough to fix this, so they passed me on to the second level. We were getting somewhere when she asked me to reboot my computer. I forgot that I called them through Skype that was on my computer and when it shut down … well I lost my connection. Oops.  I called back and they passed me back to 2nd level. It was a different person, but the key to fixing it all was for him to email me a registry cleaner to get rid of any bad Epson registry entries. I uninstalled everything, ran the cleaner, reinstalled, and the Start Button in Scanners and Cameras now had Document Capture Pro as an option, and it worked perfectly.  It took about 2 hours to sort this all out with Epson support, but we did fix the problem and I was happy.

One last thing to do. At work, when the scans produced the PDFs, Even though the PDF assembly software was meant to handle this, I often found a few pages rotated because they were oriented landscape instead of portrait, or blank pages left in because they had some marks on them that fooled the software. At work we had the full version of the Adobe Acrobat editor we could use, and I was easily able to fix the problem. At home I don’t have that, and the Adobe editing software is not a light or inexpensive tool. Their new version, Adobe Acrobat DC, is really souped up and meant to work well with the cloud. But you have to purchase a non-inexpensive subscription at $13 US a month to use it. This was a bit of overkill for what I had to do which was change orientation and delete pages.

So I did a search for some inexpensive PDF editors. I found a few.

First I tried Wondershare PDF element which costs $70. I downloaded the trial, and it wasn’t bad, but I still thought I could get something as good but less expensive.

I found Classic PDF editor for $25. It also seemed okay, but as I was testing it out, it froze. Oooh. Bad sign. Try something else.

One nice site I use in these cases is Alternate To. I entered Wondershare PDFelement into their search box and the first program it gave was Adobe Acrobat DC. The second was one called PDF-XChange Editor for $43.50. I tried that one out and I really liked it. It has a nice thumbnails setup on the left for quick moving, rotating or deleting. It includes an OCR feature, which PDFelement had as an extra-cost add-on. They even had a SDK (Software Development Kit) that programmers could buy to include PDF functionality in their program. That tells me they know what they’re doing because development of an SDK takes expertise. Finally, this news item they put on their news page caught my attention and being Canadian, not only made me laugh, but also got me to purchase the product from them:

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After using it for a while, I found I liked PDF-XChange Editor so much, that I made it my computer’s default PDF reader, taking the honour away from Adobe Reader.

Finally, all set up, and the scanning quickly produces PDFs that Windows can word index. Now I can use the search in Windows Explorer to find articles I’ve scanned by the keywords in them, for example:

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… and I can throw the hardcopy originals into the recycling bin.

So I’m all set up, but I’m still planning to go to meet and listen to Janine and Brooks at their RootsTech talk. I’m sure they’ll have lots of good ideas about workflow and setting up scanner jobs and organizing and naming your scanned files on your computer that I will be interested in.

Cast and Crutches - Sat, 31 Dec 2016

On Monday Dec 19, it felt like I might have sprained my ankle. It was my first squash game of the day and I planted my foot and I felt a tiny pop in my ankle. It wasn’t too bad and I tried to continue but less than a minute later I felt another pop in the ankle. Now it felt like a badly sprained ankle.

I immediately told the guys that’s it for me today, got some ice and iced it for 40 minutes while my buddies finished up their matches. It didn’t feel too bad after the icing and fortunately I was carpooling with Rob and it was his turn driving and he took me home.

That night it didn’t swell up much, but it hurt like crazy. The next morning, my wife took me into our nearby Sports Medicine clinic. They took X-rays and could see on the X-ray (I’ll try to get it and post it here), that I had an avulsion fracture of the ankle. That means the place the peroneal tendons (which go from the outside of foot back to the calf) are attached to the ankle broke off taking a tiny piece of the bone with it. The X-ray can’t see the tendons, but it did show the bit of bone.  

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The peroneal tendons (which I never knew existed two weeks ago) are like two rubber bands glued to the bottom of the fibula. Both the rubber bands and the “glue” are stronger than the bone and with pressure, something had to give. Now the two tendons were held in place at the top and bottom but not in the middle and were floating. The doctor put me in a solid cast which could bear weight, and made an appointment with the foot surgeon to see if I would need an operation.

So a week of hobbling around in that cast and crutches, with my wife and daughters driving and otherwise helping me. On Wednesday Dec 28, I met with the foot surgeon. She told me this is unlikely to heal well on its own. I had peroneal tendon subluxation which means the tendons were out of place.

Yesterday, Dec 30, I went in for day surgery. I had my wisdom teeth removed 40 years ago, but this is my first surgery in a hospital. I got changed and they set me up on an IV in the waiting room. I would be getting a spinal, which would freeze my lower half and I’d be awake. They asked me if I wanted to have a sedative applied so that I wouldn’t remember the surgery. i turned it down because I wanted to experience it.

When surgery time came, they rolled me into the operating room. There were two doctors and about 4 others there, including the anaesthesiologist who would then administer the spinal. Barely felt that. The IV previously was worse. The operation was to take about 45 minutes. I couldn’t see anything because they had a big canopy over me. I couldn’t make out much of what the doctors were saying because they were talking very quietly. I only had the anaesthesiologist who came around to check on me every few minutes. The spinal was great. I felt nothing! When they came to cut a small groove in my fibula so that they could place the tendons, I got to enjoy a few minutes of listening to what sounded like a circular saw, but again I felt absolutely nothing and couldn’t tell anything was being done to me. My anaesthesiologist asked me if the saw sound bothered me, but I said no, it was just like being at the dentist.

The operation took about 1 hour and 15 minutes, which was 30 minutes longer than expected because when they got in, they found the tendons were quite frayed and needed repair, which they did. It actually was a good thing I did the surgery because the state of the tendons would have caused me problems in the not too distant future if I had chosen not to have the surgery.

imageAfter surgery, I was taken to the recovery room for an hour and I was watched closely. My surgeon came in and said everything went well and told me about the frayed tendons that they repaired. They also put me in a new non-weight bearing cast which I would have to be in for 6 weeks and then a walking boot for 4 weeks. I had appointments set up for 2 weeks and 6 weeks from now with the surgeon to check progress, but she said I can come in 5 weeks instead of 6, and we’d see if I could switch to the walking boot to make RootsTech easier for me. Either way, crutches or boot, I wasn’t going to miss RootsTech. Hopefully it will be the boot. Crutches would make quite a scene as I go up onstage to present Double Match Triangulator in the Innovator Showdown semi-finals.

After the recovery room, my wife joined me back to the staging area to ensure that the spinal wears off which takes a few hours. After I could get up on my own steam, I was released and my wife drove me home.

It took until 10 p.m. or so until the full spinal wore off. Then the pain started and it was bad. I took two Tylenol 3’s which the doctor gave me but that hardly seemed to do anything. I barely slept last night. In the morning, my wife who is a pharmacist, recommended two Ibuprofens. Within an hour, that did the trick and most of today has been pain free. I must have had swelling from the operating I couldn’t see under the cast and those helped relieve this.

So, what a way to start a new year. At least I will be on my road to recovery now and I’ll do what I need to do to make it to RootsTech. This is likely the end of my 30 years of playing squash. My last major injury from squash was a completely torn achilles 5 years ago on the same leg, which was fully healed and unrelated to this new injury. I’ve had other aches and pains and nagging injuries from squash, but these two, with the out-of-action time that they cause to the rest of my life, are just not worth it anymore to me. This one just came too close to ruining RootsTech for me. So lots of walking, biking and swimming should do well to keep up my fitness levels. I will miss my squash guys and their camaraderie over the years though.

A side benefit of the next six weeks: I’ll have lots of time at my computer to work on Behold and do genealogy stuff.


Update:  Monday, Jan 16, 2017

imageLast Friday, two weeks after the operation. They took the cast off and removed the stitches. They put a rectangular bandaid over it and a sock over that, and no longer did I have to wear a cast, but I’m in a walking boot – actually the same one that I got for my achilles tear 5 years ago, so for up to 8 more weeks, I’m a stormtrooper again. Four weeks non-weight bearing with the boot with crutches, and 4 weeks after that still in the walking boot weight bearing without crutches. I’ll wear the walking boot during the day and at night.

Up to today, I was taking a shower sitting on the edge of the tub with my right foot out of the tub with the cast and then the boot in a bag so it wouldn’t get wet. On Friday the doctor told me that starting today, I could take off the boot a few times a day to shower and to do exercises to bend my foot up and back (but not side to side). So today I took off the bandage and washed my right foot and leg for the first time in 2 1/2 weeks. It felt so good to do that.

The incision was a slight curve about 3 inches long. You can see where the stitches were removed but it’s all healing nicely. It’s a bit tender but doesn’t hurt and there’s very little swelling. My right calf muscle is going to pot though. I’m sure I’ll bring that back up to snuff not too long after the boot comes off and biking season starts.image

My next appointment is in 2 1/2 weeks which will be 5 weeks from the operation. That was supposed to be at 6 weeks when I can start weight-bearing, but my doctor moved it up because I was going to be out of town at RootsTech the next week. She’ll evaluate then and tell me if I’ll be taking crutches to Salt Lake CIty.

Funny that my right leg feels fine. It’s the upper quad in my left leg that I partially tore 3 months earlier that’s giving me more problems, especially at night. But all the extra work my left leg is doing now to support all of me is helping it.


Update:  Thursday, Feb 2, 2017

Had my post-op five week appointment today. It’s looking really good. There’s no pain whatsoever. Foot can move any direction nicely.

So the word for now is that I can wean off the crutches and start weight bearing on the boot. By Monday, I should be good to go without crutches and can make my trip to Salt Lake City in the boot and not have the hassle of taking the crutches. That means I’ll be able to pull my carry-on behind me rather than have to wear a backpack. This will make the trip much easier than it would have been if I couldn’t weight-bear.

The added bonus: I only have to wear the boot while walking. I can take it off if I’ll be in one place for a while, and I also won’t have to wear it to bed any more.

In two weeks, I’ll start physiotherapy to get the foot and leg muscles back in shape and will also get some home exercises to do. In five weeks, I can stop using the boot completely (and likely will be able to start driving again), and in seven weeks, I’ll have one more visit with my surgeon for what will hopefully be a final inspection.

Probability of No X Segments Matching - Sun, 25 Dec 2016

Okay. Let’s do what we did last post for autosomal this time for the X chromosome.

I’ll assume you already know the unique pattern of how the X chromosome get’s passed down, where males get their one X from their mother and females get one of their Xs from their mother and the other from their father. The mother’s is from both of her parents and since the X chromosome (according to FamilyTreeDNA) is 196 cM, that means it recombines with an average of about 1.96 crossovers, which I will round to be 2.. The father’s is passed intact only to his daughter without recombining.

So a son only gets one X chromosome from his mother which will have on average 2 crossovers. A daughter gets one from her mother with 2 crossovers and one from her father with zero crossovers.

This is interesting. That means is a 50% chance of 2 crossovers if it is a son, and that leaves a 25% chance of 2 crossovers and a 25% of zero crossovers if it is a daughter. That works out to 75% chance of 2 and 25% chance of zero giving an expected value of 1.5 crossovers per generation.

And that seems to make sense, since if you got up the female line via mother-mother-mother-mother…, you’ll get 2 crossovers each generation.If you go up the most possible male line which is father-mother-father-mother…, you’ll get zero,2,zero,2,… crossovers which average 1 crossover each generation. So 1.5 seems like it could very well be the average over all lines.

For autosomal, we started with the 23 chromosomes pairs and increased them by 34 segments each generation since both pairs total about 3400 cM. Here for the X chromosome, we’ll start with 1 and increase by 1.5 segments per generation. It’s okay if we use fractional segments here because we’re dealing with averages.

For autosomal, we doubled the number of ancestors each generation. The X chromosome grows not by doubling, but via a Fibonacci sequence. As a lover of mathematics, I must say it’s nice to get good old Fibonacci into DNA. A Fibonacci sequence starts with 1 and 1 and then the next number is always the sum of the previous two, so it’s 1, 1, 2, 3, 5, 8, 13, 21,… A male starts with one X chromosome parent, whereas a female starts with two, so they are offset with one another and an overall average can be taken.

Now lets put the generational levels together:

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There you see the segments growing 1.5 per generation, the male and female Fibonacci sequences and their average that represents the expected number of ancestors.

The “P(NoMat)” column is the probability of no segments matching a specific ancestor given that there are N ancestors and S segments and is calculated as:

(1 – 1 / N) ** S

Finally, we can work out the expected number of ancestors that match on the X chromosome by multiplying the number of Ancestors by the probability of matching (which is 1 – the probability of not matching). For higher generations, this number is the same as the number of segments, because it is very unlikely that such a distant ancestor will contribute more than one segment each.

N * P(NoMat)

What this table says is that after 13 generations of X chromosomes, you will have on average 20.5 segments. 95.93% of the 493.5 possible X ancestors will not contribute meaning the 20.5 segments come from 20.1 ancestors, so there is still a chance one or two of them may contribute more than one segment.

Comparing the probabilities of not matching with autosomal is interesting:

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With autosomal, it takes 9 generations before there’s less than a 50% chance that an ancestor won’t pass you a segment. For the X chromosome, it only takes 6 generations for less than a 50% chance. And there’s even a small chance that you won’t inherit an X-segment after 1 generation. This could happen if the X chromosome from the mother’s side has no crossovers and comes just one of her parents. See the section: The X Doesn’t Recombine as Expected.

Back to statistics: The Poisson distribution can approximate the number of crossovers per generation. Assuming we are talking about the mother’s X chromosome which has an average of 2 crossovers, a Poisson distribution wiith mean of 2 can give a reasonable estimate of the expected chance of each number of crossovers in one generation on the X chromosome:

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One thing left to do. Like we did for autosomal in my last blog post, we also want to determine the average segment length of a match. So we get this:

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Comparing average segment length of an autosomal match with that of an X chromosome match (above) gives:

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This shows that autosomal matching segments at any generation are on average a bit longer than X chromosome matching segments.

So now I have everything I need to program this into Behold. Behold will be working with the actual ancestors and know whether it’s a male or female and will take this into account. This will enable to Behold will give more accurate information than what I’ve shown above which are just averages. Also, Behold will correctly add the probabilities and compute the expected lengths when there’s pedigree collapse and one ancestor is an ancestor on multiple sides. This should be really useful information that I don’t believe is available anywhere else.

My calculations and assumptions above and in my previous post are as far as I can tell, correct for the averages. I would love to get these two posts peer-reviewed by some genetic genealogists and/or genetic researchers. With encouragement, I could turn these posts into a submission for a publication like the Journal of Genetic Genealogy. I’d be happy to have any problems pointed out and will make any clarifications or corrections that are necessary.