Book is done (for now anyway)

I released the final version of the book today, with all my edits from the summer and fall. No more edits are expected until summer 2019—unless a big error is found that I need to correct quickly.

Although I’ve raised the minimum price (to $5.99 from $4.99), the coupon LeanpubHolidaySaleHoHoHo is good through 2019 Jan 1 for the old price.

Students in BME 51A for Winter 2019 should have gotten their coupons for free copies.

Anyone who bought the book or used a free coupon in the past can get the new version for free.  The URL is now https://leanpub.com/applied_analog_electronics, though the old URL should re-direct.

I’m offering a token payment for the first report of any error (25¢ per error, and I’ll scale that up for bigger errors).  For students or tutors in the class, I’ll pay cash at the end of BME 51B.  For anyone else, I’ll pay by PayPal.

The book now has

603 pages
302 figures
12 tables
475 index entries
142 references

 

Dante Labs is probably not a scam

As readers may remember from Spit kit sent, I spent $500 in March 2018 in an attempt to get my genome sequenced through Dante Labs. I worried at the time that their price was too low for current sequencing capabilities, but I thought that I’d give them a try.

I am now convinced that Dante Labs is indeed a scam. (Update: 2019 March 15—I’m an no longer convinced one way or the other.  They have, finally, sent me the promised data.)

On 2018 August 31, they sent me an e-mail:

Your Raw Data are ready!

Dear Customer, 

We’re excited to let you know that we completed the sequencing of your sample. 

Over a month later, I asked when I would get the data they claimed to have.  On 2018 Oct 9, they sent me an e-mail:

Dear Kevin,

we apologize for this delay.

Your hard disk is among the next few to be shipped.

Again, we are sorry for this inconvenience.

Best regards,

Paul

Dante Labs

It is now four months since they claimed to have data for me, and almost three months since they claimed that mine was “among the next few to be shipped”.

It is clear now that they are incapable of delivering the whole genome sequence that they promised.  I suspect that they are doing a variant of a Ponzi scheme, where they use the money of new customers to pay for sequencing of a few select early customers, so that they don’t have all their customers complaining about non-delivery.

For my part, I’ve given up on ever expecting anything from them—now I have to decide if it is worthwhile to report them to the Better Business Bureau and appropriate district attorneys.  I can, at least, warn all my readers not to do business with them.

I’ll also have to look for a different, more reputable business to get my whole-genome sequencing done.  While I’m looking, I wonder whether it would be worth the $200 for a SNP panel from 23andme—that would not answer the most interesting question for me (the genetic cause of our family’s inherited bradycardia), but it might provide some data of interest.

If anyone has suggestions for whole-genome sequencing companies I should check, please let me know.

UPDATE: 2019 March 8.  Dante Labs informed me today that my data “has been ready for a while” and there is indeed a VCF report for me on their web site (with an 2018 August 11 date on it, though I don’t believe it was there then).   They had promised me the raw data, which they never sent.

I will check the VCF file to see whether it is consistent with 23andme data for me, and see whether Promethease can process the data (there is mention on the Promethease website that they have had trouble with Dante Labs data, though no reasons are given).  I have also ordered another whole-genome sequencing from fullgenomes.com, which I will also check for consistency.

If the VCF file for Dante Labs turns out to be correct and usable, I will remove the accusation of “scam” and just say that their customer service is terrible.

UPDATE: 2019 Mar 15.  The hard disk with the FASTQ and and alignment files (the raw data Dante Labs promised me last year) arrived yesterday.  After I catch up with my grading (only 51 more hours to go—10 hours more grading on Lab 5, then 41 hours of grading on Lab 6, which comes in on Monday), I’ll be consulting with the experts at UCSC about the best way to re-analyze the data.

Promethease had no trouble processing the VCF file from Dante Labs, but their analysis assumed that any variant not mentioned vas not tested, while most were sequenced but homozygous for the reference allele.  There needs to be a better format for communicating genotypes!

The preliminary results from the Promethease analysis are compatible with the 23andme data, but I’ll need to write a Python program to compare the 23andme genotype with the VCF file to see how much they differ.  This may be a bit tricky, as I’ll probably first have to create a 23andme reference, so that I can guess what the genotype is where the VCF has no variant reported or remove from the comparison any places where my 23andme genotype matches the reference.  Again, this will have to wait until my grading is done.

Right now, I am cautiously optimistic that Dante Labs is not a scam—though their delays in delivering data are not real encouraging.   If they really deliver whole-genome data at scale at the prices they are currently charging, I’ll be impressed.  If they are only delivering to a few selected customers, then not so impressed.

If the data checks out ok, I will have some of my relatives send samples to Dante Labs for sequencing—the prices is so much lower that it is worth some risk.

Textbook on sale

My textbook is part of LeanPub’s special holiday sale.  For the rest of 2018, you can get it for only $4.99 (instead of the usual $5.99) with the coupon

http://leanpub.com/applied_analog_electronics/c/LeanpubHolidaySaleHoHoHo

Note: students in BME 51A should have gotten a coupon to get the textbook for free.

Latest book release

I released the new version of the book today, with all my edits from the summer and fall.  I’ve also raised the minimum price (to $5.99 from $4.99).  Anyone who bought the book or used a free coupon in the past can get the new version for free.  The URL has changed—it is now https://leanpub.com/applied_analog_electronics, though the old URL should re-direct.

Students in BME 51A for Winter 2019 should have just gotten their coupons for free copies.

I expect to do a few more edits in the later chapters (those for BME 51B instead of BME 51A) in the next couple of weeks, with another release in the first week of January, but the book is basically done (for this year anyway).

I’m offering a token payment for the first report of any error (25¢ per error, and I’ll scale that up for bigger errors).  For students or tutors in the class, I’ll pay cash at the end of BME 51B.  For anyone else, I’ll pay by PayPal.

The book now has

593 pages
302 figures
12 tables
473 index entries
140 references

 

Changes in student populations

There has been a lot of discussion at Inside Higher Education (and other higher-education media sites) lately about colleges failing because of enrollment difficulties due to the declining number of high-school graduates.

I think that this discussion has been colored largely by strongly regional phenomena.  A report by the National Center for Education Statistics shows that the Northeast and Midwest are dropping in K–12 students, but the West and South are increasing.  Overall, the K–12 population is growing, though very slowly: projected growth is 0.18% a year, while past growth has been about 0.22% a year. So the story should not be of shrinking numbers of students for college, but a shift in where the students are coming from.  We may indeed have an oversupply of colleges in New England, with a shortage in the South and West.

Even more strongly, the report shows a shift in racial/ethnic demographics of the K–12 population, with a strong growth in Hispanic students (1.3% a year) and a shrinkage in white students (-0.5%/year).  The Asian/Pacific Islander category is expected to grow strongly also (1.4%/year), but black student population should remain fairly flat.  I wonder how much of the panic about colleges not being able to get students is due to the colleges marketing only to white students, who formed their traditional core, and not to the growing numbers of Hispanic students.

For projected number of high-school graduates, the racial shift is even stronger: White -0.7%/year, Black +1.2%/year, Hispanic  +1.9%/year, Asian/Pacific Islander +1.2%/year.

UCSC, where I teach, is bursting at the seams with far more students than we have the facilities for, with no signs that demand is shrinking.  UCSC qualifies as a Hispanic-Serving Institution, with about 26% of students being Hispanic, and UCSC also has a fairly large Asian enrollment (again, about 26%). Source: http://mediafiles.ucsc.edu/iraps/student-characteristics/2017-18/enrolled-students/new-continuing-and-returning-students-by-ethnicity-87697.pdf

I wonder how much of the discussion of the problem of shrinking enrollment in colleges is due to regional blinders and how much is due to racial blinders.