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Journal Journal: Transcribing WW1 biography 5

My great great grandmother wrote a biography of her three brothers killed in WW1. I'm typing it all into a LaTeX editor and will be adding a family tree along with a sketched outline of their lives and newspaper clippings.

A best-seller it ain't, but it may interest a few here as these guys show autistic traits and are geeks from just over a century ago.

User Journal

Journal Journal: Review: Bird of Prey 4

TL;DR version: 80s dystopian techno-horror geekfest with relatively accurate portrayal of cryptography and hacking.

Long version: Pretty much the same as above. It's a low budget BBC production that scores highly on accuracy of methods, exploits and technology of the era, insofar as TV ever gets.

The premise: a low-rank civil servant, tracking down bank fraud, discovers a trail of blackmail, corruption by intelligence services, deliberate weaknesses in security and criminal gangs operating with impunity.

By season 2, he's keeping himself alive the same way the Wikileaks journalists did, his wife has what we would call severe PTSD and the body count isn't slowing down.

Given trauma was barely understood in the 80s, the portrayal there and the bouts of temporary insanity are extremely close to what happens, again allowing for this being TV drama and not a psychological documentary.

The storyline deals with cryptography, surveillance society, backdoors and institutional corruption. All hot button issues of today. It even covers the inevitable issues of DIY security.

The conspiracy aspect is a trifle OTT bit, again, it's TV. It has to be to have a program.

It's geared to nerds, geeks and dystopia lovers, though, rather than the mainstream. I saw more reviews in computer journals than in TV guides.

It's the sort of show that would really need updating to be watchable by modern audiences, but fans of older shows would likely enjoy it.

It wasn't unusual for the time, which is the great thing

The 80s were a time for really bleak geek television - Codename Icarus (for the younger viewers), Edge of Darkness, Terry Nation's Survivors, Threads - all productions in this decade.

(Even late 70s had some dark stuff, Blake's 7, The Omega Factor, Day of the Triffids, and ABC/Central's Sapphire & Steel were not light watching. You have to go back to the start of the decade and Doomwatch to see a plausible contemporary dystopia.)

The stuff of a thousand bad dreams, these shows.

User Journal

Journal Journal: Teaching history via RPGs 3

There's a new RPG pack under development, called Carved In Stone. Well, it's called an RPG pack, but basically it's a fairly comprehensive history lesson about the Picts that can be used in roleplaying games. This is quite a neat idea and it got me wondering.

There were, at one point, quite a few historical wargames (Britannia, Decline and Fall, etc) but they were mostly about large-scale strategy rather than the history itself (which was mostly an excuse for blowing up other people's counters). History lessons via roleplaying games sounds quite an interesting approach and could be used to cover all kinds of events.

The expansion pack isn't out yet (it's still in kickstart) but there's enough information about it to get a good feel for how much depth there is in there. If it's done well, it could be very effective in the same way "...and then the Huns came and beat the sh*t out of the Romans before leaving again" isn't. Unless you're a Hun.

I'd like to get people's views on the use of roleplaying games and which system would be best for such gaming. Rolemaster? Call of Cthulhu? The ever-present Dungeons and Dragons? ("My 20th level mage casts a fireball at the fleeing Scots" sounds ahistorical.)

User Journal

Journal Journal: Consumer Genetics, the current state of play

Ok, so let's start be defining a few terms, as it is obvious from Facebook genetic genealogy groups that people are truly ignorant on the subject. (Not that I believe this is common on Slashdot, where we're all much more knowledgeable.)

First off, most genetic testing is NOT carried out by sequencing all of your DNA, a widespread belief that resulted in outrage on one Facebook group when I pointed that out.

The vast majority of consumer testing is done by SNP genotyping. They look at very specific genetic markers and see if those markers have changed from one base pair to another. That's the only type of mutation looked for and they typically look at only a few.

So we've our first way to group companies: sequencing vs genotyping.

SNPs (single nucleotide polymorphisms) are, as mentioned above, one type of mutation. Another is called STR (short tandem repeat), where a block of DNA is duplicated.

FamilyTreeDNA does both STR and SNP testing, STRs mostly for the Y chromosome. Both can be used for family history.

Most labs, though, use only SNP tests. It's quicker and cheaper than counting repeats but with many of the more interesting ones covered by patents or kept private by other means, there's a lot more secrecy involved.

(Note: This has doubtless led to a lot of unnecessary deaths, as genetic markers indicating a high probability of getting certain forms of cancer are being milked by private companies for profit. Few people get more than one test, so most people won't know if they carry such markers and can't take action in advance.)

So the second piece of jargon is SNP vs STR.

Finally, we come to the different areas of DNA. There are regions that are especially good for ancestrial reserch (mostly non-coding DNA), then there's the exome (which is where most of the protein coding takes place), you've telomeres (suicidal buffers between chromosomes, which have a function in longevity), and so on. I won't list them all.

The Y chromosome is particularly good for ancestry, but only has 9 coding genes left in it. It's possible it will vanish in time, but it seems to be fairly stable for right now.

Most companies test only DNA that is good for ancestral research in the autosomal regions (aDNA, the regions outside the sex chromosomes). This allows you to identify anyone who is genetically connected, but because you (on average) get just under 50% (remember, there's mutations in each generation and that DNA comes from neither parent) of your DNA from each parent, the distance you can track depends on how many markers are tested (very few). Reliability falls off sharply.

YDNA (Y chromosome DNA) tests only test for paternal ancestry, but if two people have a common paternal-line ancestor, it's a lot more precise once you're past about second cousins. It's popular with anthropologists as it's very good for tracking how men have migrated.

mtDNA (mitochondrial DNA) is only inherited through the maternal line. Again, it's very popular, this time for tracking how women have migrated. There are certain forms of mtDNA that are linked to health benefits and others to genetic diseases, so this one tends to be the most controversial of the ancestral DNA tests. It also changes very slowly, so you don't get high resolution on population movements.

These two (YDNA and mtDNA) tests can tell you a lot about whether societies are open or closed, and whether it was men who travelled to find partners, women, or both. So we can know something of the culture of even long-extinct societies.

The data I have been able to find is for 2019. It shows: Myheritage tests for 702,442 autosomal SNPS, AncestryDNA for 637,639, FTDNA for 612,272 and 23andme for 630,132. This is out of a total of 3 billion base pairs. So the best test that year looked at 0.0023% of the genome.

ISOGG produced a chart as well, but it's far older. Their chart is dated around 2013.

Since you inherit a random 50% from each parent, the assumption that this is statistically meaningful for such a small fraction of the DNA is questionable. It seems to work adequately, but I'm not sure what the error bars are.

FTDNA also tests up to 111 STRs on regular tests and 600+ STRs for their "BigY" (it depends on the quality of the genetic sample).

Companies that do sequencing sometimes offer partial kits (in the order of tens of millions of SNPs) or full sequencing (which is what the same suggests). These are rarer and more expensive.

Most DNA companies allow you to access the raw data, some only allow it if you pay vast sums of money, and some don't allow you to at all. Always check in advance.

When you download your own data, you can use public databases to search for matches (either for relatives or genetic conditions). The quality of public databases is less controlled, both in terms of privacy and quality of data. However, corporate databases will usually be smaller for both types of data and will also usually not contain data from rivals. If you want broad data sets, public databases are the way to go.

I've only tested with 23&Me, FamilyTreeDNA, CRI Genetics and Nebula Genomics, so can't tell you anything much about the quality of the other companies.

(Ok, I also tested with uBiome, a microbiome testing company in the US, but they had their computers seized some time back due to fraud. I have no idea what happened to my data on there, or whether there's a way to access it.)

The quality seems to be reasonable for all four.

FTDNA is the most expensive for a lot of things, but has less of a sticker shock than Nebula and gets more data than 23&Me. It looks like there are a few companies that are better for ancestry but it's one of the best and the one the Genomics Project used. They're the only ancestral company that gives you STRs AFAIK and they give you a much more detailed evaluation of haplogroups than anyone else I've tested with.

Nebula does up to medical grade (100x oversampling) DNA testing, so if you want results a hospital will trust, that's where you part with a vast amount of money.

23&Me is good for a lot of medical stuff and if you want to help with research is probably the best.

CRI Genetics produces a lot of data with much higher reliability than most of the others, but you can't access the raw data and their databases won't be as extensive. However, because you can't access the raw data, you have to test with them to compare against their database.

User Journal

Journal Journal: Tea 7

I have now passed the total of 30 different black teas. Not fruit, not spice, not herbal, not even green, white or red tea. Just black teas. No, blends like PG Tips and Yorkshire Gold don't count either.

Why so many? Aside from being my current monomania, it's because I'm fascinated by how different they are.

I couldn't tell you the chemistry that makes that difference, nor could I tell you what difference it makes in terms of the various compounds affecting alertness or sedation. (It contains both), in terms of health benefits or even in the simplest term of how water is retained in the body.

But I'm determined to find out at least some of this. It'll have to be on my own, as essentially no research is being done on the subject, and I've no idea of what that'll require beyond a very good gas spectrometer (I'm going to have to count molecules, not atoms).

But I think it would be fun to find out, and definitely worth doing as long as I can figure out how to (a) control the parameters, and (b) afford said piece of gear.

User Journal

Journal Journal: Fare thee well, Slashdot 6

I've been on slashdot since the early days. I've seen meme after meme come and go from the trolls, I've seen the internet grow from 28.8 modems to multi-megabit pipes. During those years we moved from 386's measured in MHz to Core CPUs measures in GHz.

But along with all the other changes, the internet itself has changed. The quality of comments on Slashdot has changed. Even the quality of selected articles has changed.

And most of it has not changed for the better.

So while I'll still be using Sourceforge.net, I don't think I'll be coming back to Slashdot any more.

Quite frankly, it's boring.

User Journal

Journal Journal: MSS Code Factory 2.3.12994 Service Pack 1

This release refactors and rearchitects the core objects of the system using diamond inheritance of the interfaces so that you can cast between the defining schema names for the objects and the current project's schema names. All of the methods of the new interfaces rely on the defining schema names, but you can safely cast the returned objects to your current schema names.

The goal of this effort was to make it easier to write custom GUI components that rely on the defining schema names for object interfaces, so that you should be able to just reference the jars that provide those custom GUI components, wire them to your projects GUI factories, and automatically use the customized screen components.

It isn't perfect, but it's the best I could do to address what I saw as a glaring flaw with the code base. Of course, the downside is that you may have to do more typecasting in some of your code. There are always trade-offs when designing an architecture.

Another benefit of the new approach is that it is made very clear that you are using the objects and interfaces from a referenced schema/project, an issue which was concerning me as some people might have taken the approach of ignoring the license requirements of the referenced schemas because the code gets re-manufactured into their project. Now there is a clear delineation between the referenced objects and the current project, preventing anyone from pretending they "didn't know" they had to abide by the licenses of referenced projects.

http://msscodefactory.sourceforge.net/

User Journal

Journal Journal: MSS Code Factory 2.3.12932 Released to production!

MSS Code Factory 2.3 adds support for the specification of ServerProc, ServerObjFunc, and ServerListFunc methods that are performed at the server end and atomically committed when invoked by an XMsgClient application.

The 2.3 series also reworks the way that licensing and copyright information are tracked by the manufactured code. Now the license and copyright information of the originating project is used, instead of that of the project that is being manufactured. Just because you included a model someone else designed does not mean you get to take credit for that work.

There will be additional service packs adding new functionality to the 2.3 series, but those enhancements will not require further changes to the GEL engine, only the rule base.

http://msscodefactory.sourceforge.net/

User Journal

Journal Journal: I don't understand this Google vs. Oracle thing

For the life of me, I do not understand why Google doesn't just ship an ARM64 build of OpenJDK instead of futzing around with this fight against Oracle. From a pure developer's perspective, the whole thing is flat out STUPID.

Oracle is not preventing Google from shipping their own build of the JDK. They're just stopping them from breaking Java's portability requirement by shipping non-Java bytecode.

Java is not a compiler kit.

User Journal

Journal Journal: April 2015 has been a busy month

April 2015 has been a busier month than I'm used to.

I got MSS Code Factory 2.1 Service Pack 1 out the door after over two months of work.

I packed up and moved to a new apartment.

Last but not least, I installed Ubuntu 14.04.2 LTS on my failing Debian box. I still haven't done any more work on the Windows 7 laptop to get it into a development-usable state, but since I did all that performance tuning on MSS Code Factory 2.1, I really don't need to use the Windows laptop. In fact, the poor beast is so I/O bound when running 2.1 that it sounds like the hard drive is about to rupture and spew it's guts out the keyboard when MSS Code Factory is running.

The shift to Ubuntu 14.04.2 from Debian 7 was a last-ditch attempt to resolve an X-Server crash issue (white-out screen in NVidia 8600-series hardware with NVidia drivers.) Although I did see one such crash on Ubuntu 14.04.2 since installing it in the first week of April, I have not seen it in the ten days since Ubuntu released some X-Server input patches.

So it wasn't entirely the NVidia driver's fault that my X-Server was crashing; there seems to have been some bugs in the input stream processing.

I'm still not 100% confident that the X-Server bug has been resolved, but it's looking like it has. Which is a good thing -- I can't afford to buy a new computer at this time (nor in any reasonably near future, as I'm on disability and get less than $17,000/year to live on here in Saskatchewan, Canada.)

User Journal

Journal Journal: Windows 7 laptop is toast -- hello, Debian 1

My Windows 7 laptop was finally nuked. It was only a matter of time before something got to it -- Windows is a virus vector hell.

I'm downloading Debian for my Lenovo IdeaPad Z580 -- I hope it works. I've never tested the system for Debian compatability, though Lenovo has a good reputation for it.

Sadly, I'm pretty sure it's going to mean losing my glorious 192/24 audio playback, as I can only get 44.1/16 working on the desktop despite it having a HD soundchip. I'm going to miss that...

More to the point, I won't be able to do any further work with Oracle, Sybase ASE, or SQL Server for my pet project. Such is life. What's there at this point works; someone else will just have to pick up the ball for those databases.

User Journal

Journal Journal: MSS Code Factory 1.11.12558 Service Pack 6: It is done!

Service Pack 6 provides move up/down functionality for the Chains for all of the supported databases. Note that the RAM storage does not support Chains or complex object deletes at all -- it's intended for high volume read/update/delete data, such as the call record information for an Asterisk or FreeSwitch PBX system, or the internals of MSS Code Factory itself.

There are some critical bugs fixed with Service Pack 6, including cache integrity bugs that were discovered during testing of the move up/down functionality.

With this release, I think I'm pretty much done with MSS Code Factory 1.11. I can't think of any more functions I'd want to add that I have experience with. Sure I could implement proper login security with hashing algorithms, a JEE server to receive and respond to X(ml)Msg requests, and polish the prototype GUI some more, but that's really not my forte. I spent 30 years as a back end database programmer, tuning servers and wringing every last bit of performance out of database engines that I could.

MSS Code Factory 1.11 now incorporates everything I ever learned about making an RDBMS sing and dance. It provides all the functionality points that I was ever asked to deliver to a front end application programming team, and does it all automagically from a Business Application Model.

It's been 18 years of long hours working on this project to get to this point. The idea was around even longer (I came up with the concept way back in 1987, before I'd even had any experience with data modelling tools.)

Service Pack 6 is, in essence, my life's work. My magnum opus. I have climbed my mountain, and the view is great.

http://msscodefactory.sourceforge.net

User Journal

Journal Journal: MSS Code Factory 1.11 Service Pack 1 released

MSS Code Factory is a model-to-code development tool that provides Java 7 using JDBC and stored procedures for DB/2 LUW, Microsoft SQL Server, MySQL, Oracle, PostgreSQL, and Sybase ASE.

Service Pack 1 corrects defects in the manufactured database schema installation scripts, the core Java ORM objects, the stored procedures, and the JDBC layer. It also adds in the production of an XML messaging based communications framework for doing client-server or web development (you have to code the transport layer, but the message parsers and processing are provided.)

Service Pack 1 also provides a prototype Swing GUI that can be used as-is for performing demos and walkthroughs of a business application model for users, rather than counting on users to understand ERD or UML diagrams. The prototype is entirely factory and interface based, so it can form the basis of a custom user interface by either subclassing the manufactured GUI components produced, or by replacing them wholesale with JInternalFrame and JPanel instances as appropriate (the only requirement is that they implement the interfaces specified by the manufactured objects.)

The source code for the project is hosted at github, but the main project is on SourceForge at http://msscodefactory.sourceforge.net.

The project has been under research and development since Java 1.1 was released in 1997, with the past two years focusing on the 1.11 release.

User Journal

Journal Journal: 24/192 Audio Redux

A while back I put my laptop into forced 24bit/192kHz output mode in order to be able to play some Grateful Dead tracks that were recorded in that format. I've left it at that setting on the Windows 7 laptop because it plays back lower resolution audio just fine.

In fact, it seems to upsample lower resolution audio rather nicely. So while CDs and MP3s still are far from as clean sounding as the Grateful Dead tracks, the upsampling prevents "digital fatigue" and sounds more "musical" than 44.1 Hz output does on my Linux box. So I find myself spending more and more time listening to my music under headphones plugged into the laptop (a rather nice set of Sony noise cancelling full-cup headphones that cost nearly $300 15 years ago -- a gift from good friends.)

For the life of me, I do not understand people who claim they can't hear the difference between 44.1 audio and higher resolutions. They must be deaf. The difference is obvious as night and day, if you know what to listen for.

User Journal

Journal Journal: MSS Code Factory 1.11 has been released to production

This day had to come eventually. It was just a matter of patience, persistence, and time.

Today I released MSS Code Factory 1.11 to production.

This is the first time I've ever released a piece of software because I honestly believe it's ready to be released rather than because some marketing/sales rep or management had set an arbitrary delivery date.

This release was 4 years in development. The project itself was started 18 years ago.

But my baby has all grown up, and it's time to send her out the door into the wild, wild world.

If I were to die today, I'd die knowing I accomplished something with my life.

This has been the mountain I had to climb; the ocean I had to sail; the desert I had to cross. It has been my mission ever since I first conceived of the idea of manufacturing code by reversing the logic of a compiler/parser way back in my University days.

For those of you who are programmers, please download and play.

http://msscodefactory.sourceforge.net/

By the way, as a side effect of the testing and validation of MSS Code Factory itself, I produced CFUniverse, a conglomerate business application model project that is nearly 14,000,000 lines of source code. To put that in perspective, the biggest project I ever worked on was about 1.5 million lines, coded by a team of over 150 developers over a 3 year period. Were you to print out CFUniverse at 100 lines per page, double-sided, you'd need 5 cases of paper plus another 20 reams to do it.

I'd love to dump that sucker on someone's desk for a code review!

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I tell them to turn to the study of mathematics, for it is only there that they might escape the lusts of the flesh. -- Thomas Mann, "The Magic Mountain"

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